Table 3

Repeat gap polymorphic variants
Ensembl ID
 Locus link ID
 AA
 Position*
 Size*
 Size variant
 Len. protein*
 Number of ESTs†
 Codon max run‡
 Codon hom.§
 Max run size‡
 Description
ENSP00000282388
 ZFP36L2
 Q
 394
 7
 9
 494
 195
 CAG
 1
 7
 Butyrate response factor 2 (TIS11D protein)
ENSP00000324790
 TDE2L
 Q
 363
 5
 6
 455
 56
 CAG
 1
 5
 Tumor differentially expressed 2-like
ENSP00000317661
 CACNA1A
 Q
 2,311
 13
 11
 2,505
 10
 CAG
 1
 13
 Voltage-dependent P/Q-type calcium channel alpha-1A subunit (CACNA1A)
ENSP00000280665
 DCP1B
 Q
 251
 10
 11
 617
 7
 CAG
 0.90
 9
 mRNA decapping enzyme 1B
ENSP00000348018
 ZNF384
 Q
 439
 16
 15
 516
 23
 CAG
 0.88
 14
 Zinc finger protein 384 (nuclear matrix transcription factor 4)
ENSP00000264883
Q
 92
 5
 6
 507
 33
 CAG
 0.80
 4
 Nucleoporin p54 (54 kDa nucleoporin)
ENSP00000229279
 ATN1
 Q
 482
 19
 16
 1,189
 7
 CAG
 0.79
 15
 Atrophin-1 (dentatorubral-pallidoluysian atrophy protein; DRPLA)
ENSP00000265773
 SMARCA2
 Q
 215
 23
 22
 1,590
 8
 CAG
 0.57
 13
 Possible global transcription activator SNF2L2 (SNF2-alpha)
ENSP00000354597
 KIAA0476
 Q
 815
 16
 13
 1,417
 8
 CAG
 0.56
 9
 Unknown function
ENSP00000272804
 KIAA1946
 Q
 42
 14
 15,16
 428
 4
 CAG
 0.43
 6
 KIAA1946
ENSP00000313603
 ABCF1
 Q
 63
 10
 9,11
 845
 20
 CAG
 0.40
 4
 ATP-binding cassette. sub-family F, member 1
ENSP00000252891
 NUMBL
 Q
 426
 20
 18
 609
 9
 CAG
 0.35
 7
 Numb-like protein (Numb-R)
ENSP00000304689
 THAP11
 Q
 103
 29
 28
 314
 12
 CAG
 0.34
 10
 THAP domain protein 11 (HRIHFB2206)
ENSP00000345671
 NCOA3
 Q
 1,243
 29
 28
 1,420
 8
 CAG
 0.31
 9
 Nuclear receptor coactivator 3 isoform b
ENSP00000301187
 TMC4
 E
 56
 5
 4
 706
 12
 GAG
 1
 5
 Transmembrane channel-like 4
ENSP00000315064
 MAGEF1
 E
 152
 6
 4,7
 307
 49
 GAG
 1
 6
 Melanoma-associated antigen F1 (MAGE-F1 antigen)
ENSP00000340702
E
 630
 10
 9,11
 686
 6
 GAG
 1
 10
 106 kDa O-GlcNAc transferase-interacting protein
ENSP00000262680
 NRD1
 E
 149
 5
 4
 1,219
 33
 GAA
 0.80
 4
 Nardilysin precursor (EC 342461) (N-arginine dibasic convertase)
ENSP00000252455
 PRKCSH
 E
 312
 13
 12
 528
 15
 GAG
 0.77
 10
 Glucosidase II beta subunit precursor (PKCSH)
ENSP00000253237
 GRWD1
 E
 123
 6
 5
 446
 79
 GAA
 0.50
 3
 Glutamate-rich WD-repeat protein 1
ENSP00000262710
 ACIN1
 E
 269
 12
 11
 1,341
 5
 GAG
 0.50
 6
 Apoptotic chromatin condensation inducer in the nucleus (Acinus)
ENSP00000346324
E
 60
 7
 8
 109
 249
 GAG
 0.43
 3
 Predicted: similar to prothymosin alpha
ENSP00000263274
 LIG1
 E
 152
 6
 5
 919
 19
 GAG/GAA
 0.33
