General information for g3237.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 g3237 is located on chr_3: 23949749..23950560 (- 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_3 | g3237 | g3237.t1 | isoform | g3237.t1 | 23946447 | 23950360 |
| chr_3 | g3237 | g3237.t1 | exon | g3237.t1.exon1 | 23946447 | 23947606 |
| chr_3 | g3237 | g3237.t1 | cds | g3237.t1.CDS1 | 23946447 | 23947606 |
| chr_3 | g3237 | g3237.t1 | exon | g3237.t1.exon2 | 23947663 | 23947746 |
| chr_3 | g3237 | g3237.t1 | cds | g3237.t1.CDS2 | 23947663 | 23947746 |
| chr_3 | g3237 | g3237.t1 | exon | g3237.t1.exon3 | 23947817 | 23948253 |
| chr_3 | g3237 | g3237.t1 | cds | g3237.t1.CDS3 | 23947817 | 23948253 |
| chr_3 | g3237 | g3237.t1 | exon | g3237.t1.exon4 | 23948328 | 23948353 |
| chr_3 | g3237 | g3237.t1 | cds | g3237.t1.CDS4 | 23948328 | 23948353 |
| chr_3 | g3237 | g3237.t1 | exon | g3237.t1.exon5 | 23948417 | 23948605 |
| chr_3 | g3237 | g3237.t1 | cds | g3237.t1.CDS5 | 23948417 | 23948605 |
| chr_3 | g3237 | g3237.t1 | exon | g3237.t1.exon6 | 23948671 | 23948786 |
| chr_3 | g3237 | g3237.t1 | cds | g3237.t1.CDS6 | 23948671 | 23948786 |
| chr_3 | g3237 | g3237.t1 | exon | g3237.t1.exon7 | 23948842 | 23949916 |
| chr_3 | g3237 | g3237.t1 | cds | g3237.t1.CDS7 | 23948842 | 23949916 |
| chr_3 | g3237 | g3237.t1 | exon | g3237.t1.exon8 | 23949989 | 23950360 |
| chr_3 | g3237 | g3237.t1 | cds | g3237.t1.CDS8 | 23949989 | 23950360 |
| chr_3 | g3237 | g3237.t1 | TSS | g3237.t1 | 23950728 | 23950728 |
| chr_3 | g3237 | g3237.t1 | TTS | g3237.t1 | NA | NA |
Sequences
>g3237.t1 Gene=g3237 Length=3459
ATGAATGAATCAACTGGAGAGCCTGGAAGTGCCTCAAAATTTAAGTTTAAAAAGAGCTCT
AATCAAGATCAAAAAAATTCTCAATTCTTTATTGATAATGACGATGACGATTATTTAAAA
GACATTTTTCCACTTAAGAACCCTACAAAGAAGGCAGAAAATGATACAAAAATAGTACAT
TTATGCAAACCTAAAGAAACAACATCACACGAGACACCACTTTTGAATGAAGACAAGAGT
ATCTTGAGTAATTCTAAAACAATTCAATTACCTACTAAATCACTTGAGAATATTCTTCTT
AATGAAAGAGAAATCAATATAACTTCTGCTAAAAGTGAAACAACAACAATCGACTTGAAA
AAACCATCTAAGTCATCTCCTGGAAAACTAATGGCAGCAAAAATCAGCAACCAGCTAGCA
GCAATAGTGAATTTAAAAAAAAATGATGAAATTGATTCACCTTTATCATCATTTTATCAA
AGAGAATCATGTAACATAAATGTGTTAAGTAATTCACCACAGGCGACGAAAGTTAAAATT
AATATCGACAATCAAAAAATAATGAATATGCTTTATGAATATTCGTCAAGTAATTTCGAA
