Gene loci information

Transcript annotation

  • This transcript has been annotated as Regulator of nonsense transcripts 2.

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 g13055 g13055.t1 isoform g13055.t1 27675273 27678890
chr_1 g13055 g13055.t1 exon g13055.t1.exon1 27675273 27675581
chr_1 g13055 g13055.t1 cds g13055.t1.CDS1 27675273 27675581
chr_1 g13055 g13055.t1 exon g13055.t1.exon2 27675641 27676229
chr_1 g13055 g13055.t1 cds g13055.t1.CDS2 27675641 27676229
chr_1 g13055 g13055.t1 exon g13055.t1.exon3 27676291 27678290
chr_1 g13055 g13055.t1 cds g13055.t1.CDS3 27676291 27678290
chr_1 g13055 g13055.t1 exon g13055.t1.exon4 27678348 27678890
chr_1 g13055 g13055.t1 cds g13055.t1.CDS4 27678348 27678890
chr_1 g13055 g13055.t1 TSS g13055.t1 27679034 27679034
chr_1 g13055 g13055.t1 TTS g13055.t1 NA NA

Sequences

>g13055.t1 Gene=g13055 Length=3441
ATGAGTGAAGAAAATAAAGAAGTAATAGTTGATAATACAACTGTGGAAGATTCAGCAGCA
GAAGAAGAACAGGAACGTGCAGAATTACAGAAATATATTGAAGAATTGAATGAAAAGTTG
AAAACAAAAAATGAATTACGTGATAAAAATGTTAATCGTGTATTACCAGCTGATAACTAC
TTCTTCAAACTAGATTCGAGTTTGAAAAAGAACACTGCTTTCGTGAAGAAGCTAAAACAA
TTCACAGCGGCTCAATTAGATGCATTATTAAAAGATATGAGTGGTTTAAATTTGACAAAG
TATATTTCTGAAGTATCAGCAGCTCTGCTTGAAGCAAAATTAAAGATGACAGATATTCCA
GCTGTAATTATATTGTGTTCTCAATTACATCAAATTTATGGTGACTTCTCTCAACAATTT
TTCGAAAGTTGGCAAAAGAATTTAACAATAAAACCGGGCGAGAAGATACAAAACATCAGT
AAATTGCGAGTAGATTTGAGGTTTTATTGTGAAATTGTCAGTGTTGGAATTTTCACTAAT
AAGATGGGATTGCCTCTACTTGGATCGATTTTGACAAATCTCATAACACAAGACAAAGAA
GAGCACATGAATCTGTCAATCATTCTTTCTTTCTGTAAACATTGTGGTGAAGAGTATGCT
GGATTAACGCCAAGGAAAATATTACTACTTTCAAAGAAATATGATATTCAATTGCCATCT
TCAACACTTCTACCACCAGATAAACAGCAAAATTTAAAAAATTTATTGCGTGATTATCAT
CAAACTCTATGCAAGCATCTTAAAAGTGAGCATAAAGAATTACAGTCAGCTGAGAGAGGT
AAGAAAAAGGCAATGGAAGCGCGAGGAGAAATTTCCAACGAAAAACGAGAACAACTTGAA
TTATTGCAATCAAATTATGAGAAATTACTGCAGTCCACAACGACTCTGAGTGATTTACTT
AATGAAAATATGCCAGAATTGCCAAAAGAACCTGAAATTCAAAATGAGGGTAATGTCATT
GAATTATCAGAAGACTTGAACGATGTACAACTCGATCCATGGGGAGATGAAGATACGAAA
TCATTTTATGTTGATTTGCCTGATCTAAGACAATTTTTACCAAATTTTCATGGAAGAAAA
GAATCATCTGAACCACTACCTGAAGTCGAACAAGTTACAGAAGCAGCTTTAGATGAAGAA
AATCCAGCTGAACCAGAATTGAATGTTGAAGAAGAAGCAATGCTTAAAGAAATTGAATTA
GAAGCAACTAAGCCTGATGGTGAAAAGAGTGCAATTGAAAAACCACCAGAAGAAACTGAA
