Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Protein SMG5.

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_2 g5201 g5201.t1 TSS g5201.t1 7627601 7627601
chr_2 g5201 g5201.t1 isoform g5201.t1 7627787 7631414
chr_2 g5201 g5201.t1 exon g5201.t1.exon1 7627787 7627818
chr_2 g5201 g5201.t1 cds g5201.t1.CDS1 7627787 7627818
chr_2 g5201 g5201.t1 exon g5201.t1.exon2 7628086 7629856
chr_2 g5201 g5201.t1 cds g5201.t1.CDS2 7628086 7629856
chr_2 g5201 g5201.t1 exon g5201.t1.exon3 7629913 7630894
chr_2 g5201 g5201.t1 cds g5201.t1.CDS3 7629913 7630894
chr_2 g5201 g5201.t1 exon g5201.t1.exon4 7630955 7631113
chr_2 g5201 g5201.t1 cds g5201.t1.CDS4 7630955 7631113
chr_2 g5201 g5201.t1 exon g5201.t1.exon5 7631182 7631414
chr_2 g5201 g5201.t1 cds g5201.t1.CDS5 7631182 7631414
chr_2 g5201 g5201.t1 TTS g5201.t1 7632003 7632003

Sequences

>g5201.t1 Gene=g5201 Length=3177
ATGGAAAATTCAGAATTGAAAGCAAAAACAAAGAATGTTTATCAGATAATTAAAGCACTG
GATGAGCATAAACAAACATCAAAAACAATTTCATCGCTATTCAGTGACATTGGAGTAGAG
GTCTTACGCAAGAAACTTGTAATTTTAATAGAATCAATTTTGTTAGAGGATTTTGAGACC
ATCGGGAAGAAAACAAGAGATATATTATGGCGAAAAATGTATTACGATCCAATTTCAACA
TCAAAAAAATTATGGAAGAAGAGTGAAAGGGAGTTGACTGACTCGGAAGCGACTGTTTTA
TATGAGTTTATCAAAAGTGGGATAAAGCACTACAAGACATTGATTCTTAAATTTGAAGAT
ATTTTCAATCTTGATATACGCTACATCATTGACTTTAGTATCATCGCTAATGGTGCTGAT
CCTTTTGAGAAACGCAGTGAAAAAGAAATTTATACAGTGAATGAGACGAATCATGCAATT
GAGACTATACATAACTTTTTAATCAGTCTCGGTGACCTTCATCGTTATTGCATTGAATTT
AAATTTGCTGAAAGAGAAAAATTTTTAGCATGTGGCAATAAACAACTTGCTGCTAGCTAC
TACATTGAGGCGTTCAAGTTAAATCCAAAAGTTGGAATGCCACATAATCAACTTGGAACA
TTGTTGTCTGGTGAAAATTATGAGATTGATTCAATTTTTCACTATCTTTATTCACTTTGT
TCACCTATTCCCGTTGAATTGAGTGAAGCAAATGTCAGCAAAATTTTTCAACAAAATAAC
GAAATGCTTGTCACTATAGAGCCTTCTTGCGATGGATTTAACATTCGAGACTTTATGATG
CAAGTTATTCTTCTCATTGACATTTTTTTCTACGATAAAGAAATTGTTGACTTTAATTCG
ATCTGCTTTAGTGTTCTTTTGAATTTTAAAGATTATTTAATCAAATGCAATCGCAACTCA
CAATCTGATGTTACTTTTCAACTTACATCAATCTTTATGCTTTGCTTATTAAAGCTCAAA
CGAAATAATTCTCCAAAGGTTCAGTGCTTGAATGCCTTTCTTGTAGCATTTTGTGCAAAA
ATTGTTGATATTGTCATTGAGAAAATTGACGACTATATAGCCGAACACAAGAATGAAAAT
