Gene loci information

Transcript annotation

  • This transcript has been annotated as Bloom syndrome protein-like protein.

Parent gene

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.t2 TTS g13013.t2 27498501 27498501
chr_1 g13013 g13013.t2 isoform g13013.t2 27498558 27499807
chr_1 g13013 g13013.t2 exon g13013.t2.exon1 27498558 27499807
chr_1 g13013 g13013.t2 cds g13013.t2.CDS1 27498558 27499730
chr_1 g13013 g13013.t2 TSS g13013.t2 NA NA

Sequences

>g13013.t2 Gene=g13013 Length=1250
GTCGTGCAGGTCGTGATGGTGCATTAGCGACATGTATTCTCTATTATAATTATAGCGATA
GAGCTCGTCTAGTAAATATGATATTAAAAGATCAGCAATCACATAAAACTCGACAAGTTT
CTATGGAAAACATAAATTTGGTAGTGAATTTTTGTGAAAACATGATCGATTGTCGACGTA
TAACACAACTTAATTATTTTGGAGAACATTTTACTAGAGAACAATGCCTTGCAAATCGCG
CATCAGCATGTGACAATTGTAGTAGAATATCTGAATATAAAAACATCGATGCTACTGAAA
TAGCACGAACTATTATTAGTTCTGTACAAGAACTGTGTGAACGCAGTCGATTTACGTTGT
TGCATATGATCGATGTTTTTAAAGGAGCAGAAACGAAAAAAGTTGTCGATTCAGGTCATA
AAAATACTCGATATCATGGACATTTAAAGCAATGGGATCGAACAGATATTCAAAGAATCT
TTCATAAATTAGTTATTGAAAATTACTTGAGAGAAGATATAACAGTAATTAATGATATTC
CCATTGCATATCTAAAACTTGGAGAAAAAGTTGCAGACATTATGAGAGGAAACAAGAAAA
TTGAGTTCGCCGTACAAGAAAGACAATTGTTTGCAAATAGAAAGAAGAATGAAAATATTC
CAGCTAAAACAAGCGACATACTCACAGATGATCCACTTATGGAAGAATTACAAGATCAAT
GCTATCACGAACTTATGGAAGTCGCTAAATTAATTGCGGATGAACGTAATTTGGCAATAC
AACAAGTTATGAATATGGAAGCACTTCGACAAATGTCAATCAAAATACCAAAGACTGTTG
AAGAAATGCTAGAAATTCCACACGTTACAAAGGCAAACTTCAATAAATATGGTCAAGGAT
TTTTGAACGTATGTCAGTCATATCGTATTAAGAGAACTGATTACGAAATGGCAAGACAAT
TACAACGTGAAGAAGATCGTATGAATGAATCTTATGAAGATACCGATAATGAAGAAGATG
ATGATAATGTTGATTGGGATGCACTTGGTCGGCAAGCAACGACAAGTAGCGCAAAAGTTT
CTGGTTATAAACGAAAAGGTTCATTTCGTGCATCAAATATTGCTAAGAGATACAAACGAT
CATTTTCAAAGAAAACACCTACTAAGAAGAAAACTTCTGCCACGAAAACAAAAGGTGCAA
AATCGAAAACAGGAAAATCATTATTACCACCACCAAGAATTTCTTTTTGA

>g13013.t2 Gene=g13013 Length=390
MILKDQQSHKTRQVSMENINLVVNFCENMIDCRRITQLNYFGEHFTREQCLANRASACDN
CSRISEYKNIDATEIARTIISSVQELCERSRFTLLHMIDVFKGAETKKVVDSGHKNTRYH
GHLKQWDRTDIQRIFHKLVIENYLREDITVINDIPIAYLKLGEKVADIMRGNKKIEFAVQ
ERQLFANRKKNENIPAKTSDILTDDPLMEELQDQCYHELMEVAKLIADERNLAIQQVMNM
EALRQMSIKIPKTVEEMLEIPHVTKANFNKYGQGFLNVCQSYRIKRTDYEMARQLQREED
RMNESYEDTDNEEDDDNVDWDALGRQATTSSAKVSGYKRKGSFRASNIAKRYKRSFSKKT
PTKKKTSATKTKGAKSKTGKSLLPPPRISF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g13013.t2 Coils Coil Coil 292 315 -
8 g13013.t2 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 1 190 3.9E-44
9 g13013.t2 Gene3D G3DSA:1.10.150.80 - 207 294 3.3E-21
16 g13013.t2 MobiDBLite mobidb-lite consensus disorder prediction 296 319 -
13 g13013.t2 MobiDBLite mobidb-lite consensus disorder prediction 305 319 -
14 g13013.t2 MobiDBLite mobidb-lite consensus disorder prediction 331 390 -
15 g13013.t2 MobiDBLite mobidb-lite consensus disorder prediction 344 371 -
4 g13013.t2 PANTHER PTHR13710 DNA HELICASE RECQ FAMILY MEMBER 8 354 1.0E-37
5 g13013.t2 PANTHER PTHR13710:SF128 ATP-DEPENDENT DNA HELICASE Q-LIKE 4A 8 354 1.0E-37
1 g13013.t2 Pfam PF16124 RecQ zinc-binding 1 61 2.3E-12
2 g13013.t2 Pfam PF09382 RQC domain 67 182 3.1E-27
3 g13013.t2 Pfam PF00570 HRDC domain 212 278 4.5E-12
17 g13013.t2 ProSiteProfiles PS50967 HRDC domain profile. 209 289 14.37
11 g13013.t2 SMART SM00956 RQC_2 71 181 1.4E-30
12 g13013.t2 SMART SM00341 hrdc7 209 289 3.1E-13
7 g13013.t2 SUPERFAMILY SSF46785 Winged helix DNA-binding domain 68 179 6.26E-22
6 g13013.t2 SUPERFAMILY SSF47819 HRDC-like 211 283 4.8E-14

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:0006260 DNA replication BP
GO:0000166 nucleotide binding MF
GO:0043138 3’-5’ DNA helicase activity MF
GO:0044237 cellular metabolic process BP
GO:0003676 nucleic acid binding MF

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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.

Raw TPM values