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_3 g3237 g3237.t8 isoform g3237.t8 23946447 23947606
chr_3 g3237 g3237.t8 exon g3237.t8.exon1 23946447 23946931
chr_3 g3237 g3237.t8 cds g3237.t8.CDS1 23946447 23946931
chr_3 g3237 g3237.t8 exon g3237.t8.exon2 23947043 23947606
chr_3 g3237 g3237.t8 cds g3237.t8.CDS2 23947043 23947442
chr_3 g3237 g3237.t8 TSS g3237.t8 NA NA
chr_3 g3237 g3237.t8 TTS g3237.t8 NA NA

Sequences

>g3237.t8 Gene=g3237 Length=1049
GACGCGCTGGTCGTGATGGAAAATTATCAACGTGTATACTTTATTATAGTTATTCTGATC
GAACTCGACTTGTAAATTTGATAACCCGCGACAAGAAATCATCATCAAAAATTCAAAAAA
TCGCTATAAATAATATAGATTTAGTAGTGAGTTTTTGCGAAAATATGATCGACTGTAGAC
GACAAGCACAATTAAATTATTTTGGAGAGCATTTTTCAAGAGAAAAATGTATTGAAAATC
GCGAATCTGCCTGTGATAATTGTACAAGAAATGCTGACTATATAATGATTGATATTACTG
AAATATCAAGAACTATTATTAGCTCTGTACAAGAACTTTGTGAATGCAACCGTTTTACAT
TGTTGCATATGATTGATGTTTTTAAAGGTGCGATGACAAAGAAAATTGTTATTTCAGGTC
ATCAGAATACTCGATATCATGGATATTTGAGAGAATGGGATCGTCTTGATATTGAGAGAA
TTTTTCACAAACTAGTCATTGAAAATTATTTAAAGGAAGAATTAACGGTTGTTAAAGATA
TTCCTATTCCATATTTAAAACTTGATGATCCACTTATGGAAGAACTTTATAGTCAATGTT
ATCGTGAACTTTTAGAAGTTGCTAAAATAATTGCTGATGAACTTAATGTAGCTGTAAATC
AAATTATGAATATGGAAGCAATTCGTCAAATGTCTATTAAATTACCAAAAACTTTGGAAG
AGATGCTAGACATTCCACATGTCACAAAAGCTAATTTTGAAAAGTATGGTCATGGATTTT
TGAATATATGCCAGTTATATCGTTCCAAAAAAATTGACTACGAAATGGCAAGAGAAATGC
AACGTGAAATAGATCTAGAAATGGAAAATTCTACCGAACTGATCGATTATGAAGAAGATG
ATGATGATGATGATAATAATATTGATTGGGATACATTTTATCAGCAAATAATGACAAGTA
GCCAAAATGTTGCAGGCTTTAAACGTAAAGGTACAGGACGTAAAGAAATTGTTGCTAAAA
AATACAAGCAAACATTAACAAAGAAATGA

>g3237.t8 Gene=g3237 Length=294
MIDCRRQAQLNYFGEHFSREKCIENRESACDNCTRNADYIMIDITEISRTIISSVQELCE
CNRFTLLHMIDVFKGAMTKKIVISGHQNTRYHGYLREWDRLDIERIFHKLVIENYLKEEL
TVVKDIPIPYLKLDDPLMEELYSQCYRELLEVAKIIADELNVAVNQIMNMEAIRQMSIKL
PKTLEEMLDIPHVTKANFEKYGHGFLNICQLYRSKKIDYEMAREMQREIDLEMENSTELI
DYEEDDDDDDNNIDWDTFYQQIMTSSQNVAGFKRKGTGRKEIVAKKYKQTLTKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g3237.t8 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 2 133 0.00e+00
13 g3237.t8 Gene3D G3DSA:1.10.150.80 - 138 223 0.00e+00
4 g3237.t8 PANTHER PTHR13710 DNA HELICASE RECQ FAMILY MEMBER 2 120 0.00e+00
6 g3237.t8 PANTHER PTHR13710:SF128 ATP-DEPENDENT DNA HELICASE Q-LIKE 4A 2 120 0.00e+00
5 g3237.t8 PANTHER PTHR13710 DNA HELICASE RECQ FAMILY MEMBER 139 273 0.00e+00
7 g3237.t8 PANTHER PTHR13710:SF128 ATP-DEPENDENT DNA HELICASE Q-LIKE 4A 139 273 0.00e+00
1 g3237.t8 Pfam PF16124 RecQ zinc-binding 3 34 1.60e-06
2 g3237.t8 Pfam PF09382 RQC domain 41 134 0.00e+00
3 g3237.t8 Pfam PF00570 HRDC domain 144 208 0.00e+00
14 g3237.t8 ProSiteProfiles PS50967 HRDC domain profile. 139 219 1.35e+01
10 g3237.t8 SMART SM00956 RQC_2 43 150 0.00e+00
11 g3237.t8 SMART SM00341 hrdc7 139 219 0.00e+00
9 g3237.t8 SUPERFAMILY SSF46785 Winged helix DNA-binding domain 41 142 0.00e+00
8 g3237.t8 SUPERFAMILY SSF47819 HRDC-like 143 215 0.00e+00

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