TTAGAATTTGTTGAAGAATACAATAGAAAGTACTATGAATTTGATAAACAAATCAAAAGA
GCACGTGACATTAATCGTAATCAAAAAAGTAAACAATTTGGAGAATCTTTGAAAGATTCG
GGAATAGAAAAAAATGGAAGCAGTAACAGTCAAAAAGATGGTTCAGGAAGTAATCGTATG
TCTAATGAAAGTAAAGTTACTATGTCTCAATCGTCGGGAAAGTCTCAACCAGGCGATATC
AAAATTGTAAAAAGACCGCAACCACAGCAAAGTAATGCTAATAATAATCATCGTCGTCGA
AGAAAACGTAGAGGTTTCACTGAAAGTACTAGCAGTGATGAGTCCGAAACAGAATCATTA
TTTAGTGAAGATAACAGCGATGTTGAGTCAATGAATAGTGATTTCGATTCATACGATGAA
GATGATTTTCATGTTAAAATGCGATTCTCTTCGGACGAAGATTCTGAAGAAGATGATGAT
GACGATGATATTTTAATTGAAAGTGAAGAAATTGTTTATAAGAAAAATGAAGAAACTCCA
AATCAATTGACTTTTCATGAAGAGAATAGCGATGACATCATTGTTGAAGAAGAGAAAATT
GTCTTTCAAGAAGAACAACCGGATGAGGAAATTGCTAAAATGTTAAAAATGAAATATAAA
AAGAAATATACTAAAGTTGATCCAAACTTGATTTTGGAATTTAGTAAAATTCATGAAGGA
TGGATGAAAAGTTTGAAGATTTTGTTTGATTGGTTGCATTTGGATAATGAAACCATCGAA
AGTTGTTACCGTAGCAATCCAGAATTTATTGGAAAAATCATTCGACTTATGAATTTCATT
AACATTGACATTTTTACTCGTAAAATTTATTTTGATCGCTCAATGATCAAGTTTAAAAAT
GTTCGTGAAGATTTACGTTACATTTTTGACAATCGTCACCAAATTGCAACAACTGAGGAC
ATAATTTTCAAGAAAAATGTAATATTTGAAGAACTTCAACAAACAATTGATTGGAATTTG
AATTATAAATTGCAAATAACACCAGAAGAGGATGTCATATTGAGAATTTTTAAAATGATT
GATTTTGGTTTTCATTTGATCAAGATTAAAAAGTTTAACTACAATTTTTGTGCTCGTTCG
AGAGTTTTTATTGAAAAGACCAATCGTCGCAGATCAAGAAAAACTAGCGATGATTCTCGT
AGAAAATTCAAAAATGAAGAGCGTGGCAATCGACGTGAACGTAAAAGAAATCGTCGTAGG
AAGAGACGTGAAGAAAGAAAGTTGAGAAACTCTGAAAGCGATCGTTTTGAACGACTTTCT
ATTAAAACTCATTCACAAGGAAGTCAAGAAATTGAAGAATTTCCTTCAATTGAAAAATCA
AATCAATGCAGTGTTCGTAAAGGATATTTGTCAAATAAAATTGCTGAAAGAGAAAAATCT
GAAGCAGAAAAGAAAGAGATGATGGGAAAACTTGGAAAATTATGGTTGAAGAATGAAGTT
CAAACTTTGGAGTCACGTTCAAAACCAGTCAACACCAATATGACACCATTTTTGATGCTC
GATACTAATGCACTCACTGACTATTTGTATGTCGTAAAAGCCTTGGTCAAAACTAAAAAA
TTCATTGTATTGATTCCCAAAGCAGTTTTACAAGATATTGATGGATTAAAGAAAAATAAG
GAAAGTGCTCGTAATGCAATCAAATGGCTCGAAACAGAATTTCAAAAAGGAAATCGTTTT
CTCAGAACTCAACGTGACTCAGAAATTTTACAAATGCCATACTTGAAAGTTCCATCAAAA
TTGGAACGTGAGGATGCAGTTTTCATGAACATCGTTCCATTTGCAAATTTTATTGTATCA
AATAACACGAGCGATTGTGGATCAGATTTGCCAATTTTGACATTGCTAACAGGCGAAAAT
TTGGATACTAAAAAATCATCTACCACAAGCAACATCAATCAGATTGGAATCTTACAGTCG
ATTCCGGTCAAATATGATCAAATTTATCGTTTCTTTTCAAAATATAAAAAGAAGTGA

