General information for g13013.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Bloom syndrome protein-like protein.
Parent gene
- The parent gene g13013 is located on chr_1: 27502166..27502962 (- 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_1 | g13013 | g13013.t1 | TTS | g13013.t1 | 27498501 | 27498501 |
| chr_1 | g13013 | g13013.t1 | isoform | g13013.t1 | 27498558 | 27502962 |
| chr_1 | g13013 | g13013.t1 | exon | g13013.t1.exon1 | 27498558 | 27499807 |
| chr_1 | g13013 | g13013.t1 | cds | g13013.t1.CDS1 | 27498558 | 27499807 |
| chr_1 | g13013 | g13013.t1 | exon | g13013.t1.exon2 | 27499866 | 27499949 |
| chr_1 | g13013 | g13013.t1 | cds | g13013.t1.CDS2 | 27499866 | 27499949 |
| chr_1 | g13013 | g13013.t1 | exon | g13013.t1.exon3 | 27500025 | 27500461 |
| chr_1 | g13013 | g13013.t1 | cds | g13013.t1.CDS3 | 27500025 | 27500461 |
| chr_1 | g13013 | g13013.t1 | exon | g13013.t1.exon4 | 27500536 | 27500561 |
| chr_1 | g13013 | g13013.t1 | cds | g13013.t1.CDS4 | 27500536 | 27500561 |
| chr_1 | g13013 | g13013.t1 | exon | g13013.t1.exon5 | 27500628 | 27500816 |
| chr_1 | g13013 | g13013.t1 | cds | g13013.t1.CDS5 | 27500628 | 27500816 |
| chr_1 | g13013 | g13013.t1 | exon | g13013.t1.exon6 | 27500875 | 27500990 |
| chr_1 | g13013 | g13013.t1 | cds | g13013.t1.CDS6 | 27500875 | 27500990 |
| chr_1 | g13013 | g13013.t1 | exon | g13013.t1.exon7 | 27501046 | 27502780 |
| chr_1 | g13013 | g13013.t1 | cds | g13013.t1.CDS7 | 27501046 | 27502780 |
| chr_1 | g13013 | g13013.t1 | exon | g13013.t1.exon8 | 27502843 | 27502962 |
| chr_1 | g13013 | g13013.t1 | cds | g13013.t1.CDS8 | 27502843 | 27502962 |
| chr_1 | g13013 | g13013.t1 | TSS | g13013.t1 | 27503111 | 27503111 |
Sequences
>g13013.t1 Gene=g13013 Length=3957
ATGTCGAAAAATGGATCAGAAAAAGGAAAACAAATGCGCCTTGATAACTTCTTTTCGAAA
AATAATTCGAACAATAACAAACCAGAAAATCAGTCAAAATTATCAATTAAAAAGAGAATA
AAAAGCTTTAATTTATCAGATGATGATTCTATCGAAACTCCTACAAAAATATTAAATGGT
TTCAATTGTTCAGAGATTAAAGAGAATCTCGATAATTTATCAAGAACTATGAATGAATCA
ACACCAACACCTGGAAGTGCCTCGAAATTTAAATTCAAAACAAGCTCTAATAAAGATCCT
CCATCGTCTTCAACCTCAAATACAATACAATCATTAGATTTGAATAGTGAACCGAAAAAA
AGCGTTTTTGGTAAACAATCACAATTTTTCATAAATGATGATAGCTTAGAAGATATTCTT
CCACTTAAAAAACCAACACAAAAGACAGAGAATATTATAAAACCTGAACCTTTATTTAGA
ATTAAAGGTAAAATAACAGAATCATCACAAAAAACATTTTTAAATGAAGACAAAAATTCA
CTTTTTAAGTCAAATCAAATTCAATTACTAACCAAACCACCAATTGAGAAAATTTTATTA
AATGAACGGGAAGTTAACATGACTTTTGCAAAAAGTGAAACAGCAGCATCTAATCAACCA
AAATCAACAAAAGACCAATTTGAGTTTCTCAATTCTGATATTGATAGTTCACCTCATCCA
GTTGTTGATTTAACAGCAAAACATTTATCTCCTACAAAATTTAAAACTTCTACAATCAGT
GATCAATTAGCATCTATGATTCATTCAAAGAAAACTGATGAATTTGATTCACCTTTGTCT
TCATTTTATCATAAAGAATCATTAAGTCCAAATTTATCGACTCCTAGTAGCTCACAACAG