GATGCCAATGTTGATATCTTAAAAGATGAAAAGCTCAAGTTTCAAGATGTATGCTTGAAT
TATTTTAATCAAATTCCGTTATCATTTTTCGAACCAATTGAGGGTTTTGACAAAACTGCA
ATTATTAGACTTAAAGGTGTCATTCAATCACTTAATGTAAAACTACGAAAACAAAATGTA
AAGAATTTACAGCCATCAACTCCTCATCAACAAATTGAAAAAGCACAATCAAACTCTATC
AACAGTTTCTTTGATGATAATGAAGACTTTGATTTGAATGAAATTGCTAATAATATTGAA
GAAGAAGAGAGAAACCGCATCGAAAAATTAAAGAATTTTAAAGACCTTCCATTGACATCA
GCAATGGAATCTTCATTAACACCTAAATTTAAGAACCAAACGAATTCATTATCTGCAAAG
AAAAAACTTTCATTCAGTCAATGTAGTGAAGATAATGCAAAAGCGGATGATGATGGCTTT
CCTATTCTCGATTATAGTATGTTGCAAAATGTAATTCCAATAGAATCAATATCAAAAATG
TCAATACCCTCAACGTCAAACAATCCATTGAAAGAAATTGAATCAACAAAAAAAATCGAT
TTGATGATTACAGACAACTCTGATAAAACTCAATTTAAAGACACCTCATTTGTCGGTGTT
TTTTATAATGATGTGAAAAATGATGGAATCAGTGGTGAATTTGATGGTACAAATTATCCA
TTCTCTAAGGAGCTTCAGCATGTTTTTGAAAACACTTTTGGTCTTCGAAAATTTCGTCAA
AATCAACTTCAAGCAATAAATGCAGCATTACTCGGACATGATTGTTTTATTATAATGCCA
ACTGGAGGAGGAAAATCATTATGCTATCAGTTACCTGCTCTGCTCTGTGACGGTGTCACA
ATCGTTATTAGTCCCTTGAAAAGTTTGATATTAGATCAAGTTAATAAGCTGAAATCTTTA
GATATAAGAGCAGCAGCTCTCTCAAGTGACGTTCCTCTTGATGAATCACAATATGTTTTC
AATGACCTTAAATTGAATAATCCCACAATCAAACTTTTATATGTTACTCCTGAAAAAATA
TCAATATCGACAAATTTTCGAGATACTATGACTTTGATGTATCGAAATAGAACAATCTCT
AGAATTGTGATTGATGAAGCTCATTGTGTTTCAACATGGGGCCATGACTTTCGACCTGAT
TATAAAAAGTTAGGTATACTTAGAACATTATTTCCTTTTGTACCTTTTATGGCTTTAACT
GCAACTGCAAATATTCGAGTAAGAGCAGATGTAATTAATCAATTGAAAATTGAAAAGTGC
AAATGGTTCTTATCGAGTTTCAATCGCCCTAATTTAAAATACATTGTTACACAAAAGACT
AGTTCAAGAACTTTAACCGACATTATAAATTTAATTAAAACGAAGTATAGCAAAGCAAGC
GGTATCATCTATTGTCTTGCACGAAAAGATTGTGACCAAATGGCAGAAAAATTACAGATT
TTAAATATAAAAGCAATTAGTTATCACGCAGGACTATCTGATGAAGTACGAAAAAAAGTT
CAAAATGACTGGTTTACCAACAAATATCTAGTAGTTTGTGCAACAATTGCTTTCGGTATG
GGTATTGACAAGCCAGATGTACGATACGTTATTCATTATTCGATGCCTCAATCAATAGAA
GCATACTATCAAGAATCAGGACGCGCTGGTCGTGATGGAAAATTATCAACGTGTATACTT
TATTATAGTTATTCTGATCGAACTCGACTTGTAAATTTGATAACCCGCGACAAGAAATCA
TCATCAAAAATTCAAAAAATCGCTATAAATAATATAGATTTAGTAGTGAGTTTTTGCGAA
AATATGATCGACTGTAGACGACAAGCACAATTAAATTATTTTGGAGAGCATTTTTCAAGA
GAAAAATGTATTGAAAATCGCGAATCTGCCTGTGATAATTGTACAAGAAATGCTGACTAT
ATAATGATTGATATTACTGAAATATCAAGAACTATTATTAGCTCTGTACAAGAACTTTGT
GAATGCAACCGTTTTACATTGTTGCATATGATTGATGTTTTTAAAGGTGCGATGACAAAG
AAAATTGTTATTTCAGGTCATCAGAATACTCGATATCATGGATATTTGAGAGAATGGGAT