>g5201.t1 Gene=g5201 Length=1058
MENSELKAKTKNVYQIIKALDEHKQTSKTISSLFSDIGVEVLRKKLVILIESILLEDFET
IGKKTRDILWRKMYYDPISTSKKLWKKSERELTDSEATVLYEFIKSGIKHYKTLILKFED
IFNLDIRYIIDFSIIANGADPFEKRSEKEIYTVNETNHAIETIHNFLISLGDLHRYCIEF
KFAEREKFLACGNKQLAASYYIEAFKLNPKVGMPHNQLGTLLSGENYEIDSIFHYLYSLC
SPIPVELSEANVSKIFQQNNEMLVTIEPSCDGFNIRDFMMQVILLIDIFFYDKEIVDFNS
ICFSVLLNFKDYLIKCNRNSQSDVTFQLTSIFMLCLLKLKRNNSPKVQCLNAFLVAFCAK
IVDIVIEKIDDYIAEHKNENLEFVEEYNRKYYEFDKQIKRARDINRNQKSKQFGESLKDS
GIEKNGSSNSQKDGSGSNRMSNESKVTMSQSSGKSQPGDIKIVKRPQPQQSNANNNHRRR
RKRRGFTESTSSDESETESLFSEDNSDVESMNSDFDSYDEDDFHVKMRFSSDEDSEEDDD
DDDILIESEEIVYKKNEETPNQLTFHEENSDDIIVEEEKIVFQEEQPDEEIAKMLKMKYK
KKYTKVDPNLILEFSKIHEGWMKSLKILFDWLHLDNETIESCYRSNPEFIGKIIRLMNFI
NIDIFTRKIYFDRSMIKFKNVREDLRYIFDNRHQIATTEDIIFKKNVIFEELQQTIDWNL
NYKLQITPEEDVILRIFKMIDFGFHLIKIKKFNYNFCARSRVFIEKTNRRRSRKTSDDSR
RKFKNEERGNRRERKRNRRRKRREERKLRNSESDRFERLSIKTHSQGSQEIEEFPSIEKS
NQCSVRKGYLSNKIAEREKSEAEKKEMMGKLGKLWLKNEVQTLESRSKPVNTNMTPFLML
DTNALTDYLYVVKALVKTKKFIVLIPKAVLQDIDGLKKNKESARNAIKWLETEFQKGNRF
LRTQRDSEILQMPYLKVPSKLEREDAVFMNIVPFANFIVSNNTSDCGSDLPILTLLTGEN
LDTKKSSTTSNINQIGILQSIPVKYDQIYRFFSKYKKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g5201.t1 CDD cd09884 PIN_Smg5-like 896 1056 1.86813E-52
9 g5201.t1 Coils Coil Coil 794 814 -
8 g5201.t1 Coils Coil Coil 933 953 -
10 g5201.t1 Coils Coil Coil 1056 1058 -
7 g5201.t1 Gene3D G3DSA:3.40.50.1010 - 894 1058 7.3E-43
14 g5201.t1 MobiDBLite mobidb-lite consensus disorder prediction 403 519 -
19 g5201.t1 MobiDBLite mobidb-lite consensus disorder prediction 403 418 -
18 g5201.t1 MobiDBLite mobidb-lite consensus disorder prediction 419 457 -
17 g5201.t1 MobiDBLite mobidb-lite consensus disorder prediction 497 516 -
15 g5201.t1 MobiDBLite mobidb-lite consensus disorder prediction 768 834 -
16 g5201.t1 MobiDBLite mobidb-lite consensus disorder prediction 768 792 -
13 g5201.t1 MobiDBLite mobidb-lite consensus disorder prediction 806 821 -
4 g5201.t1 PANTHER PTHR15696:SF7 PROTEIN SMG5 15 1024 6.5E-122
5 g5201.t1 PANTHER PTHR15696 SMG-7 SUPPRESSOR WITH MORPHOLOGICAL EFFECT ON GENITALIA PROTEIN 7 15 1024 6.5E-122
2 g5201.t1 Pfam PF10374 Telomerase activating protein Est1 64 180 1.3E-16
3 g5201.t1 Pfam PF10373 Est1 DNA/RNA binding domain 197 383 1.7E-23
1 g5201.t1 Pfam PF13638 PIN domain 899 971 1.4E-6
12 g5201.t1 SMART SM00670 PIN_9 896 1007 0.0016
6 g5201.t1 SUPERFAMILY SSF48452 TPR-like 11 765 6.07E-52

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5201/g5201.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5201.t1.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005515 protein 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