General information for g1607.t3
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.t3 | TTS | g1607.t3 | 12097000 | 12097000 |
| chr_3 | g1607 | g1607.t3 | isoform | g1607.t3 | 12098013 | 12101444 |
| chr_3 | g1607 | g1607.t3 | exon | g1607.t3.exon1 | 12098013 | 12099276 |
| chr_3 | g1607 | g1607.t3 | exon | g1607.t3.exon2 | 12099507 | 12099571 |
| chr_3 | g1607 | g1607.t3 | cds | g1607.t3.CDS1 | 12099549 | 12099571 |
| chr_3 | g1607 | g1607.t3 | exon | g1607.t3.exon3 | 12099626 | 12100033 |
| chr_3 | g1607 | g1607.t3 | cds | g1607.t3.CDS2 | 12099626 | 12100033 |
| chr_3 | g1607 | g1607.t3 | exon | g1607.t3.exon4 | 12100322 | 12100566 |
| chr_3 | g1607 | g1607.t3 | cds | g1607.t3.CDS3 | 12100322 | 12100566 |
| chr_3 | g1607 | g1607.t3 | exon | g1607.t3.exon5 | 12100837 | 12101069 |
| chr_3 | g1607 | g1607.t3 | cds | g1607.t3.CDS4 | 12100837 | 12101069 |
| chr_3 | g1607 | g1607.t3 | exon | g1607.t3.exon6 | 12101331 | 12101444 |
| chr_3 | g1607 | g1607.t3 | cds | g1607.t3.CDS5 | 12101331 | 12101444 |
| chr_3 | g1607 | g1607.t3 | TSS | g1607.t3 | 12101603 | 12101603 |
Sequences
>g1607.t3 Gene=g1607 Length=2329
ATGAGTGAAAACGTACATGACGGCGAATGCAGCAATGCTCAAATGGAAAATTCCGAAATG
AATGGAAATAACGAGCATTATGAAGACAATGGTAATCAAAATGAACAATATGATGATGAT
ATTAAAGAACCAGAATGCACGCGAAAACTTTTTATTGGTGGGCTTGACTATAGAACAACT
GACGAAACATTAAAGAGTTATTTTGAAAAATGGGGAAAAATAGTTGATGTAGTTGTAATG
AAAGATCCTAAGACTAAACGTTCACGTGGGTTTGGTTTCATCACTTACTCGCGTTCAAGC
ATGGTTGATGCAGCACAAGCAGCTCGTCCTCATAAAATTGACTCTCGTACTGTTGAACCA
AAACGTGCGGTGCCTAGAAATGATATTAATCGCCCGGAGGCGGGTTCTTCTGTGAAGAAA
CTGTTTGTTGGAGGCCTTAAAGACGACTTTGAAGAAGAAGATTTGCGTGAATATTTCTCA
CAATTTGGAAATATCACATCTGTAATCATTGTTAGTGATAAAGAAAGTGGAAAAAAACGT
GGATTTGGATTCGTTGAATATGACGATTATGATCCTGTTGATAAAATTTGCTTGCAAAAG
ACACACACAATTAAGAACAAGATGCTTGACGTGAAAAAAGCAATTAGTAAGCACGATATG
GATCGCTTTAGGAATGACCAACGTGGGATGATGGGAAATAATTATAGTGGAGGTAATTAT
GGATCGGGCTATGGCAGAAATCAAGGAAGCTGGGGAGGACGAAATAATAATGGAAATTGG
GGGCAATGGTCAAATGATTCTTATGGAGGAAATTCAGGTTGGAGTAACGATAATGGACCA
TGGGATAGTCAAAGTAGTTGGTCCAATAATAATGGCGGATACAATCAAAATTGGTCAAAT
GATAGTTTCGGTAATAATTATCAACAAAGCTATAATAACGGTGGCGGACCAGTTCGAGGT
AGAAGCAGTTATGGCAATCGTTCAGCACCATACAACCAAAGAAGTGGAAATCGACGCTAC
TAAGAAAATAACATACATTTTAGTATGAAAAACTTGTGTGTCATGGTTTCAATATGCAAA
AGTATAAAGATTTATTCATAAGACAAAACAAAATTGTAAATGTTTTTCCTTCAAATTTAA
ACTTCTACTATACAAGAGACATAATCATGTGAGAAGCATAGAGTTTTTAGTTATTGGGCC
TTCCACTTCAAGAAAAATAAATCCAACGACAAATTCATACAGAGAGAGATTGAGAGAAAG
AGATAAGCCGATATATATGTTAGACAGAAACCAAAAATGAAGGCGCGTGAGAATAGAAAT
TACACAAGTGAGATATCAAGACAGAAAAAGAAAGATCTTCAAGATGAAATGCAATTGCAT
TTTCCTTCTCAATAAGAATAATAGTTGTGTAGGAAGAAGAAATTGCGTGATGACAGGAGA
GATAAGTTTTTTTTCTTTAGTTTTGAAGTTTCTCCAGAAGACGATGATAATCAACATTTT
ATTTGTTCAGTTTTTTATATAATTCATTTTTCACAATTTACGTGCTATTTTATAATTTAT
ACATATATAAAATAATATCTATTGGATAGAATGTAAGCATACTTTTAATTACAAAACGCT
GATGAGAATTAGTTGTTAAAAAAAGATTGAAATATGTGTTTTTTTTTCATGATAAAATGA