CGTCTTGATATTGAGAGAATTTTTCACAAACTAGTCATTGAAAATTATTTAAAGGAAGAA
TTAACGGTTGTTAAAGATATTCCTATTCCATATTTAAAACTTGGTCCGAACGTTGCAAGT
ATAATGAAAGGAAGCAAGAAAATTGAATTTGTCGTACAAAAATCAAATAATAAGAATAAC
ATTTTACTTAAAGCAACAAATGATACAATCACAGATGATCCACTTATGGAAGAACTTTAT
AGTCAATGTTATCGTGAACTTTTAGAAGTTGCTAAAATAATTGCTGATGAACTTAATGTA
GCTGTAAATCAAATTATGAATATGGAAGCAATTCGTCAAATGTCTATTAAATTACCAAAA
ACTTTGGAAGAGATGCTAGACATTCCACATGTCACAAAAGCTAATTTTGAAAAGTATGGT
CATGGATTTTTGAATATATGCCAGTTATATCGTTCCAAAAAAATTGACTACGAAATGGCA
AGAGAAATGCAACGTGAAATAGATCTAGAAATGGAAAATTCTACCGAACTGATCGATTAT
GAAGAAGATGATGATGATGATGATAATAATATTGATTGGGATACATTTTATCAGCAAATA
ATGACAAGTAGCCAAAATGTTGCAGGCTTTAAACGTAAAGGTACAGGACGTAAAGAAATT
GTTGCTAAAAAATACAAGCAAACATTAACAAAGAAATGA
>g3237.t1 Gene=g3237 Length=1152
MNESTGEPGSASKFKFKKSSNQDQKNSQFFIDNDDDDYLKDIFPLKNPTKKAENDTKIVH
LCKPKETTSHETPLLNEDKSILSNSKTIQLPTKSLENILLNEREINITSAKSETTTIDLK
KPSKSSPGKLMAAKISNQLAAIVNLKKNDEIDSPLSSFYQRESCNINVLSNSPQATKVKI
NIDNQKIMNMLYEYSSSNFEDANVDILKDEKLKFQDVCLNYFNQIPLSFFEPIEGFDKTA
IIRLKGVIQSLNVKLRKQNVKNLQPSTPHQQIEKAQSNSINSFFDDNEDFDLNEIANNIE
EEERNRIEKLKNFKDLPLTSAMESSLTPKFKNQTNSLSAKKKLSFSQCSEDNAKADDDGF
PILDYSMLQNVIPIESISKMSIPSTSNNPLKEIESTKKIDLMITDNSDKTQFKDTSFVGV
FYNDVKNDGISGEFDGTNYPFSKELQHVFENTFGLRKFRQNQLQAINAALLGHDCFIIMP
TGGGKSLCYQLPALLCDGVTIVISPLKSLILDQVNKLKSLDIRAAALSSDVPLDESQYVF
NDLKLNNPTIKLLYVTPEKISISTNFRDTMTLMYRNRTISRIVIDEAHCVSTWGHDFRPD
YKKLGILRTLFPFVPFMALTATANIRVRADVINQLKIEKCKWFLSSFNRPNLKYIVTQKT
SSRTLTDIINLIKTKYSKASGIIYCLARKDCDQMAEKLQILNIKAISYHAGLSDEVRKKV
QNDWFTNKYLVVCATIAFGMGIDKPDVRYVIHYSMPQSIEAYYQESGRAGRDGKLSTCIL
YYSYSDRTRLVNLITRDKKSSSKIQKIAINNIDLVVSFCENMIDCRRQAQLNYFGEHFSR
EKCIENRESACDNCTRNADYIMIDITEISRTIISSVQELCECNRFTLLHMIDVFKGAMTK
KIVISGHQNTRYHGYLREWDRLDIERIFHKLVIENYLKEELTVVKDIPIPYLKLGPNVAS
IMKGSKKIEFVVQKSNNKNNILLKATNDTITDDPLMEELYSQCYRELLEVAKIIADELNV
AVNQIMNMEAIRQMSIKLPKTLEEMLDIPHVTKANFEKYGHGFLNICQLYRSKKIDYEMA
REMQREIDLEMENSTELIDYEEDDDDDDNNIDWDTFYQQIMTSSQNVAGFKRKGTGRKEI
VAKKYKQTLTKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 18 | g3237.t1 | CDD | cd18794 | SF2_C_RecQ | 649 | 782 | 1.84317E-66 |
| 17 | g3237.t1 | Coils | Coil | Coil | 292 | 312 | - |
| 14 | g3237.t1 | Gene3D | G3DSA:3.40.50.300 | - | 422 | 648 | 3.7E-88 |
| 13 | g3237.t1 | Gene3D | G3DSA:3.40.50.300 | - | 649 | 857 | 6.6E-67 |
