Gene loci information

Transcript annotation

  • This transcript has been annotated as Signal recognition particle subunit SRP72.

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 g10523 g10523.t1 TSS g10523.t1 10343484 10343484
chr_1 g10523 g10523.t1 isoform g10523.t1 10343550 10345647
chr_1 g10523 g10523.t1 exon g10523.t1.exon1 10343550 10343661
chr_1 g10523 g10523.t1 cds g10523.t1.CDS1 10343550 10343661
chr_1 g10523 g10523.t1 exon g10523.t1.exon2 10343722 10345459
chr_1 g10523 g10523.t1 cds g10523.t1.CDS2 10343722 10345459
chr_1 g10523 g10523.t1 exon g10523.t1.exon3 10345521 10345647
chr_1 g10523 g10523.t1 cds g10523.t1.CDS3 10345521 10345647
chr_1 g10523 g10523.t1 TTS g10523.t1 10345707 10345707

Sequences

>g10523.t1 Gene=g10523 Length=1977
ATGTCGTCTAGAGAAGAAATTAAGGCGCAAAATATAAGGCAATACTATACAGAGTTGAGT
AAATTTGGTCAAGCAGGAGAATATGAAAAAGCAATCAAATCTGCTAATAAAATTATTAGT
ATTGCACCTGAAGAAGTGAAAGCAGTTCATTGCAAATTAGTTTCTTTAATTCAATTATCC
AAATTTGATGAGGCCCTCAAATTTATTGAAAAAACACCTTCTGCTCAATCACTTTTATTT
GAGAAGGCCTATTGTGAATATCGTCTCAATAAACCAGAAGTTGCATTGAAAACAATCGAG
AGTGCAAAAATCAATCCACTTCCACCAAATTTGAAAGAATTAAAAGCTCAAGTTTTATAC
AGATTGGAGCAATTTGATGAATGCTTCAATCTTTATCGTGACATAATTAAAAATTCAACT
GACGATTATGAAGAGGAGAGAACAACGAACTTGTCAGCTGTTTGTGCTAATTTAGCTATA
GAAGGCACTGATAAAAAAATCCCTGAACTTGGAGAGAATACTTATGAATTGGTCTATAAT
TCAGCAGTTGCTCTCTCAGGTATAGGAAAATATAATGAAGCTGAGAAGAAACTTAAAATC
AGTGAAAAGATGTGTCGAGAATTCTTGGAAGAAGACGAAGCAACAACTGAAGAAGATATT
CAAAATGAGCTAGCTATTATTCGAGTTCAATTGGCCTACTGCTTACAAATGCAAGGTCGC
AATAAAGAAGCATCTGCTATTTATGCTGAAACTCTTAAAAATAAACCTAATGATCAAGCA
CTAACTGCAGTTGCTTCAAATAACTCAGTTGTTATTAATAAAGATCAAAATGTTTTTGAT
TCAAAGAAAAAAATTAGAGCCGCTATGATTGAAGCAGTTGAACATAAACTTAATAGTCGT
CAAAAAAAGAGCATTGCCATCAACAACTGTATTTTAGCATTATTCACTCATCAAGGAGAC
CTCAATCAACTTGTTCATAAACTCGTTCAGAAATATCCAGATCTCGAGTTTAATGGATGT
CTTATTCAATCATGTTCGCTTATTAAAGAAAAGAAGTATAAAGAAGCAAGTGAAGTTTTA
GAAAAATTTGCCCAGAAAAATCCAAAATCATCTCTTGAAATCAAATTTGCTCTTATTCAA
TTGCATTTGATGGCTGGAAATAAAACAAAAGCTATCGAAGTTCTTCAATCATTAGAGAAT
TCAACAAAATTTAGTCCAGGTGTTGTTTCTGCACTCGTTTCACTTTATTTGGGAACTAAT
GATAAATCTGCCGCATCCGATCTTCTTAAAGTAGCTGTTGATTGGTACAAGCAAAATAAA
TCTACGGAAGTAGGTGATTTAACTGACATGTGGCGCCATGCTGCTGATTTTCATTTGCGA
GGTGGAGATGCACCTACTGCAGCCAAGAGTTTAGAAGAATTGCATCGTTCTAATCCGAAA
GACATGAAAACACTCGCTCAACTTGTAATAGCTTATGCTCAGTTTGATCCGAAGAAAGCT
CAAGATTCATCTAAAAAATTACCTGCACTTGAAACATTAACCACACAAGCTGAAATTGAT
GAATTAGAAGCAACTAATTGGACTATGATAACAAAAGCTGTTAAAAAGAAGACATCAACA
AAATCTGATCAATCTCCTGGTACACCAGGAAGTGAAACTGCCTTAAAGAAAATGAAAAAG
AAGAAGCGAAAGAATAAATTACCCAAGTACTATGATCCAAATGCAAAACCTGACCCTGAG
CGATGGTTGCCAAAGCAAGAACGTACTGGTTATAGGAAAAAACGCGATAGAAGAGTTAAA
GAAGTGATGAAAGGTTCTCAAGGAATGGCTTCAACACAAGCCGATATGTATGATATGACT
AAAGCCCAAAATTTGGGTCAAAATGTCAAAGCATCAAGTTCTCGAGAAGAGACTACTCCA
GGTCCCCGCCAGCAGCAACGCAAGCACCAACAAAAAAAGAAGAAGGGCAAACATTAA