TGATGAGAAATGAAAAATAGTAATCAATACATGCACATAAATAAATGTCTCATTTTTTTG
AATTAAGTATTCACATTATAATTTCCTGTGCATAATAATGTACATTACAATTTATAATAT
TTCCTTTGATTAAACTGAATTTTAATTCAGAATTTCAGAGGCAATTTGATGTAGACATTA
AGAATGAAAGAAAAAAGTTACAGAACCAATTAGCGAGTATATTTAATACACACATATGAG
AAAGAGAGAATCGAAAGTTTATAGCATAAATATGAAAACATGTGTAGTCACTTAACATTT
AAAAAAATTTACCTTATTACACATTTTTAGAGTAATCATTAAATTGGTAAAAAATATTGC
TAAAAATAATGAAAAATAAACTTAGAAAATAATTTGTTCATTTTTCTTTTTTGTATGCTA
AACAACTTTTCATCAAATATTTTATGAAAATCATGAAATTTATCATAAAACATATACACA
TAATTAGCAGAAAAATTTATTATCGTTTTAAAAAATCCTTTTTTTGAGAATAGAGAAAGG
CAAAAAAATAAATGTAGGTAAAATTACGTAGGATGACAGAAGAGTATGAAAAAGAGTTTC
AAGAATCCTTCAGCAAAGTACAGGAAAAAGATAAAATTATATTTACTTA
>g1607.t3 Gene=g1607 Length=340
MSENVHDGECSNAQMENSEMNGNNEHYEDNGNQNEQYDDDIKEPECTRKLFIGGLDYRTT
DETLKSYFEKWGKIVDVVVMKDPKTKRSRGFGFITYSRSSMVDAAQAARPHKIDSRTVEP
KRAVPRNDINRPEAGSSVKKLFVGGLKDDFEEEDLREYFSQFGNITSVIIVSDKESGKKR
GFGFVEYDDYDPVDKICLQKTHTIKNKMLDVKKAISKHDMDRFRNDQRGMMGNNYSGGNY
GSGYGRNQGSWGGRNNNGNWGQWSNDSYGGNSGWSNDNGPWDSQSSWSNNNGGYNQNWSN
DSFGNNYQQSYNNGGGPVRGRSSYGNRSAPYNQRSGNRRY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g1607.t3 | CDD | cd12578 | RRM1_hnRNPA_like | 49 | 126 | 4.55552E-49 |
| 10 | g1607.t3 | CDD | cd12328 | RRM2_hnRNPA_like | 140 | 212 | 1.14138E-39 |
| 9 | g1607.t3 | Coils | Coil | Coil | 10 | 30 | - |
| 7 | g1607.t3 | Gene3D | G3DSA:3.30.70.330 | - | 9 | 135 | 8.2E-25 |
| 8 | g1607.t3 | Gene3D | G3DSA:3.30.70.330 | - | 137 | 214 | 4.0E-24 |
| 14 | g1607.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 30 | - |
| 16 | g1607.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 41 | - |
| 15 | g1607.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 316 | 340 | - |
| 3 | g1607.t3 | PANTHER | PTHR48026 | HOMOLOGOUS TO DROSOPHILA SQD (SQUID) PROTEIN | 40 | 332 | 2.4E-83 |
| 4 | g1607.t3 | PANTHER | PTHR48026:SF2 | HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN A1-RELATED | 40 | 332 | 2.4E-83 |
| 2 | g1607.t3 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 50 | 116 | 7.9E-16 |
| 1 | g1607.t3 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 141 | 196 | 4.8E-15 |
| 18 | g1607.t3 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 48 | 125 | 15.75 |
| 17 | g1607.t3 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 139 | 216 | 17.182 |
| 12 | g1607.t3 | SMART | SM00360 | rrm1_1 | 49 | 121 | 6.0E-23 |
| 13 | g1607.t3 | SMART | SM00360 | rrm1_1 | 140 | 212 | 3.0E-22 |
| 6 | g1607.t3 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 46 | 132 | 1.48E-24 |
| 5 | g1607.t3 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 123 | 246 | 1.61E-29 |
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 transcript has been annotated with K12741 (heterogeneous nuclear ribonucleoprotein A1/A3)
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.
