General information for g7486.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as DNA repair protein complementing XP-C cells-like protein.
Parent gene
- The parent gene g7486 is located on chr_2: 23978853..23979370 (+ strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_2 | g7486 | g7486.t1 | TSS | g7486.t1 | 23974796 | 23974796 |
| chr_2 | g7486 | g7486.t1 | isoform | g7486.t1 | 23974806 | 23978853 |
| chr_2 | g7486 | g7486.t1 | exon | g7486.t1.exon1 | 23974806 | 23975083 |
| chr_2 | g7486 | g7486.t1 | cds | g7486.t1.CDS1 | 23974806 | 23975083 |
| chr_2 | g7486 | g7486.t1 | exon | g7486.t1.exon2 | 23975140 | 23975732 |
| chr_2 | g7486 | g7486.t1 | cds | g7486.t1.CDS2 | 23975140 | 23975732 |
| chr_2 | g7486 | g7486.t1 | exon | g7486.t1.exon3 | 23975879 | 23978042 |
| chr_2 | g7486 | g7486.t1 | cds | g7486.t1.CDS3 | 23975879 | 23978042 |
| chr_2 | g7486 | g7486.t1 | exon | g7486.t1.exon4 | 23978106 | 23978460 |
| chr_2 | g7486 | g7486.t1 | cds | g7486.t1.CDS4 | 23978106 | 23978460 |
| chr_2 | g7486 | g7486.t1 | exon | g7486.t1.exon5 | 23978521 | 23978853 |
| chr_2 | g7486 | g7486.t1 | cds | g7486.t1.CDS5 | 23978521 | 23978853 |
| chr_2 | g7486 | g7486.t1 | TTS | g7486.t1 | NA | NA |
Sequences
>g7486.t1 Gene=g7486 Length=3723
ATGAGACCGAAACGAGAAGCAGCAAGAAAATCACAATTGCGACTGAAAGAAAAAAAAATT
GATTTGCAACTTTCAGAAGATGAAGAAGAGAATATTGACAGTGAAGATGATTTTTCTGAT
GGGTCTTCTGATGATTATAAACCAAATGAGTCTGCAGACAAAGATGAAGAGTCAGCTCAT
GAGTCTGAAGAAGAGCCAATGAGCGAAGATGAAGATGATAGTGCTGATGAAGAAGATGAG
CAAGATAGCTTTGCTACAAATATTAAAGAAATAAACAAGAAAAAAGGTAGTAAAGTTGCA
AGTTTGAAAAAAGACGCAATCAACAAGTTTAAAAGAAAGCAGAGCAGTTTACATAAAAAT
AATTTGAGTCTTAAATTAAAAGATGTTTTAAAGAAAGCCGAATATACTAGGGGAAAACAA
AAGAGTTTATTCAGTCAATCAGATGATGATAATGAGAGAGAAAAGTCTCCAATATTTGAT
TGCTCAGGCGGTGTTAATTTATCTGATTCGTCGAGCGAATCTGATGACGATGGATCACAA
AAAATTCAAAAAAAAGATTCAACTAAAAACAAACCTAATTTGCTTAACAGTATTAATGAA
TCATCAGATACAGAGGAGGTAGATTTAAATTCCATTCATATTAAGTTAAAAGAAATTGAA
AATGCAAAAGAAAAACTTTCAAATTATAAGCATCCAAAGAAAATCATTACTTCAACCCAA
AGTCAAAAAGAAAATATAGATATAGCAGATTTGTTAGCAATGGGAGAAAATGAAACATCA
GTGAAACGTACAAAGTCAAATGATTCACAAAAGCGAGCAAAACCTACTCAAGGTGATGAT
TCAGATTCTGATAACTGGGAGGATGTTGAAGAAAACGATTCAAGCAGTAAGCAAACACCA
AAGGAAAGTGTTGAGATTGTCTTGGATGAGTTTGGAGATATTCAAAAGAAAAAGTTAGAG
AAATTAGTTGATGTTGAAGCACAATTGAAAAGGAAATTCAACAAGAGACGCAAGGAAATG
CAAGAATACCTTCATAAAACTGAACTCATATGTTGGATTTCTCATTACAGTTTTGTAAAC
AAGCGACTCAACGATATGAATTTAATTAATTCTGCTCTTAAAATGCTACCTGAAAACAGT
AAGCAATGTTATCCAAAAGAAAAAACCGATATAGACTATTTTAAGCAAATCACCAAATGG
TACAAATCTATAATGACCTTGAAGAACACAAAAATGTATTGTGAAAAACTAAAGAAACGT
CCACCACTTATGATGAGTTTAGCTATACAAATGAAATTTAAAGCAGCTATTTGTCGACGA