GATACAAAAGTTAAAATTAAAGTCGACAATCAAGAAATAGCAAGTATGATTGGCGAATAT
TCATCAAAGAATTTAGAAGGTGCCAGTGTGGAGCGCTTAAAAGAGGAAAAACTCAAATTT
CAAGATGTCTGGTTCAATTATTTTAACCAAATTCCATTCACAGTTTTTGAATCAATTGAG
GGTTTCGACAAAACTACAGTTATTCGACTTAAAGGTGTCATTCAATCACTAAATGCAAAA
ATACGAAAGCAAAGCGCTAAAAGTTCACAACCATCAACTCCTCATCAGCAAAAACCTCAA
CAATTGGCAAAGCCAAGTACAAACTCTATCAACTTTTCATTTAGTGACGATGATGAACAA
TTTGGTCTCAATGAGATTATTAATAATATTGAGGAAGAAGAGAAGAAAATGTCTGGAAAG
TTTGACAATAATTTTATTGATCTCTCAGTATCACCAGCAATGAAATCTTCATTTAAACCT
AGAGTTAATATGAAAGATCAAACAACAAATCCTACAACATCAAGAACTCAACTTTCAAAT
GTCTTCGGACATCATAGTGAAGTTAATGCTGAAGCAGATAACGATGGTTTTCCAATTTTT
GATTATAGTTCATTAGAAGATGTAGTTCCAATTGATTCAACACCTATACCTTCATCATCA
AATAGCTCTCTAAAAGAAAATAAGAGACCAGTAAAACAAACAATCGATTCAATGATTCCA
GATAATCCAGATGAAATTCAATTTAAAAACACCTCATCAGTTGGTGTTTTTTACAATAAT
GTTACAAATGATGGAATCAGTGGTGAATTTGATGGCATGAATTATCCATTCTCAAAGGAA
CTTCAGCGTGTATTTGAAAATATTTTTGGTCTTCGCAAGTTTCGTCAAAATCAACTTCAA
GCTATAAATGCAGCATTACTTGGTCATGATTGTTTTGTTCTAATGCCAACTGGAGGAGGA
AAATCATTATGTTATCAATTGCCTGCCTTGCTAAGTCGAGGTGTTACAATTGTCATTAGC
CCTTTAAAAAGTTTGATCTTAGATCAAGTTAATAAGCTAAACTCTCTAGATATTAGAGCA
GCAGCTCTCTCAGGTGAAGTTTCACAAGCTGAAGCGCGGGAAATTTTTAGTGACATTAAT
AAAAATAATCCAACAATCAAGCTTTTATATGTTACACCAGAAAAAATATCAGCATCTACA
TTTTTCCAAGATACTTTAACTTCAATGCATCAAAAAGGAACACTTGCTAGATTTGTTGTT
GATGAAGCTCATTGTGTCTCAACATGGGGACATGACTTTCGACCTGATTACAAAAAGTTA
GGTGAATTGAAGAATCGATTTTCAAATGTGCCTGTCATGGCTTTAACTGCTACTGCCAAT
ATTCGAGTAAGAGCTGATGTAATTCATCAATTAAAAATTGCAAAGTGCAAATGGTTCTTA
TCGAGTTTTAATCGTCCAAATTTAAAATATATTGTTACACAAAAAACTGGTGCGAAATCT
TTAACCGACATCATCAATTTAATCAAAACAAAATTTATCAGAGCTAGCGGTATCATCTAT
TGCCTTTCAAGAAAAGATTGTGATACAACTGCTGAAAAATTACAATTGTCGAATATCAGA
GCAATAAGTTATCATGCTGGTTTGACTGATAAAGTGCGAGAAAAAGTTCAAAATGATTGG
CTAACAGATAAATATCGGGTAGTTTGCGCAACAATTGCTTTCGGTATGGGCATCGACAAG
CCAGATGTACGATATGTTATTCATTATTCAATGCCAAAATCAATTGAAGGATATTATCAA
GAATCAGGTCGTGCAGGTCGTGATGGTGCATTAGCGACATGTATTCTCTATTATAATTAT
AGCGATAGAGCTCGTCTAGTAAATATGATATTAAAAGATCAGCAATCACATAAAACTCGA
CAAGTTTCTATGGAAAACATAAATTTGGTAGTGAATTTTTGTGAAAACATGATCGATTGT
CGACGTATAACACAACTTAATTATTTTGGAGAACATTTTACTAGAGAACAATGCCTTGCA
AATCGCGCATCAGCATGTGACAATTGTAGTAGAATATCTGAATATAAAAACATCGATGCT
ACTGAAATAGCACGAACTATTATTAGTTCTGTACAAGAACTGTGTGAACGCAGTCGATTT
ACGTTGTTGCATATGATCGATGTTTTTAAAGGAGCAGAAACGAAAAAAGTTGTCGATTCA
GGTCATAAAAATACTCGATATCATGGACATTTAAAGCAATGGGATCGAACAGATATTCAA
AGAATCTTTCATAAATTAGTTATTGAAAATTACTTGAGAGAAGATATAACAGTAATTAAT
GATATTCCCATTGCATATCTAAAACTTGGAGAAAAAGTTGCAGACATTATGAGAGGAAAC
AAGAAAATTGAGTTCGCCGTACAAGAAAGACAATTGTTTGCAAATAGAAAGAAGAATGAA
AATATTCCAGCTAAAACAAGCGACATACTCACAGATGATCCACTTATGGAAGAATTACAA
GATCAATGCTATCACGAACTTATGGAAGTCGCTAAATTAATTGCGGATGAACGTAATTTG
