General information for g5579.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Thrombospondin type-1 domain-containing protein 4.
Parent gene
- The parent gene g5579 is located on chr_2: 10384132..10393036 (+ 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_2 | g5579 | g5579.t1 | isoform | g5579.t1 | 10384132 | 10393036 |
| chr_2 | g5579 | g5579.t1 | exon | g5579.t1.exon1 | 10384132 | 10384151 |
| chr_2 | g5579 | g5579.t1 | cds | g5579.t1.CDS1 | 10384132 | 10384151 |
| chr_2 | g5579 | g5579.t1 | exon | g5579.t1.exon2 | 10384711 | 10384801 |
| chr_2 | g5579 | g5579.t1 | cds | g5579.t1.CDS2 | 10384711 | 10384801 |
| chr_2 | g5579 | g5579.t1 | exon | g5579.t1.exon3 | 10385378 | 10385981 |
| chr_2 | g5579 | g5579.t1 | cds | g5579.t1.CDS3 | 10385378 | 10385981 |
| chr_2 | g5579 | g5579.t1 | exon | g5579.t1.exon4 | 10386045 | 10386087 |
| chr_2 | g5579 | g5579.t1 | cds | g5579.t1.CDS4 | 10386045 | 10386087 |
| chr_2 | g5579 | g5579.t1 | exon | g5579.t1.exon5 | 10387710 | 10387800 |
| chr_2 | g5579 | g5579.t1 | cds | g5579.t1.CDS5 | 10387710 | 10387800 |
| chr_2 | g5579 | g5579.t1 | exon | g5579.t1.exon6 | 10387862 | 10388116 |
| chr_2 | g5579 | g5579.t1 | cds | g5579.t1.CDS6 | 10387862 | 10388116 |
| chr_2 | g5579 | g5579.t1 | exon | g5579.t1.exon7 | 10390533 | 10390734 |
| chr_2 | g5579 | g5579.t1 | cds | g5579.t1.CDS7 | 10390533 | 10390734 |
| chr_2 | g5579 | g5579.t1 | exon | g5579.t1.exon8 | 10390863 | 10391068 |
| chr_2 | g5579 | g5579.t1 | cds | g5579.t1.CDS8 | 10390863 | 10391068 |
| chr_2 | g5579 | g5579.t1 | exon | g5579.t1.exon9 | 10391313 | 10392043 |
| chr_2 | g5579 | g5579.t1 | cds | g5579.t1.CDS9 | 10391313 | 10392043 |
| chr_2 | g5579 | g5579.t1 | exon | g5579.t1.exon10 | 10392106 | 10392189 |
| chr_2 | g5579 | g5579.t1 | cds | g5579.t1.CDS10 | 10392106 | 10392189 |
| chr_2 | g5579 | g5579.t1 | exon | g5579.t1.exon11 | 10392245 | 10392336 |
| chr_2 | g5579 | g5579.t1 | cds | g5579.t1.CDS11 | 10392245 | 10392336 |
| chr_2 | g5579 | g5579.t1 | exon | g5579.t1.exon12 | 10392395 | 10392585 |
| chr_2 | g5579 | g5579.t1 | cds | g5579.t1.CDS12 | 10392395 | 10392585 |
