Table 2.
Features of the Human Class III Genes
| Human gene | mRNA length | Evidence for gene model | ATG exon | CDS length | Alternative promoter | Alternative splice forms | Read-through transcripts | Notes |
|---|---|---|---|---|---|---|---|---|
| BAT1 | 2128 | mRNA/ESTs | 1 or 2 | 1284 | Start at exon 1 or 2 | Alternative exon 2 length | mRNA/ESTs | |
| ATP6V1G2 | 1631 | ESTs | 1 or 2 | 354 | Start at exon 1 or 2 | Alternative exon 1 length | mRNA/ESTs | May be brain-specific |
| NFKBIL1 | 1394 | mRNA/ESTs | 2 | 1074 | Two alternative exon 1 | No | No | Mouse may have an extra 3′ exon |
| LTA | 1408 | mRNA/ESTs | 2 | 615 | Two start sites for exon 1 | Alternative exon 1 length; combine exons 2 and 3 | No | |
| TNF | 1675 | mRNA/ESTs | 1 | 699 | No | No | No | |
| LTB | 1542 | mRNA/ESTS | 1 | 918 | No | Exon 2 skipped | No | 3 or 4 exons |
| LST1 | 818 | mRNA/ESTs | 2 | 291 | Four alternative exon 1 | Exons 3 and 4 skipped | No | 2, 3, 4, or 5 exons |
| NCR3 | 1043 | mRNA/ESTS | 1 | 603 | No | Alternative location for exon 4 | No | |
| AIF1 | 691 | mRNA/ESTs | 1 | 441 | No | Alternative exon 1 length; other minor splice variants | No | |
| BAT2 | 6879 | mRNA/ESTs | 2 | 6468 | No | Alternative exon 2 length | No | |
| BAT3 | 3696 | mRNA/ESTs | 2 | 3378 | Four alternative exon 1 | Alternative exon 7 length; exon 24 skipped in several ESTs | No | |
| APOM | 854 | mRNA/ESTs | 2 | 670 | Two alternative exon 1 | No | No | |
| C6orf47 | 2476 | mRNAs (2) | 1 | 882 | ND | No | No | Single exon gene |
| BAT4 | 1778 | mRNA/ESTs | 2 or 3 | 1068 | Start at exon 2 or 3 | Alternative exon 2 length | No | |
| CSNK2B | 1055 | mRNA/ESTs | 2 | 645 | Two alternative exon 1 | No | No | |
| LY6G5B | 2589 | mRNA/ESTs | 1 or 2 | 438 | Start at exon 1 or 2 | Exon 1 and 2 conjoined | No | |
| LY6G5C | 951 | mRNA/partial ESTs | 5′ partial | 675 | Four alternative exon 1 | Variable location for exon 2 | No | No mouse ESTs/ATG start unclear |
| BAT5 | 2065 | mRNA/ESTs | 1 | 1674 | Two alternative exon 1 | No | No | |
| G6F | ND | GenScan | ND | 873 | ND | ND | mRNA | |
| LY6G6E | 383 | mRNAs (3) | ND | 378 | No | Exon 2 and 3 conjoined | mRNA | Probable pseudogene |
| LY6G6D | 1266 | mRNAs (3) | 1 | 399 | No | Alternative exon 3 length; exons 1 and 2 conjoined | mRNA | |
| LY6G6C | 991 | mRNA/ESTs | 1 | 375 | Two alternative exon 1 | Extra exon in one EST | No | |
| C6orf25 | 2394 | mRNAs (8) | 1 | 711 | No | Exons 3 and 4 skipped | No | |
| DDAH2 | 1685 | mRNA/ESTs | 2 | 855 | Two alternative exon 1 | No | No | |
| CLIC1 | 1222 | mRNA/ESTs | 1 or 2 | 723 | Start at exon 1 or 2 | ND | No | |
| MSH5 | 2887 | mRNA/ESTs | 2 | 2505 | No | Alternative exons 1 and 7 length | mRNA/ESTs | |
| C6orf26 | 1055 | ESTs | 1 | 444 | Two alternative exon 1 | Exons 4 and 5 conjoined | mRNA/ESTs | |
| C6orf27 | 4337 | mRNA (2) | 2 | 2673 | ND | ND | No | |
| VARS2 | 4169 | mRNA/ESTs | 2 | 3795 | No | No | No | GC splice donor at exon 19 |
| LSM2 | 864 | mRNA/ESTs | 1 | 285 | Two minor EST variants | No | No | |
| HSPA1L | 2539 | mRNA/ESTs | 2 | 1923 | No | No | No | |
| HSPA1A | 2337 | mRNA/ESTs | 1 | 1923 | No | No | No | |
