Gene loci information

Transcript annotation

  • This transcript has been annotated as Ribonucleases P/MRP protein subunit POP1.

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 g9511 g9511.t2 isoform g9511.t2 3829549 3832249
chr_1 g9511 g9511.t2 exon g9511.t2.exon1 3829549 3831937
chr_1 g9511 g9511.t2 cds g9511.t2.CDS1 3829549 3831921
chr_1 g9511 g9511.t2 exon g9511.t2.exon2 3831991 3832249
chr_1 g9511 g9511.t2 TSS g9511.t2 NA NA
chr_1 g9511 g9511.t2 TTS g9511.t2 NA NA

Sequences

>g9511.t2 Gene=g9511 Length=2648
TTTTATTTACTTATTTATTATTGTCTTGTTTTAAAATGATAATTTTATATTAAATTACTT
TTTTGAGATCTATTTAGTTACTTTTATTGGTTATAAAACTTCTTTTTAGTGGAGAATTTA
TTGATGGAATAAAATTTTATCAAATTTCAAAATTGAAATATTTTTTGAACTTCCGGAGTT
CAAAAATTTCAAAACAAACAAAAAAGCATGATTTTTCTAATTGAAATTTATTAAAATTTA
ATTGTTAAGAATTTATAAGTTTTAGTTTATTCATCATGGATCAAGATAGTGAAGTTGTAA
AAAAGCGTGAAAATATAAATATTGTGAATCACATTGCCGGTCGTTTGAAAGAATTAAAGA
GATTGTACAATGATGTGGTTACTACAAAATCTGATATGCTGGTTCATCAAATGCTACCTA
ATCATTTGAGAAGACGTGCAATGAGTCATAATCCGAAAAGACTTCCACGAAAATACCGGC
AAGCACATATTAATCAAATGACAAAATCTGGACTTGAAGGTGCAAAAAAGAAGAGACCAT
CTAGAAAATATCGTCGTAGACCATCAAATCTTATGAAAGAATATAATAGACGAAAGCAGA
AAAATGTATGGCTAGAAACTCATGTTTGGCATGCAAAACGTTTTAGAATGAAGAATATGT
GGGGATATCGAGTGCCTTTTACACCGACAGATAAACGATATAGAGCATCATATAAAGGTG
CAAATCATCATTGTTTAGTTCAAGACATCAGTTATTATTCATGTATTGAAATATCTGGAG
CTTTTGAAGATTTACAAGCTGGATTTCGTCGAATAACTTCGGTTGAATGTGGCTTAACTT
TAAATGCAAAATGTTTATTAAATGGTACTCGCGAAGGTAATGTAATGATTTTTAAAACGG
ATTCATATCCACTTCATGCTATAGCTCGTATTTCATTCTTATGGAGACCATCAACTGATT
TATCACATCGAACTATTTGGATATTTGTTCATCCTGGTGTCTATAAAGAAACTTTAAAAG
AGTTTCTTGAGCTGTTTGATGCAAAAGAAAATGGTTCAAATTCTAAATTAATTCGCAATC
CAAAATATACCAACACAACTTCATCAATTGAAATAATTGAATTGAAAGATACTTTAAATC
GAATTCAATTAACTGGACCCTATTCGAGTGCTGTCTTATTTAAAACTCTCAAATTATCAA
CAAACTTTAAAAATAATTGGACTGAAATGCATTATGATGAAAATTCAATTTATAAAAAAG
CTCATATAGAACAAGAGATTGTATGGAAAAAATTACAACAAACCACATCACATTTAGAAT
ATCAACTATATGGAGTACTAGGTTTAACAGTTCAAGATCCACGAATTAATCGTCCATTAA
AAACGACTAAAGCTGTGAATGAATCACAATCCTTTCAAAAAGATAACTATCTTTTTGAAG
ATGTGCCTCAAATAACTTCAATATCTGCAATTTGGAATAAAGAAATTAGAGATGAACTTA
TCAAAACTAAAATGTCAAACAGTGAACTATGTAAACTTCGAAATAAGAATCAATTAGTGC
CAGGAATCGCTTCATTATGTGAAAAAGATCTTCAGCCTATTCCTATACTTTTAATACAAC
GACCATCAGTTGCAAGTAATAATATTCGTAAGAATGCATTTGGTAGCGGTTGGGATTTAA
TAATTCCTGCATCATATGGACTTCATTTCTGGTTAACACTTGTTAAATTTGGTGCTAAAC
CAATAGGATTGAGAGAACGATATATGATAATGAATGAAGCAGGTTTAAATGCATTTGATC
CTGATTCATTACTTGGAAAGAAAGAGTATGAGCAAATTAAACAAGAAAAAACTGATCAAT
ATTTCAAACTTCCACCTAATAAACGCACAAATTATACTAAAATGAAAATTGCTTCGCCAT
TTGCATTACCATTCAAACAATTGATTAATGAATGGGGATCAGAAAATAATGAATTTTATT
TATTAAGGAATATTTCTCTTTTAAATGAACTTGATAATGCTGTGAGGAAAAGAATCAATT
ATAATTTTGATAAGATTGATACTAATGCTTTAATTCCAATTTATTTAATTAATGAGGGAA
GTCGTAACGATAGTTATTTCAATTTAATTTGTCTGCCAAAAAAGTGTGACATTAAAAAGG
CATTAAATCAAAAATATTTTCGTGTCAATGAGCCTGTATTTATTGAAACAACAGGAGAAG
ATAAAAATGCTGTAGAAAGAAAGAATATCAGACTTAACCACAAGAAAGCACTAAAACGTC
TAAGAAATCGTCGAGTGAGACTAAAGAGAAAACTTCAAGCGACATCAGAGTATTTTGTAA
AAATACAGAAATCAAATACTGAAAAGATGATCGAAGAGCAATTTAAGAAAATGTGTGAAT
TATGGCTGCCATCAAATCAACCGACAATCAGAAATCAATGTTCTCGTGAAGTGATTGGAT
ATATTACAAAATCACGTTTCTGTTTCTCAGAAGGAAAAGTTTGTGCGATTGGATATGTAA
CTCGAAACGGATTTAAAGAATTATTACAAGTTTTTCAAAAATTCAAAGGACTTAAATCAT
TTGTCATTACTCGCAATACAAATAGCCAGAATTATTATCAATCAAATTTTATAATCAATC
CGCAATAA