| chr_2 | g5579 | g5579.t1 | exon | g5579.t1.exon13 | 10392646 | 10392796 |
| chr_2 | g5579 | g5579.t1 | cds | g5579.t1.CDS13 | 10392646 | 10392796 |
| chr_2 | g5579 | g5579.t1 | exon | g5579.t1.exon14 | 10392861 | 10393036 |
| chr_2 | g5579 | g5579.t1 | cds | g5579.t1.CDS14 | 10392861 | 10393036 |
| chr_2 | g5579 | g5579.t1 | TTS | g5579.t1 | 10393652 | 10393652 |
| chr_2 | g5579 | g5579.t1 | TSS | g5579.t1 | NA | NA |
Sequences
>g5579.t1 Gene=g5579 Length=2937
ATGGAATATTCAAATTTAAGAAAAATTATTGTCGGAATTATAATTTATGTTGCTATAATG
TGTAACGATGTTAGTATAAATGCAGAAGAAAGTACAAAAGACAGGATTCAGAAACATAGA
GCATGGCTCAATCAGAGAACTAAAGATAGACAATTGGTTGGCTATGTTGAAACTAATGAT
CCATTTCAAAAGATTAAGTACTTTAAAAAGCTGATAAAATTCAAAAACAAAAGCGATCAT
GAAAATATAATTTCATTTGTGCCACATGAGAACAATGTAAATGAATTGACAACCATTGCT
ATTGATACAGGAAATAAGTTCGCGTATGATACTGTTAATAATAATGAGGCAAACAAATAT
GATTTGGACATCACAAACGACGTTTTGCCATCATCAGCAGAACGTAACATAAATAGCAAC
ATTATCACGGACGTCGATAAACAAATTATTTTCGAGACGACTACGACGAGCAAAGACATT
AGAAACAATGAGATCGAACGAGGCAAAATTGATGACTTCGACAACTCCAACATGCATAAT
TCGATTGAAGCGACAACATCATCAATTGATTCCAAGAACTCTTTGAATGCTACTTCAAAT
GATGTTGAAATAGAACGATTTTTATCGGAGCACATAAAGTACAAGTCGAGTGATGTGACA
ATTAAAAAATCTTGGGGAAAATGGGGTCCATGGACACAATGCAGTAGAACGTGTGGTGAA
GGAGTTACATCACAATCAAGAGAGTGCATTTTGAGGCACTACAAAAATGGAAAACGAATT
AATGTAACAACAATAGCCCTTAATGAATGTATTGGATTCTTTCGTCGTTTTCGTATTTGT
AATGAGAAGAAATGTCCTGAAGAAACGGATTTACGAGCTGAACAGTGCAGTTCATTTAAT
AATCAAAGTTTTCGCGGTATTCAATACACATGGGAGCCTTACATTAAAGAAGATTCTGAA
TGTGAGCTCAATTGTAAGCCAATTGATCAAAAGTATTTTGCAAAACTCAAAGACTTTGTG
ATTGATGGAACACCATGTAAAAAAGTCAAAAATAATGCGAATATTTCATTTGATAAGGCA
GTTTGTGTAGAAGGAAAATGTAAGGCTGTCCTTAAAAACGGTATGATATCAGGATCTGGT
TTCATGAACAGTGGAAATGTGCGTTGTGGTTCTTCAATTTGTCGACCTTTATCCGGAACT
TTTCTGAAAAATCCACTGCCAAATGGATATGTACATGTTACAACAATTCCCGCCACGGCA
TCAAATATAACAATCACAGAACTACGGGATAGCATCAATCTTTTAGCTCTGAAATCTATA
GAATCTGAATTTATCATAAACGGAAATTATACTGCAACTCCGAGTGGAAAATATTATGCT
GCCGGTGCTGAATTTAAATATCATCGAATTGATAGTAGTAGCAGTGATTCAAAAGAGAGG
GATGATAAAAATGATGAAATAACTGAATGGATAACTTGTGCTGGTCCACTTCATAACCCA
ATTCACATTATGGTTTTATCACAGCAACAAAATCCAGGAATCAAATATGAATATTTGATA
CCAATAAATTTTGCTTCATCATCAGAAGAGAGTGGATCAGAAGTTGATAATTCGGCAGAA
GAAAATTTATCTATTAATAGACGTCTAAAAGCAGCTAATTATCAAACTAATTCAACAGCG