GATTATGTACTTATTTACATTGTGCTTTTACGAGCTTTGGGGATTCAATGTAGAATGGTT
CAGTCTGCTGTCTGCGATCCAAAAATTTGTCCTAAAAGCGAACTCATGAGTCTTTCTAAA
AATGATAGTAAGAAAACTGAAAAGAATGCTAAAAAAACAAACAATAAATCAAAAACTACA
AAAAAATCGAACAAATCGAGTAAGAGTCAAAAATCTGCTAAATCTATGAAAATTCCTCAA
TTGGATGGTGCTGATGATTTACTTGATCGTAAGAAGACAAAGAAACAAATGAAATTAAAA
GGAGCATCAGAGTACAAAGTTGATGAATCGTTTGTGAGCGTTAGCAAGGAAAGTCTCAAG
TCAAATGCAGGAAATTTATCACCTAAAATCAAGATTGAAATTAATCCACCTAATAGTATT
AATACAAAAGCATCATCCTCAAAAGTATCACAAAACGGTCCAACTAAAAGCACTTCAAAA
TTGAACATTTTTTCACCACGAAAGACTAGAAGTCGAGATACTAGAGTTGAAACATCTGTA
AAAAAAACAATAACACTACCTCAAGCAACACAAAAAAGTAAAAATTCAGGATTGATCAAA
AAAGAAGAGAAAAATGAAAAGACTACAAAAGAAACATTAAAATTACTTTCACCTCGTCGA
ACAAGAAGCATCTCTAACAGTCCATCAACTACAATTCGAAGCAATGCTAAAGAATCGAAT
TTAAAAGATAAGAAAAAAAGCGAAAACATTACTACATCTATTTCTCATCGATTAGAAAAT
AGATCTCGTAGTCCATGTACATCAGCTGAAGTTCAAAAACTAGACGCGCAAAAGTTGAAA
CAAAATGTGAAAACTGACGCACTCAAAGTTAATACTCCTATTTCTCGTCGTTTGAGAAGT
AAAAGTACTGATAATAATCCAAATTTGAGTGCAAATGATTCACGAAAGCGCACATCAACT
GTAAAAGATGAGATTGAAAATAAGAGAATGAGGATGAATTCAAATGCAAAAAAGAAACCT
GCTGAAGTAATAAAAAGTGACGAAAAATCAAAAAAGCGTAATGCACCATCTGAAGAAAAA
GATGATGTTGCATCGAAGAAGAAAAAGCTTTATGAAAATAATTTTTTGCAAAACTTCTTT
GGAGAACCTGAATCAGATTCAGATGAGAGCTTAAAATATTTTAAATCAACTACCAAAAAG
GGAAGCAAAGCTGAAAAGTCTGTAAAGAACGAACATCCTTCAACATCATCAAAAGTTGAC
ACAGCACCACGCACAACTTCAACAAAAATCGATCGCAGAATTCTCTCATCCGATGATGAA
GAAAATTTGAACGTGGCTGCTGATCAAAGTGGTTCATCAGCTAAGAAATCAAAAGGAATC
GATATTTGGGTAGAAGTTTATTCTGAAAAAGATGAGAAATGGATTGCAATAGATGTTTTC
CAAAATAAAATTGATTGTGTAAAAGATATAATGGCAAAGGCAACTCATCCATTAGTGTAT
GTTTTCGCTTGGAACAATGATAATTCTCTCAAGGATGTGACAGCTCGTTATTGTCCTAAT
TTAAACACAACTGTTAGAAAAATGAGAGTCGATCGTGACTATTTGAACAAAATTTTAATT
ATGTATCCTGGAACAAAGACAGCGCGTGATTTGAAAGAAGACGATGAGCTGAATAAATTA
CAATTAGCTCAACCAATGCCAACTTCTATCGCAGAATTTAAAAATCATCCTCTTTATGCA
CTAAAACGTCATCTTTTGAAGTATGAAGCTATTTATCCACCTGAACCACCGATTTTGGGC
TACATTCGAGATGAACCGATTTATCCTCGAGATTGTGTCTTTGTTTGTCGTTCAAGAGAA
ACATGGTTGAAAGAAGCTCGTGTTGTGAAATTATATGAAGAGCCATATAAAATTGTCAAA
ACCATGAAATGGAACAAGCCAACTAACAAACTCATGAAAGATGTGCCATTAGAATTGTTT
GGTATATGGCAAACAAAAGATTATGAGCCACCAACAGCTGAAAATGGAATAGTACCACGC
AATGGCTATGGCAATGTAGAGCTGTTTAAGCCTCAAATGTTACCTTATGGTACAGTGCAT
TTACAACTACCTGGCCTTCAAAAAGTTTGCAAAAAACTAGGCGTTGATTGTGCTCAAGCA
GTTGTTGGATTTGATTCGAGTGGAGGTTGGCCTTATCCGGTTTATGATGGTTTCGTAATT
TGCAAAGAATTCGAGGAAAAAGTTGTTGATGCCTGGAATCGAGAACAAGAAGAAATTGAA
CGAAAGGAAAGAGAAAAAATCGAAAAACGTGTTTACGGAAATTGGAAAAAGCTTATTAAA
GGATTACTTATTCGCGAGCGTTTAAAGTTGAAATATAATTTTGATAATAATTTGGATGAT
TAA
>g7486.t1 Gene=g7486 Length=1240
MRPKREAARKSQLRLKEKKIDLQLSEDEEENIDSEDDFSDGSSDDYKPNESADKDEESAH
ESEEEPMSEDEDDSADEEDEQDSFATNIKEINKKKGSKVASLKKDAINKFKRKQSSLHKN