 2
 DNA ligase I (polydeoxyribonucleotide synthase [ATP])
ENSP00000304498
 PODXL2
 E
 161
 11
 9
 529
 39
 GAG
 0.27
 3
 Endoglycan
ENSP00000345444
 APLP2
 E
 220
 7
 5
 707
 84
 GAG/GAA
 0.14
 1
 Amyloid-like protein 2 precursor (CDEI-box binding protein)
ENSP00000350479
 RPL14
 A
 149
 10
 11,12
 215
 213
 GCT
 1
 10
 60S ribosomal protein L14 (CAG-ISL 7)
ENSP00000255608
 BTBD2
 A
 40
 14
 15,16
 525
 9
 GCC
 0.93
 13
 BTB/POZ domain containing protein 2
ENSP00000305783
 RBM23
 A
 368
 9
 10
 423
 53
 GCT
 0.56
 5
 RNA-binding region containing protein 4 (pplicing factor SF2)
ENSP00000346678
A
 130
 6
 5
 232
 50
 GCA
 0.33
 2
 Similar to splicing factor. arginine/serine-rich 4 isoform c
ENSP00000330188
A
 266
 5
 6
 434
 50
 GCA/GCT
 0.20
 1
 Similar to splicing factor. arginine/serine-rich 4 isoform c
ENSP00000324573
 FLII
 A
 410
 6
 5
 1,269
 25
 GCA/GCT
 0.17
 1
 Flightless-I protein homolog
ENSP00000255631
G
 24
 6
 9
 359
 96
 GGC
 0.83
 5
 hsp70-interacting protein
ENSP00000246533
 CAPNS1
 G
 36
 20
 21
 268
 100
 GGC
 0.50
 10
 Calpain small subunit 1 (CSS1)
ENSP00000218072
 SRPX
 L
 16
 7
 6
 464
 21
 CTG
 1
 7
 Sushi repeat-containing protein SRPX precursor
ENSP00000315602
 CHRNA3
 L
 16
 7
 6
 505
 5
 CTG
 1
 7
 Neuronal acetylcholine receptor protein, alpha-3 chain precursor
ENSP00000344134
 MOG
 L
 16
 6
 5
 206
 13
 CTC
 1
 6
 Myelin-oligodendrocyte glycoprotein precursor
ENSP00000240617
L
 17
 8
 7
 553
 22
 CTG
 0.88
 7
 Unknown function
ENSP00000304072
 DDX54
 K
 89
 5
 6
 882
 97
 AAG
 1
 5
 DEAD-box protein 54
ENSP00000285814
 MKI67IP
 K
 211
 5
 6
 293
 79
 AAG
 0.60
 3
 MKI67 (FHA domain) interacting nucleolar phosphoprotein
ENSP00000276212
 GPC3
 P
 25
 6
 5
 580
 54
 CCG
 0.83
 5
 Glypican-3 precursor (Intestinal protein OCI-5)
ENSP00000312296
 CKAP4
 P
 42
 5
 4
 602
 11
 CCG
 0.80
 4
 Cytoskeleton-associated protein 4
ENSP00000286910
 PCGF6
 P
 23
 5
 7
 350
 7
 CCT
 0.40
 2
 Polycomb group ring finger 6 isoform a
ENSP00000301653
 KRT16
 S
 72
 5
 6
 473
 248
 AGC
 1
 5
 Keratin, type I cytoskeletal 16 (cytokeratin 16)
ENSP00000307804
 MLLT3
 S
 382
 9
 7
 568
 5
 AGC/TCC
 0.11
 1
 AF-9 protein

*Refers to the Ensembl protein. Len., length. Size, size of repeat. †Number of ESTs covering the repeat. ‡Max run, longest pure codon run within the repeat-encoding sequence. §Codon hom. (homogeneity), size of Max run divided by size of the repeat. AA, amino acid. Size variant can include several size variants (for example, 15,16)

Mularoni et al. Genome Biology 2006 7:R33   doi:10.1186/gb-2006-7-4-r33