| 15 | g3237.t1 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 858 | 974 | 2.6E-27 |
| 16 | g3237.t1 | Gene3D | G3DSA:1.10.150.80 | - | 996 | 1080 | 4.7E-20 |
| 24 | g3237.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 32 | - |
| 25 | g3237.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 28 | - |
| 6 | g3237.t1 | PANTHER | PTHR13710 | DNA HELICASE RECQ FAMILY MEMBER | 427 | 941 | 3.0E-202 |
| 8 | g3237.t1 | PANTHER | PTHR13710:SF128 | ATP-DEPENDENT DNA HELICASE Q-LIKE 4A | 427 | 941 | 3.0E-202 |
| 7 | g3237.t1 | PANTHER | PTHR13710 | DNA HELICASE RECQ FAMILY MEMBER | 981 | 1130 | 3.0E-202 |
| 9 | g3237.t1 | PANTHER | PTHR13710:SF128 | ATP-DEPENDENT DNA HELICASE Q-LIKE 4A | 981 | 1130 | 3.0E-202 |
| 3 | g3237.t1 | Pfam | PF00270 | DEAD/DEAH box helicase | 461 | 624 | 6.7E-17 |
| 4 | g3237.t1 | Pfam | PF00271 | Helicase conserved C-terminal domain | 666 | 772 | 5.8E-17 |
| 1 | g3237.t1 | Pfam | PF16124 | RecQ zinc-binding | 784 | 855 | 2.4E-13 |
| 2 | g3237.t1 | Pfam | PF09382 | RQC domain | 862 | 978 | 1.7E-23 |
| 5 | g3237.t1 | Pfam | PF00570 | HRDC domain | 1002 | 1066 | 8.0E-12 |
| 23 | g3237.t1 | ProSitePatterns | PS00690 | DEAH-box subfamily ATP-dependent helicases signature. | 580 | 589 | - |
| 29 | g3237.t1 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 466 | 641 | 22.373 |
| 27 | g3237.t1 | ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 664 | 815 | 20.727 |
| 28 | g3237.t1 | ProSiteProfiles | PS50967 | HRDC domain profile. | 997 | 1077 | 13.5 |
| 21 | g3237.t1 | SMART | SM00487 | ultradead3 | 454 | 655 | 1.0E-28 |
| 20 | g3237.t1 | SMART | SM00490 | helicmild6 | 692 | 773 | 1.8E-27 |
| 19 | g3237.t1 | SMART | SM00956 | RQC_2 | 864 | 974 | 1.1E-23 |
| 22 | g3237.t1 | SMART | SM00341 | hrdc7 | 997 | 1077 | 2.9E-10 |
| 12 | g3237.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 498 | 791 | 4.28E-56 |
| 11 | g3237.t1 | SUPERFAMILY | SSF46785 | Winged helix DNA-binding domain | 862 | 972 | 1.35E-16 |
| 10 | g3237.t1 | SUPERFAMILY | SSF47819 | HRDC-like | 1001 | 1073 | 2.4E-14 |
| 26 | g3237.t1 | TIGRFAM | TIGR00614 | recQ_fam: ATP-dependent DNA helicase, RecQ family | 448 | 913 | 2.8E-169 |
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.