NLSLKLKDVLKKAEYTRGKQKSLFSQSDDDNEREKSPIFDCSGGVNLSDSSSESDDDGSQ
KIQKKDSTKNKPNLLNSINESSDTEEVDLNSIHIKLKEIENAKEKLSNYKHPKKIITSTQ
SQKENIDIADLLAMGENETSVKRTKSNDSQKRAKPTQGDDSDSDNWEDVEENDSSSKQTP
KESVEIVLDEFGDIQKKKLEKLVDVEAQLKRKFNKRRKEMQEYLHKTELICWISHYSFVN
KRLNDMNLINSALKMLPENSKQCYPKEKTDIDYFKQITKWYKSIMTLKNTKMYCEKLKKR
PPLMMSLAIQMKFKAAICRRDYVLIYIVLLRALGIQCRMVQSAVCDPKICPKSELMSLSK
NDSKKTEKNAKKTNNKSKTTKKSNKSSKSQKSAKSMKIPQLDGADDLLDRKKTKKQMKLK
GASEYKVDESFVSVSKESLKSNAGNLSPKIKIEINPPNSINTKASSSKVSQNGPTKSTSK
LNIFSPRKTRSRDTRVETSVKKTITLPQATQKSKNSGLIKKEEKNEKTTKETLKLLSPRR
TRSISNSPSTTIRSNAKESNLKDKKKSENITTSISHRLENRSRSPCTSAEVQKLDAQKLK
QNVKTDALKVNTPISRRLRSKSTDNNPNLSANDSRKRTSTVKDEIENKRMRMNSNAKKKP
AEVIKSDEKSKKRNAPSEEKDDVASKKKKLYENNFLQNFFGEPESDSDESLKYFKSTTKK
GSKAEKSVKNEHPSTSSKVDTAPRTTSTKIDRRILSSDDEENLNVAADQSGSSAKKSKGI
DIWVEVYSEKDEKWIAIDVFQNKIDCVKDIMAKATHPLVYVFAWNNDNSLKDVTARYCPN
LNTTVRKMRVDRDYLNKILIMYPGTKTARDLKEDDELNKLQLAQPMPTSIAEFKNHPLYA
LKRHLLKYEAIYPPEPPILGYIRDEPIYPRDCVFVCRSRETWLKEARVVKLYEEPYKIVK
TMKWNKPTNKLMKDVPLELFGIWQTKDYEPPTAENGIVPRNGYGNVELFKPQMLPYGTVH
LQLPGLQKVCKKLGVDCAQAVVGFDSSGGWPYPVYDGFVICKEFEEKVVDAWNREQEEIE
RKEREKIEKRVYGNWKKLIKGLLIRERLKLKYNFDNNLDD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g7486.t1 | Coils | Coil | Coil | 1182 | 1209 | - |
| 9 | g7486.t1 | Gene3D | G3DSA:3.10.620.30 | - | 896 | 1005 | 7.2E-17 |
| 11 | g7486.t1 | Gene3D | G3DSA:2.20.20.110 | - | 1006 | 1043 | 2.4E-5 |
| 10 | g7486.t1 | Gene3D | G3DSA:3.30.70.2460 | - | 1124 | 1195 | 1.7E-18 |
| 41 | g7486.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 102 | - |
| 42 | g7486.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 25 | - |
| 30 | g7486.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 26 | 40 | - |
| 38 | g7486.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 41 | 56 | - |
| 28 | g7486.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 57 | 81 | - |
| 20 | g7486.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 82 | 102 | - |
| 27 | g7486.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 137 | 207 | - |
| 34 | g7486.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 137 | 157 | - |
| 32 | g7486.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 174 | 188 | - |
| 31 | g7486.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 189 | 205 | - |
| 37 | g7486.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 258 | 302 | - |
| 23 | g7486.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 261 | 281 | - |
| 22 | g7486.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 480 | 529 | - |
| 43 | g7486.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 480 | 494 | - |