AATATTGAAGCAGACACAACATCGACAAGTGAAGAAAAACCAGCGATTACTGAAAAATCT
ATTCCTGAGAAAACACAAATCTTAGGCAAACATCATCTTGAAAATTTTCTCGCAAACTTA
CCAAATTGTGTCAATCGTGAATTGATTGATTCAGCTGCCATAGATTTCCTTCTAAATTTC
AATAATAAACCAAATCGAAAACGATTGATTAAAGCACTTTTCAATGTTCACCGTACTCGT
TTGGATTTATTACCACTACTTGCACGTTTCTGTGCTATCATTAATTTAGTCACATCAGAT
GTTGCACAAGAATTATCTCAGATGCTCAAAGTTGACTTTAAATTTCATGTCAAAAAACGT
GACCAGATTAACATCGAGTCAAAGATTAAGGCAGTTCGATATATTGGTGAAATGACAAAA
TTCGCGCTTTATCCTCGTTTGGAAGCTCTCATGTGTTTGAAGCTTTTATTAAGCAATTTT
CAGCATCATCATATCGAAATGACTTGTTCTTTTCTTGAAGTTTGCGGAATGTATCTTTAT
AATTGCAAAGACTCGAGATTAAGAACTAGTGCACTCTTAGAACAGATGATGAGATTAAAG
AAAGCAATGACATTGGATACGAGACACGCAACGCAGATTGAAAATTGCTATTATTTAGTT
AAGCCACCAGAAGGAGGTATCAAAGTAAAGCAAAAGATAAGAACACCTATTCAGATGTAT
ATTAGATATCTCATATTTGAGGAGCTACATAAAGGAAATGTTGAAAAGATTGTTAAATAT
TTGAGAAAATTGAATTGGGATGATTCAGAAGTGAGCGATTATGTGATTAAATGCTTAACA
AAAGCTTATACATTTAGATGGCATTTAATTCGTTCCTTAGCTGATGTTGTCAGTGCATTG
AGCTCTTATCAAGAGAAAGCTGTCACTAGAGTTATTGATGGTGTTTTTGAAGATATTCGA
GCTGGATTAGAAATTCATTCACCAAAACTTGCACAAAGAAGAATAGCAATGGCAAAATAT
TTAGGTGAACTATATATCTATCGACTTGTCGATTCACAGAACGTGTTCAACACTCTTTAT
AGCATCATTTCATATGGTGTAACTTGGAATCATGAAATATTCTCACCAGTTGATCCACCC
GAATCAATGTTTCGACTAAAATTAGCTTGTACTATGCTTGATACATGTGGTGCATATTTT
CAAAGTTTATCGAGCAAGAAAAAACTTGATTGTTATCTTGTCTTTCTTCAAAACTATTAT
TGGTTCAAAAAGAGTCATCCTGTGTTCAAATCGACAGCTGAAAGTGGCGATTTATTTCCT
TTTCTTATCGAGCACATGTATAAAGAGTGTTTGCATAATTTACGTCCAAAACTGAAGCTT
TACAAGTCATATGAGAAGGCACAAGAGGAAATTGAAAAGCTGAAGCAGCAATTATATCCA
AATCTTGGTGAAGGTGAAAGTGACGGTAAATTGCTGAATACGATAATTGAAAATGAGAGC
GATTACACATCGGAAGCAGTAATGGAAAGTGATGATGAAATTAAGCCACGAACGGAAGTT
GATGATTTCCAAGAGGAAGATGATAATGAAGAAGTAAAAGATGAAGAAGATGAAAATTCT
CAAATGGATGATGTCAAGTCACAGGAAAATAAAGAAAAGACAGAAGAAGATTTACAATTT
GAAGCAATGTTTGATAAAATGGCTGCAGATTCATATCAAGAGAGAATAAAAGAATTACCT
AAAGTAACTACAAGAGATATTCCAGTGCCAATGTCAACTAAAGCAATCAAAAAGACCTAT
GAGCAATTACAGGAAAATGATGATAAGCAAGAAACAAATGCAGTACCATTTGTGCTTATG
GTGAGAAATTCAAAAAGTGGAAAGCAGCAATTTAAGAACTTTGTTGCACCACCTGATAGT
GATTTAGCAATGAATTTGAAAATGCAAGAGCAAAAGATAAGAGAAGAACATGAACGTGTG
AAACGTTTAACATTAAATATTACAGAAAGATTAGAGGAAGAAGATTATCAAGAATCTTTA
CAAAAATCACCTGCCATCAATCGTAGACCAAAAGTTCAAAAATTCAAACATCAAAAAGGC
GTCCCAGATATTGATTTTTAA