GCAATACAACAAGTTATGAATATGGAAGCACTTCGACAAATGTCAATCAAAATACCAAAG
ACTGTTGAAGAAATGCTAGAAATTCCACACGTTACAAAGGCAAACTTCAATAAATATGGT
CAAGGATTTTTGAACGTATGTCAGTCATATCGTATTAAGAGAACTGATTACGAAATGGCA
AGACAATTACAACGTGAAGAAGATCGTATGAATGAATCTTATGAAGATACCGATAATGAA
GAAGATGATGATAATGTTGATTGGGATGCACTTGGTCGGCAAGCAACGACAAGTAGCGCA
AAAGTTTCTGGTTATAAACGAAAAGGTTCATTTCGTGCATCAAATATTGCTAAGAGATAC
AAACGATCATTTTCAAAGAAAACACCTACTAAGAAGAAAACTTCTGCCACGAAAACAAAA
GGTGCAAAATCGAAAACAGGAAAATCATTATTACCACCACCAAGAATTTCTTTTTGA
>g13013.t1 Gene=g13013 Length=1318
MSKNGSEKGKQMRLDNFFSKNNSNNNKPENQSKLSIKKRIKSFNLSDDDSIETPTKILNG
FNCSEIKENLDNLSRTMNESTPTPGSASKFKFKTSSNKDPPSSSTSNTIQSLDLNSEPKK
SVFGKQSQFFINDDSLEDILPLKKPTQKTENIIKPEPLFRIKGKITESSQKTFLNEDKNS
LFKSNQIQLLTKPPIEKILLNEREVNMTFAKSETAASNQPKSTKDQFEFLNSDIDSSPHP
VVDLTAKHLSPTKFKTSTISDQLASMIHSKKTDEFDSPLSSFYHKESLSPNLSTPSSSQQ
DTKVKIKVDNQEIASMIGEYSSKNLEGASVERLKEEKLKFQDVWFNYFNQIPFTVFESIE
GFDKTTVIRLKGVIQSLNAKIRKQSAKSSQPSTPHQQKPQQLAKPSTNSINFSFSDDDEQ
FGLNEIINNIEEEEKKMSGKFDNNFIDLSVSPAMKSSFKPRVNMKDQTTNPTTSRTQLSN
VFGHHSEVNAEADNDGFPIFDYSSLEDVVPIDSTPIPSSSNSSLKENKRPVKQTIDSMIP
DNPDEIQFKNTSSVGVFYNNVTNDGISGEFDGMNYPFSKELQRVFENIFGLRKFRQNQLQ
AINAALLGHDCFVLMPTGGGKSLCYQLPALLSRGVTIVISPLKSLILDQVNKLNSLDIRA
AALSGEVSQAEAREIFSDINKNNPTIKLLYVTPEKISASTFFQDTLTSMHQKGTLARFVV
DEAHCVSTWGHDFRPDYKKLGELKNRFSNVPVMALTATANIRVRADVIHQLKIAKCKWFL
SSFNRPNLKYIVTQKTGAKSLTDIINLIKTKFIRASGIIYCLSRKDCDTTAEKLQLSNIR
AISYHAGLTDKVREKVQNDWLTDKYRVVCATIAFGMGIDKPDVRYVIHYSMPKSIEGYYQ
ESGRAGRDGALATCILYYNYSDRARLVNMILKDQQSHKTRQVSMENINLVVNFCENMIDC
RRITQLNYFGEHFTREQCLANRASACDNCSRISEYKNIDATEIARTIISSVQELCERSRF
TLLHMIDVFKGAETKKVVDSGHKNTRYHGHLKQWDRTDIQRIFHKLVIENYLREDITVIN
DIPIAYLKLGEKVADIMRGNKKIEFAVQERQLFANRKKNENIPAKTSDILTDDPLMEELQ
DQCYHELMEVAKLIADERNLAIQQVMNMEALRQMSIKIPKTVEEMLEIPHVTKANFNKYG
QGFLNVCQSYRIKRTDYEMARQLQREEDRMNESYEDTDNEEDDDNVDWDALGRQATTSSA
KVSGYKRKGSFRASNIAKRYKRSFSKKTPTKKKTSATKTKGAKSKTGKSLLPPPRISF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g13013.t1 | CDD | cd18794 | SF2_C_RecQ | 785 | 918 | 8.43672E-69 |
| 16 | g13013.t1 | Coils | Coil | Coil | 653 | 673 | - |
| 15 | g13013.t1 | Coils | Coil | Coil | 1220 | 1243 | - |
| 12 | g13013.t1 | Gene3D | G3DSA:3.40.50.300 | - | 558 | 784 | 3.2E-91 |
| 11 | g13013.t1 | Gene3D | G3DSA:3.40.50.300 | - | 785 | 994 | 1.1E-65 |
| 13 | g13013.t1 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 996 | 1110 | 1.5E-29 |
| 14 | g13013.t1 | Gene3D | G3DSA:1.10.150.80 | - | 1136 | 1220 | 1.8E-20 |
| 24 | g13013.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 36 | - |
| 28 | g13013.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 15 | 31 | - |
| 30 | g13013.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 72 | 112 | - |