| 24 | g7486.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 558 | 805 | - |
| 36 | g7486.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 572 | 605 | - |
| 35 | g7486.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 620 | 635 | - |
| 26 | g7486.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 636 | 657 | - |
| 25 | g7486.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 658 | 676 | - |
| 19 | g7486.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 677 | 692 | - |
| 33 | g7486.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 693 | 715 | - |
| 21 | g7486.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 724 | 755 | - |
| 40 | g7486.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 756 | 805 | - |
| 29 | g7486.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 838 | 875 | - |
| 39 | g7486.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 838 | 853 | - |
| 4 | g7486.t1 | PANTHER | PTHR12135 | DNA REPAIR PROTEIN XP-C / RAD4 | 50 | 665 | 1.3E-169 |
| 6 | g7486.t1 | PANTHER | PTHR12135:SF0 | DNA REPAIR PROTEIN COMPLEMENTING XP-C CELLS | 50 | 665 | 1.3E-169 |
| 5 | g7486.t1 | PANTHER | PTHR12135 | DNA REPAIR PROTEIN XP-C / RAD4 | 719 | 1235 | 1.3E-169 |
| 7 | g7486.t1 | PANTHER | PTHR12135:SF0 | DNA REPAIR PROTEIN COMPLEMENTING XP-C CELLS | 719 | 1235 | 1.3E-169 |
| 1 | g7486.t1 | Pfam | PF03835 | Rad4 transglutaminase-like domain | 875 | 997 | 2.0E-25 |
| 3 | g7486.t1 | Pfam | PF10403 | Rad4 beta-hairpin domain 1 | 1004 | 1053 | 2.6E-18 |
| 2 | g7486.t1 | Pfam | PF10405 | Rad4 beta-hairpin domain 3 | 1118 | 1190 | 2.7E-26 |
| 13 | g7486.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 441 | - |
| 15 | g7486.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 442 | 461 | - |
| 14 | g7486.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 462 | 1240 | - |
| 16 | g7486.t1 | SMART | SM01030 | BHD_1_2 | 1002 | 1054 | 2.3E-27 |
| 17 | g7486.t1 | SMART | SM01031 | BHD_2_2 | 1056 | 1111 | 9.0E-20 |
| 18 | g7486.t1 | SMART | SM01032 | BHD_3_2 | 1118 | 1192 | 7.3E-43 |
| 8 | g7486.t1 | SUPERFAMILY | SSF54001 | Cysteine proteinases | 345 | 1017 | 7.65E-41 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005634 | nucleus | CC |
| GO:0003677 | DNA binding | MF |
| GO:0003684 | damaged DNA binding | MF |
| GO:0006289 | nucleotide-excision repair | BP |
KEGG
Orthology
- This transcript has been annotated with K10838 (xeroderma pigmentosum group C-complementing protein)
Pathway
- This transcript belongs to the following pathways
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.
