General information for g1607.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Heterogeneous nuclear ribonucleoprotein 87F.
Parent gene
- The parent gene g1607 is located on chr_3: 12101069..12102151 (- 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 | g1607 | g1607.t2 | isoform | g1607.t2 | 12096845 | 12101444 |
| chr_3 | g1607 | g1607.t2 | exon | g1607.t2.exon1 | 12096845 | 12097463 |
| chr_3 | g1607 | g1607.t2 | exon | g1607.t2.exon2 | 12099507 | 12099571 |
| chr_3 | g1607 | g1607.t2 | cds | g1607.t2.CDS1 | 12099549 | 12099571 |
| chr_3 | g1607 | g1607.t2 | exon | g1607.t2.exon3 | 12099626 | 12100033 |
| chr_3 | g1607 | g1607.t2 | cds | g1607.t2.CDS2 | 12099626 | 12100033 |
| chr_3 | g1607 | g1607.t2 | exon | g1607.t2.exon4 | 12100322 | 12100566 |
| chr_3 | g1607 | g1607.t2 | cds | g1607.t2.CDS3 | 12100322 | 12100566 |
| chr_3 | g1607 | g1607.t2 | exon | g1607.t2.exon5 | 12100837 | 12101069 |
| chr_3 | g1607 | g1607.t2 | cds | g1607.t2.CDS4 | 12100837 | 12100946 |
| chr_3 | g1607 | g1607.t2 | exon | g1607.t2.exon6 | 12101327 | 12101444 |
| chr_3 | g1607 | g1607.t2 | TSS | g1607.t2 | 12101603 | 12101603 |
| chr_3 | g1607 | g1607.t2 | TTS | g1607.t2 | NA | NA |
Sequences
>g1607.t2 Gene=g1607 Length=1688
ATGAGTGAAAACGTACATGACGGCGAATGCAGCAATGCTCAAATGGAAAATTCCGAAATG
AATGGAAATAACGAGCATTATGAAGACAATGGTAATCAAAATGAACAATATGATGTAAGA
TGATATTAAAGAACCAGAATGCACGCGAAAACTTTTTATTGGTGGGCTTGACTATAGAAC
AACTGACGAAACATTAAAGAGTTATTTTGAAAAATGGGGAAAAATAGTTGATGTAGTTGT
AATGAAAGATCCTAAGACTAAACGTTCACGTGGGTTTGGTTTCATCACTTACTCGCGTTC
AAGCATGGTTGATGCAGCACAAGCAGCTCGTCCTCATAAAATTGACTCTCGTACTGTTGA
ACCAAAACGTGCGGTGCCTAGAAATGATATTAATCGCCCGGAGGCGGGTTCTTCTGTGAA
GAAACTGTTTGTTGGAGGCCTTAAAGACGACTTTGAAGAAGAAGATTTGCGTGAATATTT
CTCACAATTTGGAAATATCACATCTGTAATCATTGTTAGTGATAAAGAAAGTGGAAAAAA
ACGTGGATTTGGATTCGTTGAATATGACGATTATGATCCTGTTGATAAAATTTGCTTGCA
AAAGACACACACAATTAAGAACAAGATGCTTGACGTGAAAAAAGCAATTAGTAAGCACGA
TATGGATCGCTTTAGGAATGACCAACGTGGGATGATGGGAAATAATTATAGTGGAGGTAA
TTATGGATCGGGCTATGGCAGAAATCAAGGAAGCTGGGGAGGACGAAATAATAATGGAAA
TTGGGGGCAATGGTCAAATGATTCTTATGGAGGAAATTCAGGTTGGAGTAACGATAATGG
ACCATGGGATAGTCAAAGTAGTTGGTCCAATAATAATGGCGGATACAATCAAAATTGGTC
AAATGATAGTTTCGGTAATAATTATCAACAAAGCTATAATAACGGTGGCGGACCAGTTCG
AGGTAGAAGCAGTTATGGCAATCGTTCAGCACCATACAACCAAAGAAGTGGAAATCGACG
CTACTAAGAAAATAACATACATTTTAGTATGAAAAACTTGTGTGTCATGCATTTAACGTA
GAATGATATTTTGCGTACAAGCGACGAAAATGTGAGAGAGCATAATATGGGCGTGATTTT
TCTACTTTCTAAATGAAGTAAGTACTCTTCAATGTGCAAGTAAACAGCAACATTGAACTA
TGAACAGAAGGTAAGTAATGAAGAATAATATGCATGTGTGAAAGAAACTTGTGAATATGT
GACAAAACGGCATCATCGTTGTCGTCAATTTGCTGAAAGGATTTTTGAGAAACTCTTCGT
CATCACCTTCTCTCCCTGTCTTCTACAAATGTGTGGGTAAAAAAAGGTTTGGTGACAATC
GTTTTATTATTTTCATTGCTTCAATTGACCTTAGATTGCATGGCAATTATTATTATTGCT
GACTTTTATTAATTTTTAAGTATTCTATACCTCATTTATAACTTTAAAATACAAATTGAC
TTTAATTCATAGAATAAAAGTTTTTTGTTGGAAAAATTCAAATTGTCTTATTTAATTCTT
ATTTCAGTTATAATGATTTCAAAAATTTCAGAATCAGGGGGATGAAAATTAAGCAAACGA
TTTCGCTTATATTTGCTTTTTTCGCTTCAAAGTTCACATGCGACAAACACACAATTTTCA
TATTTTCA
>g1607.t2 Gene=g1607 Length=261
MKDPKTKRSRGFGFITYSRSSMVDAAQAARPHKIDSRTVEPKRAVPRNDINRPEAGSSVK
KLFVGGLKDDFEEEDLREYFSQFGNITSVIIVSDKESGKKRGFGFVEYDDYDPVDKICLQ
KTHTIKNKMLDVKKAISKHDMDRFRNDQRGMMGNNYSGGNYGSGYGRNQGSWGGRNNNGN
WGQWSNDSYGGNSGWSNDNGPWDSQSSWSNNNGGYNQNWSNDSFGNNYQQSYNNGGGPVR
GRSSYGNRSAPYNQRSGNRRY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g1607.t2 | CDD | cd12328 | RRM2_hnRNPA_like | 61 | 133 | 4.19291E-41 |
| 7 | g1607.t2 | Gene3D | G3DSA:3.30.70.330 | - | 1 | 50 | 2.3E-9 |
| 6 | g1607.t2 | Gene3D | G3DSA:3.30.70.330 | - | 58 | 135 | 2.5E-24 |
| 10 | g1607.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 237 | 261 | - |
| 2 | g1607.t2 | PANTHER | PTHR48026 | HOMOLOGOUS TO DROSOPHILA SQD (SQUID) PROTEIN | 1 | 253 | 1.3E-63 |
| 3 | g1607.t2 | PANTHER | PTHR48026:SF2 | HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN A1-RELATED | 1 | 253 | 1.3E-63 |
| 1 | g1607.t2 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 62 | 117 | 2.9E-15 |
| 11 | g1607.t2 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 60 | 137 | 17.182 |
| 9 | g1607.t2 | SMART | SM00360 | rrm1_1 | 61 | 133 | 3.0E-22 |
| 5 | g1607.t2 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 1 | 53 | 9.77E-9 |
| 4 | g1607.t2 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 42 | 150 | 7.39E-25 |
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: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.