>g13055.t1 Gene=g13055 Length=1146
MSEENKEVIVDNTTVEDSAAEEEQERAELQKYIEELNEKLKTKNELRDKNVNRVLPADNY
FFKLDSSLKKNTAFVKKLKQFTAAQLDALLKDMSGLNLTKYISEVSAALLEAKLKMTDIP
AVIILCSQLHQIYGDFSQQFFESWQKNLTIKPGEKIQNISKLRVDLRFYCEIVSVGIFTN
KMGLPLLGSILTNLITQDKEEHMNLSIILSFCKHCGEEYAGLTPRKILLLSKKYDIQLPS
STLLPPDKQQNLKNLLRDYHQTLCKHLKSEHKELQSAERGKKKAMEARGEISNEKREQLE
LLQSNYEKLLQSTTTLSDLLNENMPELPKEPEIQNEGNVIELSEDLNDVQLDPWGDEDTK
SFYVDLPDLRQFLPNFHGRKESSEPLPEVEQVTEAALDEENPAEPELNVEEEAMLKEIEL
EATKPDGEKSAIEKPPEETENIEADTTSTSEEKPAITEKSIPEKTQILGKHHLENFLANL
PNCVNRELIDSAAIDFLLNFNNKPNRKRLIKALFNVHRTRLDLLPLLARFCAIINLVTSD
VAQELSQMLKVDFKFHVKKRDQINIESKIKAVRYIGEMTKFALYPRLEALMCLKLLLSNF
QHHHIEMTCSFLEVCGMYLYNCKDSRLRTSALLEQMMRLKKAMTLDTRHATQIENCYYLV
KPPEGGIKVKQKIRTPIQMYIRYLIFEELHKGNVEKIVKYLRKLNWDDSEVSDYVIKCLT
KAYTFRWHLIRSLADVVSALSSYQEKAVTRVIDGVFEDIRAGLEIHSPKLAQRRIAMAKY
LGELYIYRLVDSQNVFNTLYSIISYGVTWNHEIFSPVDPPESMFRLKLACTMLDTCGAYF
QSLSSKKKLDCYLVFLQNYYWFKKSHPVFKSTAESGDLFPFLIEHMYKECLHNLRPKLKL
YKSYEKAQEEIEKLKQQLYPNLGEGESDGKLLNTIIENESDYTSEAVMESDDEIKPRTEV
DDFQEEDDNEEVKDEEDENSQMDDVKSQENKEKTEEDLQFEAMFDKMAADSYQERIKELP
KVTTRDIPVPMSTKAIKKTYEQLQENDDKQETNAVPFVLMVRNSKSGKQQFKNFVAPPDS
DLAMNLKMQEQKIREEHERVKRLTLNITERLEEEDYQESLQKSPAINRRPKVQKFKHQKG
VPDIDF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
27 g13055.t1 Coils Coil Coil 15 53 -
28 g13055.t1 Coils Coil Coil 277 312 -
25 g13055.t1 Coils Coil Coil 897 917 -
26 g13055.t1 Coils Coil Coil 1086 1106 -
23 g13055.t1 Gene3D G3DSA:1.25.40.180 - 19 328 1.4E-103
22 g13055.t1 Gene3D G3DSA:1.25.40.180 - 434 674 7.7E-26
24 g13055.t1 Gene3D G3DSA:1.25.40.180 - 675 923 2.1E-89
21 g13055.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 23 -
17 g13055.t1 MobiDBLite mobidb-lite consensus disorder prediction 270 292 -
13 g13055.t1 MobiDBLite mobidb-lite consensus disorder prediction 422 456 -
14 g13055.t1 MobiDBLite mobidb-lite consensus disorder prediction 422 441 -
20 g13055.t1 MobiDBLite mobidb-lite consensus disorder prediction 942 995 -
16 g13055.t1 MobiDBLite mobidb-lite consensus disorder prediction 948 962 -
15 g13055.t1 MobiDBLite mobidb-lite consensus disorder prediction 963 978 -
18 g13055.t1 MobiDBLite mobidb-lite consensus disorder prediction 979 995 -
19 g13055.t1 MobiDBLite mobidb-lite consensus disorder prediction 1112 1146 -
5 g13055.t1 PANTHER PTHR12839 NONSENSE-MEDIATED MRNA DECAY PROTEIN 2 UP-FRAMESHIFT SUPPRESSOR 2 22 1119 0.0
6 g13055.t1 PANTHER PTHR12839:SF7 REGULATOR OF NONSENSE TRANSCRIPTS 2 22 1119 0.0
3 g13055.t1 Pfam PF02854 MIF4G domain 68 256 4.2E-13
2 g13055.t1 Pfam PF02854 MIF4G domain 479 662 4.7E-15
1 g13055.t1 Pfam PF02854 MIF4G domain 682 895 9.3E-33
4 g13055.t1 Pfam PF04050 Up-frameshift suppressor 2 983 1106 7.8E-21
12 g13055.t1 SMART SM00543 if4_15 68 270 1.9E-12
11 g13055.t1 SMART SM00543 if4_15 474 663 8.3E-28
10 g13055.t1 SMART SM00543 if4_15 679 897 4.2E-29
9 g13055.t1 SUPERFAMILY SSF48371 ARM repeat 85 280 2.71E-32
7 g13055.t1 SUPERFAMILY SSF48371 ARM repeat 473 674 5.76E-48
8 g13055.t1 SUPERFAMILY SSF48371 ARM repeat 674 924 2.88E-63

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:0003723 RNA binding MF
GO:0005515 protein binding MF
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay 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