| 29 | g13013.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 382 | 406 | - |
| 27 | g13013.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1224 | 1247 | - |
| 25 | g13013.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1233 | 1247 | - |
| 23 | g13013.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1259 | 1318 | - |
| 26 | g13013.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1272 | 1299 | - |
| 6 | g13013.t1 | PANTHER | PTHR13710 | DNA HELICASE RECQ FAMILY MEMBER | 466 | 1281 | 1.1E-218 |
| 7 | g13013.t1 | PANTHER | PTHR13710:SF128 | ATP-DEPENDENT DNA HELICASE Q-LIKE 4A | 466 | 1281 | 1.1E-218 |
| 3 | g13013.t1 | Pfam | PF00270 | DEAD/DEAH box helicase | 597 | 760 | 8.8E-20 |
| 4 | g13013.t1 | Pfam | PF00271 | Helicase conserved C-terminal domain | 802 | 908 | 1.2E-17 |
| 1 | g13013.t1 | Pfam | PF16124 | RecQ zinc-binding | 920 | 989 | 3.6E-14 |
| 2 | g13013.t1 | Pfam | PF09382 | RQC domain | 995 | 1110 | 2.1E-26 |
| 5 | g13013.t1 | Pfam | PF00570 | HRDC domain | 1140 | 1206 | 2.3E-11 |
| 22 | g13013.t1 | ProSitePatterns | PS00690 | DEAH-box subfamily ATP-dependent helicases signature. | 716 | 725 | - |
| 34 | g13013.t1 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 602 | 777 | 22.147 |
| 32 | g13013.t1 | ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 807 | 950 | 20.234 |
| 33 | g13013.t1 | ProSiteProfiles | PS50967 | HRDC domain profile. | 1137 | 1217 | 14.37 |
| 20 | g13013.t1 | SMART | SM00487 | ultradead3 | 590 | 791 | 2.9E-30 |
| 19 | g13013.t1 | SMART | SM00490 | helicmild6 | 828 | 909 | 4.8E-27 |
| 18 | g13013.t1 | SMART | SM00956 | RQC_2 | 999 | 1109 | 1.4E-30 |
| 21 | g13013.t1 | SMART | SM00341 | hrdc7 | 1137 | 1217 | 3.1E-13 |
| 10 | g13013.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 418 | 923 | 4.88E-47 |
| 9 | g13013.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 783 | 1042 | 2.77E-56 |
| 8 | g13013.t1 | SUPERFAMILY | SSF47819 | HRDC-like | 1139 | 1211 | 2.62E-13 |
| 31 | g13013.t1 | TIGRFAM | TIGR00614 | recQ_fam: ATP-dependent DNA helicase, RecQ family | 584 | 1049 | 2.6E-170 |
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:0006281 | DNA repair | BP |
| GO:0005524 | ATP binding | MF |
| GO:0006260 | DNA replication | BP |
| GO:0004386 | helicase activity | MF |
| GO:0003676 | nucleic acid binding | MF |
| GO:0000166 | nucleotide binding | MF |
| GO:0043138 | 3’-5’ DNA helicase activity | MF |
| GO:0044237 | cellular metabolic process | BP |
| GO:0006310 | DNA recombination | BP |
KEGG
Orthology
- This transcript has been annotated with K10901 (bloom syndrome 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.
