Table 1.
RT–PCR analysis of 39 mammalian-wide interspersed repeat (MIR) exons in 10 human tissues
| Gene symbol | Transcript cluster ID | Probeset ID | MIR exon location (hg18) | MIR strand/mRNA | PCR skipping (bp) | PCR inclusion (bp) | Splicing pattern | Impact on mRNA/protein | Gene name | GO processes/known features |
|---|---|---|---|---|---|---|---|---|---|---|
| CSF3R | 2406783 | 2406822 | chr1:36719666-36719725 | Antisense | None | 236 | *Constitutive inclusion | 5′-UTR | colony stimulating factor 3 receptor (granulocyte) | Cell adhesion, cytokine receptor activity |
| CUL2 | 3284882 | 3284888 | chr10:35340782-35340898 | Sense | None | 268 | *Constitutive inclusion | Coding | cullin 2 | G1/S transition of mitotic cell cycle |
| FXYD4 | 3244008 | 3244011 | chr10:43188181-43188226 | Antisense | None | 115/251 | *Constitutive inclusion | 5′-UTR | FXYD domain containing ion transport regulator 4 | Ion transport |
| IL6ST | 2857416 | 2857457 | chr5:55314309-55314396 | Sense | None | 204 | *Constitutive inclusion | 5′-UTR | interleukin 6 signal transducer (gp130, oncostatin M receptor) | Cytokine-mediated signaling pathway |
| KLC1 | 3553872 | 3553899 | chr14:103221076-103221126 | Antisense | None | 221/248 | *Constitutive inclusion | Coding with ALT stop | kinesin light chain 1 | Microtubule motor activity |
| MTA2 | 3375862 | 3375867 | chr11:62118307-62118455 | Antisense | None | 373 | *Constitutive inclusion | Coding | metastasis associated 1 family, member 2 | Transcription factor |
| MTIF2 (2553751) | 2553730 | 2553751 | chr2:55348209-55348275 | Antisense | None | 313/451 | *Constitutive inclusion | 5′-UTR | mitochondrial translational initiation factor 2 | Regulation of translational initiation |
| MTIF2 (2553754) | 2553730 | 2553754 | chr2:55349218-55349379 | Sense | None | 251/224/296 | *Constitutive inclusion | 5′-UTR | mitochondrial translational initiation factor 2 | Regulation of translational initiation |
| MTX1 | 2360773 | 2360784 | chr1:153449652-153449806 | Antisense | None | 309 | *Constitutive inclusion | Coding | metaxin 1 | Protein transport |
| MYT1L | 2466822 | 2466898 | chr2:1979970-1980126 | Antisense | None | 232 | *Constitutive inclusion | 5′-UTR | myelin transcription factor 1-like | Cell differentiation, regulation of transcription, DNA-dependent |
| SLC6A12 | 3439510 | 3439537 | chr12:191453-191537 | Antisense | None | 329 | *Constitutive inclusion | 5′-UTR | solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12 | Neurotransmitter transport |
| SRRM2 | 3645253 | 3645260 | chr16:2747783-2747947 | Sense | None | 321 | *Constitutive inclusion | Coding | serine/arginine repetitive matrix 2 | Pre-mRNA splicing factor activity |
| ST3GAL1 | 3154398 | 3154432 | chr8:134580560-134580614 | Antisense | None | 226/320/351 | *Constitutive inclusion | 5′-UTR | ST3 beta-galactoside alpha-2,3-sialyltransferase 1 | Protein amino acid glycosylation |
| TFIP11 | 3955875 | 3955908 | chr22:25238065-25238141 | Sense | None | 358/435 | *Constitutive inclusion | 5′-UTR | tuftelin interacting protein 11 | RNA splicing |
| TYK2 | 3850278 | 3850327 | chr19:10351291-10351455 | Antisense | None | 410 | *Constitutive inclusion | 5′-UTR | tyrosine kinase 2 | Growth hormone receptor binding, protein amino acid phosphorylation |
| AY070437 | 2649710 | 2649716 | chr3:159942513-159942627 | Antisense | 116 | 231/458 | *ALT major | Non-coding transcript | Homo sapiens cytokine receptor CRL2 precursor, mRNA, complete cds | Receptor activity |
| C12orf52 | 3432641 | 3432648 | chr12:112108373-112108504 | Sense | 342 | 474 | *ALT major to constitutive | 5′-UTR | chromosome 12 open reading frame 52 | Unknown |
| NUMB | 3571347 | 3571378 | chr14:72903358-72903442 | Antisense | 205 | 289 | *ALT major to constitutive | 5′-UTR | numb homolog (Drosophila) | Nervous system development |
| ARNTL | 3321150 | 3321174 | chr11:13304536-13304590 | Antisense | 121 | 176 | ALT medium | 5′-UTR | aryl hydrocarbon receptor nuclear translocator-like | Positive regulation of transcription from RNA polymerase II promoter |
| TGFBR2 | 2615360 | 2615384 | chr3:30639695-30639769 | Antisense | 159 | 233 | ALT medium | Coding | transforming growth factor, beta receptor II (70/80 kDa) | Protein kinase activation, organ development |
| EIF4G3 | 2400373 | 2400483 | chr1:21310403-21310463 | Antisense | 97 | 158 | ALT minor | 5′-UTR | eukaryotic translation initiation factor 4 gamma, 3 | Regulation of translational initiation |
