Table 1.
Characteristics of human claudin transcripts and protein products
| Claudins and Their Isoforms | Characteristics of Transcripts Variants | Characteristics of Resulting Isoforms | PDZ-Binding Motif | Number of Amino Acids (N-T1-E1-T2-I-T3-E2-T4-C) | Molecular Mass, kDa | mRNA ID |
|---|---|---|---|---|---|---|
| 1 | 4 exons | Yes | 211 | 22.8 | NM_021101.4 | |
| 4 exons in CDS | (7-21-53-21-13-21-27-21-27) | |||||
| 2 | 2 exons | Variants 1–3 encode the same protein | Yes | 230 | 24.4 | NM_020384.3 |
| 1 exon in CDS | (7-21-53-21-14-21-25-21-47) | NM_001171092.1 | ||||
| 3 variants using alternate 5′ noncoding exons | NM_001171095.1 | |||||
| 3 | 1 exon | Yes | 220 (8-21-51-21-14-21-23-21-40) | 23.3 | NM_001306.3 | |
| 4 | 1 exon | Yes | 209 (7-21-53-21-15-21-22-21-28) | 22.1 | NM_001305.3 | |
| 5 | Variant 1: 1 exon | Variants 1 and 2 encode the same protein | Yes | 303 (92-21-53-21-20-21-16-21-38) | 31.6 | NM_001130861.1 |
| Variant 2: 2 exons | Long and short version due to two start codons within the intracellular NH2 terminus | NM_003277.3 | ||||
| Both: 1 exon in CDS | ||||||
| Variant 2 lacks segment in 5′ UTR | 218 (7-21-53-21-20-21-16-21-38) | 23.2 | ||||
| 6 | 2 exons | Yes | 220 (7-21-53-21-14-21-23-21-39) | 23.3 | NM_021195.4 | |
| 1 exon in CDS | ||||||
| 7 (isoform 1) | Variant 1: 4 exons | Variants 1 and 2 encode the same isoform | Yes | 211 (7-21-53-21-15-21-22-21-30) | 22.4 | NM_001307.5 |
| Variant 2: 5 exons | NM_001185022.1 | |||||
| 4 exons in CDS | ||||||
| Two alternate 5′ UTR sequences. Variants 1 and 2 | ||||||
| 7 (isoform 2) | 3 exons | Shorter and distinct COOH terminus | No* | 145 (topology not available) | 15.2 | NM_001185023.1 |
| 3 exons in CDS | ||||||
| Lacks exon 3 in the 3′ CDS | ||||||
| 8 | 1 exon | Yes | 225 (7-21-53-21-15-21-28-21-38) | 24.8 | NM_199328.2 | |
| 9 | 1 exon | Yes | 217 (7-21-53-21-14-21-22-21-37) | 22.9 | NM_020982.3 | |
| 10a | 5 exons | Yes | 226 (0-21-57-21-14-21-24-21-47) | 24.3 | NM_182848.3 | |
| 5 exons in CDS | ||||||
| 10a_i1 | 5 exons | Lacks an internal segment near the NH2 terminus (within ECL1), compared with isoform 10a | Yes | 207 (0-21-38-21-14-21-24-21-47) | 22.2 | NM_001160100.1 |
| 5 exons in CDS | ||||||
| Variant a_v1 uses an alternate in-frame splice site in the 5′ coding region, compared with variant a. | ||||||
| 10b | 5 exons | Longer and distinct NH2 terminus, compared with isoform 10a | Yes | 228 (0-21-59-21-14-21-24-21-47) | 24.5 | NM_006984.4 |
| 5 exons in CDS | ||||||
| differs in the 5′ UTR and 5' coding region, uses alternate promoter and exon 1, compared with variant a. | ||||||
| 11 (isoform 1) | 3 exons | Yes | 207 (1-21-60-21-19-21-14-21-29) | 22 | NM_005602.5 | |
| 3 exon in CDS | ||||||
| 11 (isoform 2) | 2 exons | shorter NH2 terminus, lacking aa 1-84 of variant 1 | Yes | 123 (topology not available) | 12.9 | NM_001185056.1 |
| 2 exon in CDS | ||||||
| Alternate 5′ exon, resulting in downstream in-frame AUG start codon | ||||||
| 12 | Variant 1: 5 exons | Variants 1-3 encode the same protein | No* | 244 (10-21-56-21-27-21-18-21-49) | 27.1 | NM_001185072.2 |
| Variants 2 and 3: 3 exons | NM_001185073.2 | |||||
| 1 exon in CDS | NM_012129.4 | |||||
| Variants 2 and 3 use alternate splice site and/or lack an exon in 5′ UTR | ||||||
| 14 | Variants 1-4: 3 exons | Variants 1-5 encode the same protein | Yes | 239 (7-21-53-21-13-21-26-21-56) | 25.7 | NM_144492.2 |
| Variant 5: 2 exons | NM_012130.2 | |||||
| 1 exon in CDS | NM_001146077.1 | |||||
| 5 variants differing in 5′ UTR | NM_001146078.1 | |||||
| Alternative names: | NM_001146079.1 | |||||
| variant 1 =α, 2 = ε, 3 =δ, 4 = γ, 5 =β | ||||||