| HSPA1B | 2528 | mRNA/ESTs | 1 | 1923 | No | No | No | |
| C6orf48(G8) | 1050 | mRNA/ESTs | ND | ND | Three alternative exon 1 | Variable location for exon 3/exon 3 skipped | No | Possible pseudogene |
| NEU1 | 2045 | mRNA/ESTs | 1 | 1245 | No | No | mRNA | |
| C6orf29 | 2577 | mRNA/ESTs | 1 | 2127 | No | No | mRNA | GC splice acceptor at exon 13 |
| BAT8 | 3940 | mRNA/ESTs | 1 | 3570 | Two alternative exon 1 | Exon 10 skipped | No | |
| C6orf46(G10) | 1773 | mRNA(1) | 2 | 1281 | ND | ND | mRNA/EST | Spliced to exon 4 of C2 |
| C2 | 2772 | mRNA/ESTs | 1 | 2256 | No | Alternatie exon 8 length | mRNA/EST | |
| BF | 2861 | mRNA/ESTs | 1 | 2292 | No | Alternative exons 2 and 3 length in some ESTs | No | |
| RDBP | 1476 | mRNA/ESTs | 2 | 1140 | No | No (only one minor EST variant) | No | |
| SKIV2L | 3961 | mRNA/ESTs | 1 | 3738 | No | No | No | |
| DOM3Z | 1619 | mRNA/ESTs | 1 or 2 | 1188 | Start at exon 1 or 2 | Alternative exon 4 length | No | |
| STK19 | 1720 | mRNA/ESTs | 1 | 1092 | No | Exon 3 skipped | No | |
| C4A | 5459 | mRNA/ESTs | 1 | 5232 | No | Minor EST variants | No | |
| CYP21A1P | ND | ND | ND | ND | ND | Pseudogene | ||
| C4B | 5459 | mRNA/ESTs | 1 | 5232 | No | Minor EST variants | No | |
| CYP21A2 | 2108 | mRNA/ESTs | 1 | 1485 | No | Alternative exon 2 length; exon 2 skipped | No | |
| TNXB | 13268 | GenScan/partial mRNA/ESTs | 2 | 12867 | No | Alternative exon 4 length | mRNA | |
| CREBL1 | 2655 | mRNA/ESTs | 1 | 2100 | No | Minor EST variants | mRNA | |
| FKBPL | 1344 | mRNA/ESTs | 2 | 1047 | No | Extra exon in 1 EST | No | |
| C6orf31 | 1917 | mRNA/ESTs | 2 | 918 | Three alternative exon 1 | Highly complex; internal terminations | No | No clear gene model |
| PPT2 | 2022 | mRNA/ESTs | 2 | 906 | Three alternative exon 1 | No | mRNA/ESTs | |
| EGFL8 | 1262 | mRNA/ESTs | 2 | 879 | No | Alternative exon 1 and 6 length | mRNA/ESTs | |
| AGPAT1 | 1989 | mRNA/ESTs | 2 | 849 | Four alternative exon 1 | Exons 3 and 4 skipped in 1 mRNA | No | |
| RNF5 | 1172 | mRNA/ESTs | 1 | 540 | No | Minor EST variants | No | |
| AGER | 1489 | mRNA/ESTs | 1 | 1212 | No | 1 mRNA has exon 3 length variation and skips exon 8; some ESTs skip exon 11 | No | |
| PBX2 | 3202 | mRNA/ESTs | 1 | 1290 | Minor EST variants | No | No | |
| C6orf9(short) | 1477 | mRNA/ESTs | 1 | 480 | Two alternative exon 1 | Four extra exons in 1 mRNA variant | No | |
| NOTCH4 | 6742 | mRNA/partial ESTs | 1 | 6006 | ND | ND | No | GC splice donor at exon 20 |
Gene models were constructed based on the best supporting evidence, giving highest weight to full-length cDNA sequences (mRNAs). For genes without supporting EST evidence, the number of mRNAs is given in parentheses. The length of the coding sequences was determined from the longest inframe translation. For the cases of pseudogenes (CYP21A1P), RNA genes (C6orf48), and genes for which there was minimal supporting evidence (e.g., G6F, LY6G6E, C6orf46, C6orf27, Notch4), gene models of alternative splice variants cannot be precisely determined (ND). cDNA/EST sequences were identified from the April 2003 assembly found in http://genome.cse.ucsc.edu.