>g10523.t1 Gene=g10523 Length=658
MSSREEIKAQNIRQYYTELSKFGQAGEYEKAIKSANKIISIAPEEVKAVHCKLVSLIQLS
KFDEALKFIEKTPSAQSLLFEKAYCEYRLNKPEVALKTIESAKINPLPPNLKELKAQVLY
RLEQFDECFNLYRDIIKNSTDDYEEERTTNLSAVCANLAIEGTDKKIPELGENTYELVYN
SAVALSGIGKYNEAEKKLKISEKMCREFLEEDEATTEEDIQNELAIIRVQLAYCLQMQGR
NKEASAIYAETLKNKPNDQALTAVASNNSVVINKDQNVFDSKKKIRAAMIEAVEHKLNSR
QKKSIAINNCILALFTHQGDLNQLVHKLVQKYPDLEFNGCLIQSCSLIKEKKYKEASEVL
EKFAQKNPKSSLEIKFALIQLHLMAGNKTKAIEVLQSLENSTKFSPGVVSALVSLYLGTN
DKSAASDLLKVAVDWYKQNKSTEVGDLTDMWRHAADFHLRGGDAPTAAKSLEELHRSNPK
DMKTLAQLVIAYAQFDPKKAQDSSKKLPALETLTTQAEIDELEATNWTMITKAVKKKTST
KSDQSPGTPGSETALKKMKKKKRKNKLPKYYDPNAKPDPERWLPKQERTGYRKKRDRRVK
EVMKGSQGMASTQADMYDMTKAQNLGQNVKASSSREETTPGPRQQQRKHQQKKKKGKH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g10523.t1 Coils Coil Coil 191 211 -
7 g10523.t1 Gene3D G3DSA:1.25.40.10 - 10 160 6.7E-56
9 g10523.t1 Gene3D G3DSA:1.25.40.10 - 161 270 4.5E-6
8 g10523.t1 Gene3D G3DSA:1.25.40.10 - 289 543 5.3E-12
18 g10523.t1 MobiDBLite mobidb-lite consensus disorder prediction 535 658 -
19 g10523.t1 MobiDBLite mobidb-lite consensus disorder prediction 535 551 -
17 g10523.t1 MobiDBLite mobidb-lite consensus disorder prediction 568 603 -
16 g10523.t1 MobiDBLite mobidb-lite consensus disorder prediction 606 640 -
4 g10523.t1 PANTHER PTHR14094 SIGNAL RECOGNITION PARTICLE 72 5 655 1.1E-196
11 g10523.t1 PIRSF PIRSF038922 SRP72 2 658 6.6E-221
3 g10523.t1 Pfam PF17004 Putative TPR-like repeat 34 155 3.9E-21
1 g10523.t1 Pfam PF14559 Tetratricopeptide repeat 347 404 4.2E-6
2 g10523.t1 Pfam PF08492 SRP72 RNA-binding domain 540 593 1.5E-16
12 g10523.t1 SMART SM00028 tpr_5 12 45 78.0
14 g10523.t1 SMART SM00028 tpr_5 109 142 220.0
13 g10523.t1 SMART SM00028 tpr_5 175 208 110.0
15 g10523.t1 SMART SM00028 tpr_5 225 258 11.0
5 g10523.t1 SUPERFAMILY SSF48452 TPR-like 16 202 3.32E-15
6 g10523.t1 SUPERFAMILY SSF48452 TPR-like 174 482 6.03E-11

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:0006614 SRP-dependent cotranslational protein targeting to membrane BP
GO:0005515 protein binding MF
GO:0048500 signal recognition particle CC
GO:0008312 7S RNA binding MF

KEGG

Orthology

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.

Raw TPM values