>g9511.t2 Gene=g9511 Length=790
MDQDSEVVKKRENINIVNHIAGRLKELKRLYNDVVTTKSDMLVHQMLPNHLRRRAMSHNP
KRLPRKYRQAHINQMTKSGLEGAKKKRPSRKYRRRPSNLMKEYNRRKQKNVWLETHVWHA
KRFRMKNMWGYRVPFTPTDKRYRASYKGANHHCLVQDISYYSCIEISGAFEDLQAGFRRI
TSVECGLTLNAKCLLNGTREGNVMIFKTDSYPLHAIARISFLWRPSTDLSHRTIWIFVHP
GVYKETLKEFLELFDAKENGSNSKLIRNPKYTNTTSSIEIIELKDTLNRIQLTGPYSSAV
LFKTLKLSTNFKNNWTEMHYDENSIYKKAHIEQEIVWKKLQQTTSHLEYQLYGVLGLTVQ
DPRINRPLKTTKAVNESQSFQKDNYLFEDVPQITSISAIWNKEIRDELIKTKMSNSELCK
LRNKNQLVPGIASLCEKDLQPIPILLIQRPSVASNNIRKNAFGSGWDLIIPASYGLHFWL
TLVKFGAKPIGLRERYMIMNEAGLNAFDPDSLLGKKEYEQIKQEKTDQYFKLPPNKRTNY
TKMKIASPFALPFKQLINEWGSENNEFYLLRNISLLNELDNAVRKRINYNFDKIDTNALI
PIYLINEGSRNDSYFNLICLPKKCDIKKALNQKYFRVNEPVFIETTGEDKNAVERKNIRL
NHKKALKRLRNRRVRLKRKLQATSEYFVKIQKSNTEKMIEEQFKKMCELWLPSNQPTIRN
QCSREVIGYITKSRFCFSEGKVCAIGYVTRNGFKELLQVFQKFKGLKSFVITRNTNSQNY
YQSNFIINPQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g9511.t2 Coils Coil Coil 659 686 -
4 g9511.t2 PANTHER PTHR22731 RIBONUCLEASES P/MRP PROTEIN SUBUNIT POP1 11 780 1.2E-135
5 g9511.t2 PANTHER PTHR22731:SF3 RIBONUCLEASES P/MRP PROTEIN SUBUNIT POP1 11 780 1.2E-135
3 g9511.t2 Pfam PF06978 Ribonucleases P/MRP protein subunit POP1 20 91 3.9E-11
2 g9511.t2 Pfam PF06978 Ribonucleases P/MRP protein subunit POP1 94 168 4.1E-20
1 g9511.t2 Pfam PF08170 POPLD (NUC188) domain 465 551 4.6E-19
6 g9511.t2 SUPERFAMILY SSF103025 Folate-binding domain 438 510 4.12E-5

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:0000172 ribonuclease MRP complex CC
GO:0005655 nucleolar ribonuclease P complex CC
GO:0001682 tRNA 5’-leader removal BP

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