| FGF14 | 3523499 | 3523565 | chr13:101844109-101844182 | Antisense | 148 | 222 | ALT minor | Exon in a non-coding transcript | fibroblast growth factor 14 | Cell–cell signaling |
| MYO18A | 3751323 | 3751412 | chr17:24488160-24488228 | Sense | 234/270 | None | No inclusion detected | 5′-UTR | myosin XVIIIA | ATP binding, apoptosis inhibitor activity |
| VWF | 3441685 | 3441800 | chr12:6102152-6102393 | Antisense | 156 | None | No inclusion detected | Coding with ALT start | von Willebrand factor | Cell–substrate adhesion, physiological response to wounding |
| ANKRD9 | 3580357 | 3580370 | chr14:102044731-102044936 | Sense | 90/124/159 | 365 | Tissue-specific ALT medium form in muscle and minor form in testes | 5′-UTR | ankyrin repeat domain 9 | Unknown |
| CHRNA1 | 2587937 | 2587951 | chr2:175330920-175330994 | Sense | 117 | 192 | Tissue-specific ALT minor form in cerebellum and spleen, medium form in all the other tissues | Coding | cholinergic receptor, nicotinic, alpha 1 (muscle) | Neuromuscular process, signal transduction |
| CPA5 | 3023912 | 3023916 | chr7:129772915-129772972 | Antisense | 245 | 289/303 | *Tissue-specific ALT major form in cerebellum, liver, pancreas and testes, medium form in spleen | 5′-UTR | carboxypeptidase A5 | Metallocarboxypeptidase activity |
| HORMAD1 | 2434546 | 2434564 | chr1:148953715-148953778 | Antisense | 171 | 235 | *Tissue-specific ALT major form in testes, medium form in cerebellum, spleen and thyroid | Coding, skipping causing PTC of downstream exon | HORMA domain containing 1 | Mitosis |
| IL16 | 3604287 | 3604317 | chr15:79369300-79369441 | Antisense | 212 | 354 | Tissue-specific ALT minor form in spleen and testes, no inclusion in the other tissues | Coding with PTC | interleukin 16 (lymphocyte chemoattractant factor) | Leukocyte chemotaxis |
| INPP5J | 3942766 | 3942773 | chr22:29850128-29850249 | Antisense | 225 | 346 | *Tissue-specific ALT major form in testes and kidney, ALT medium form in heart, muscle, pancreas, prostate and thyroid | 5′-UTR result in ALT start from a downstream exon | inositol polyphosphate-5-phosphatase J | Inositol/phosphatidylinositol phosphatase activity |
| MICAL2 | 3320717 | 3320794 | chr11:12227307-12227369 | Sense | 148 | 211/356/397 | *Tissue-specific ALT splicing to all degrees | Coding | microtubule associated monoxygenase, calponin and LIM domain containing 2 | Metabolic process resulting in cell growth |
| MUC15 | 3366903 | 3366911 | chr11:26545175-26545262 | Sense | 178 | 266 | *Tissue-specific ALT major form in heart, pancreas and thyroid, constitutive inclusion in the other tissues | Coding with ALT start or 5′-UTR | mucin 15, cell surface associated | Membrane protein |
| NEK11 | 2642441 | 2642445 | chr3:132229464-132229536 | Sense | 202 | 275 | *Tissue-specific ALT major form in heart and muscle, medium form in the other tissues | 5′-UTR | NIMA (never in mitosis gene a)- related kinase 11 | Cell cycle |
| RGAG1 | 3987148 | 3987152 | chrX:109575037-109575152 | Sense | 196 | 312/342/419/445/483 | *Tissue-specific ALT major form in heart, muscle, spleen and thyroid, constitutive inclusion in the other tissues | 5′-UTR | retrotransposon gag domain containing 1 | Nuclear protein |
| SCRG1 | 2794006 | 2794022 | chr4:174561800-174561919 | Sense | 82 | 202 | *Tissue-specific ALT major form in cerebellum and testes, minor form in the other tissues | 5′-UTR | scrapie responsive protein 1 | Nervous system development |
| TTLL6 | 3761551 | 3761579 | chr17:44232433-44232639 | Antisense | 206 | 412 | Tissue-specific ALT minor form in testes, higher level overall expression in testes | 5′-UTR result in ALT start from a downstream exon | tubulin tyrosine ligase-like family, member 6 | Protein modification process |
| TUSC3 | 3087167 | 3087215 | chr8:15659671-15659735 | Sense | 277/368 | 432 | Tissue-specific ALT medium form in cerebellum, prostate and spleen, minor form in the other tissues. | Coding with ALT stop | tumor suppressor candidate 3 | Protein amino acid N-linked glycosylation via asparagine |
| WSCD2 | 3430620 | 3430687 | chr12:107162429-107162488 | Antisense | 173 | 233/451 | ALT minor form in all tissues, but higher inclusion level in testes | Coding | WSC domain containing 2 | Membrane protein |
| ZFAND5 | 3209623 | 3209643 | chr9:74168206-74168342 | Antisense | 218 | 364/527 | Tissue specific alternative splicing to all degrees | 5′-UTR | zinc finger, AN1-type domain 5 | DNA binding |
ALT, Alternative; PTC, premature termination codon.
*Strongly included.