| 15 | Variant 1: 6 exons | Variants 1 and 2 encode the same protein | Yes | 228 (3-21-55-21-19-21-17-21-50) | 24.4 | NM_001185080.1 |
| Variant 2: 5 exons | NM_014343.2 | |||||
| 5 exons in CDS | ||||||
| Variant 2 has shorter and alternate 5′ UTR | ||||||
| 16 | 5 exons | Long and short version due to two start codons within the intracellular NH2 terminus | Yes | 305 (73-21-56-21-14-21-33-21-45) | 33.8 | NM_006580.3 |
| 5 exons in CDS | 235 (3-21-56-21-14-21-33-21-45) | 26.1 | ||||
| Two start codons | ||||||
| 16 | 2 exons | Lacks an internal segment, shorter and distinct COOH terminus | No* | 119 (topology not available) | 13.5 | DQ305102 |
| 2 exons in CDS | ||||||
| Lacks exons 2 to 4, frame shift results in earlier stop codon | ||||||
| 17 | 1 exon | Yes* | 224 (7-21-53-21-22-21-19-21-39) | 24.6 | NM_012131.2 | |
| 18A1 (also: 18-1) | 5 exons | Yes | 261 (6-21-53-21-21-21-31-21-66) | 27.9 | NM_016369.3 | |
| 5 exons in CDS | ||||||
| 18A2 (also: 18-2) | 5 exons | Same size but different NH2 terminus, as compared with isoform A1 | Yes | 261 (6-21-53-21-21-21-31-21-66) | 27.7 | NM_001002026.2 |
| 5 exons in CDS | ||||||
| alternate 5′ exon | ||||||
| 19a | 5 exons | No* | 224 (7-21-53-21-15-21-22-21-43) | 23.2 | NM_148960.2 | |
| 5 exons in CDS | ||||||
| 19b | 4 exons | Shorter and distinct COOH terminus compared with isoform a | Yes | 211 (7-21-53-21-15-21-22-21-30) | 22.1 | NM_001123395.1 |
| 4 exons in CDS | ||||||
| Additional segment in coding region compared with variant 1. | ||||||
| 19c | 3 exons | Shorter and distinct COOH terminus compared with isoform a | Yes* | 218 (topology not available) | 22.7 | NM_001185117.1 |
| 3 exons in CDS | ||||||
| Lacks exon in CDS, which results in frame-shift, and contains additional segment in the 3′ region compared with variant 1. | ||||||
| 20 | 2 exons | Yes* | 219 (7-21-53-21-16-21-21-21-38) | 23.5 | NM_001001346.3 | |
| 1 exon in CDS | ||||||
| 21 | 1 exon in CDS | No* | 229 (10-21-50-21-22-21-19-21-44) | 25.4 | NM_001101389.1 | |
| 22 | 1 exon | Yes | 220 (10-20-51-21-15-21-26-21-35) | 24.5 | NM_001111319.1 | |
| 1 exon in CDS | ||||||
| 23 | 1 exon | Yes | 292 (3-21-57-21-8-21-29-21-111) | 31.9 | NM_194284.2 | |
| 1 exon in CDS | ||||||
| 24 | 1 exon in CDS | (Uniprot: 205 aa, COOH terminus only 23 aa) | No* | 220 (10-21-50-21-15-21-23-21-38) | 24.4 | NM_001185149.1 |
| 25 | 6 exons | Long and short version due to two start codons within the intracellular NH2 terminus | No* | 276 (27-21-115-21-13-21-20-21-17) | 31.1 | NM_001040182.1 |
| 6 exon in CDS | 253 (4-21-115-21-13-21-20-21-17) | 28.6 | ||||
| 26 | 1 exon in CDS | No* | 223 (6-21-78-21-7-21-34-21-14) | 24.2 | NM_001146336.1 | |
| 27 | 1 exon in CDS | No* | 208 (topology not available) | 21.6 |
*
Presence of a PDZ-binding motif determined using the model suggested by Stiffler et al. (334); presence of all other motifs determined by Stiffler et al. (334). Number of amino acids is according to the uniprot database (http://www.uniprot.org/): N, intracellular NH2 terminus; T1 to T4, transmembrane regions 1 to 4; E1, E2, first and second extracellular loop, respectively; I, intracellular loop; C, intracellular COOH terminus. Molecular mass was calculated from amino acid sequence (http://www.bioinformatics.org/sms/prot_mw.html). Nomenclature follows the proposal of Mineta et al. (246) and Lal-Nag and Morin (200), taking sequence NP_001094859 as claudin-21 (NCBI: putative claudin-25), sequence NP_001035272 as claudin-25 (NCBI: claudin domain-containing protein 1, CLDND1), sequence NP_001139808 as claudin-26 (NCBI: transmembrane protein 114, TMEM114). As described by Mineta et al. (246), since August 2010 the sequence for claudin-27 (XP_946151) is no longer available through the NCBI database.