CCAGTAGGTCGTAAAAAAAGAAAATTTGCATGGCGTGTCGTTGGCTTTCAAGCATGTTCA
AAGAAATGCGGTGGTGGAATTCAACAACCAATAATTCGATGTGTTAGAGGTGAAGGTACA
AAAGCATATTCTCCAAAGAGATGTGTACATTTGCAAAAACCTTCTGTAAATGAAAATCTC
ATGAAATGCAACACTCAACCTTGCCCTGCATTTTGGAAAATATCTGAATGGTCAAATTGT
CACTGTGGAGAATTAAATGAAAAACAAGAAAAAACTCGTGACATCAAATGTGTACAAGAA
TTGATATCAGGCGTAGTAATTCAAGTAAACTCAGGAGCATGCAATCAAGATCAACCTTCG
AGTACTGCACCATGTGAATGTGTGAAACCATTAAAAGTTCACAAGATTGAAGATTTAAAA
CCATTGTCAAATCGAAATCCCTCAAAATTACAATCACAATCAAACACACAGAGTGATCAA
AAAATCAATAATATTCATCATGGAAAAAATAAAACAAAGCCACCAAAATCAAAGAAAATT
GGAGTATGGTTGACATCAGAATGGAGTGAAACATGTTCAAATGAATGTGGCGTTGGTCAA
CAATTCAGAACTATATTTTGCGATAGAAGTGTATCACCTAATGATAGGACACATATAGAG
AGATGTGATTTGCGACAAACACCTAATACTTATCGTGAATGTACAAATGAAAGTAAATGT
CATGGAGATTGGTTTATAGGTCCATGGAGCACATGTCAAGGAGATTGTTTTAATGCATCA
AGATGGAGAACAGTAGTATGTATAAAAGATGATGGATTTGCTGAAGAAAGTGAATGTGAT
TTAAAGAGTAAACCAGCAACTTTTGAAGATTGCACACCAGATGAGATGAAAGATTGCAAA
CCAAAATGGCATTTCTCTGAATGGACAGAGTGCTCAAAACCATGTGGTAATGGAATTCAA
AAGAGAACAGTCAAATGCTTGGAAATTGAGAAAAATGAAAAAGTTCTTAAAGAGTCAAAA
AATTGCAAATATTCAGAACGACCGAATGCAATGAAATATTGCAATACTCAAGATTGTTCT
GAAACGACAACAACTTACGATCCGCGTGTGGATCTTCTTCAAAATGATGACCCTACATGT
ACTGATGAATTTCCTAATTGCGAGATAATTTTAAAAGCTTCACTTTGTGGTTATCATTAT
TATAATGAAAATTGTTGTAAATCATGTCGCTCATTCTCAAATGAGCTCTATCTTTAA
>g5579.t1 Gene=g5579 Length=978
MEYSNLRKIIVGIIIYVAIMCNDVSINAEESTKDRIQKHRAWLNQRTKDRQLVGYVETND
PFQKIKYFKKLIKFKNKSDHENIISFVPHENNVNELTTIAIDTGNKFAYDTVNNNEANKY
DLDITNDVLPSSAERNINSNIITDVDKQIIFETTTTSKDIRNNEIERGKIDDFDNSNMHN
SIEATTSSIDSKNSLNATSNDVEIERFLSEHIKYKSSDVTIKKSWGKWGPWTQCSRTCGE
GVTSQSRECILRHYKNGKRINVTTIALNECIGFFRRFRICNEKKCPEETDLRAEQCSSFN
NQSFRGIQYTWEPYIKEDSECELNCKPIDQKYFAKLKDFVIDGTPCKKVKNNANISFDKA
VCVEGKCKAVLKNGMISGSGFMNSGNVRCGSSICRPLSGTFLKNPLPNGYVHVTTIPATA
SNITITELRDSINLLALKSIESEFIINGNYTATPSGKYYAAGAEFKYHRIDSSSSDSKER
DDKNDEITEWITCAGPLHNPIHIMVLSQQQNPGIKYEYLIPINFASSSEESGSEVDNSAE
ENLSINRRLKAANYQTNSTAPVGRKKRKFAWRVVGFQACSKKCGGGIQQPIIRCVRGEGT
KAYSPKRCVHLQKPSVNENLMKCNTQPCPAFWKISEWSNCHCGELNEKQEKTRDIKCVQE
LISGVVIQVNSGACNQDQPSSTAPCECVKPLKVHKIEDLKPLSNRNPSKLQSQSNTQSDQ
KINNIHHGKNKTKPPKSKKIGVWLTSEWSETCSNECGVGQQFRTIFCDRSVSPNDRTHIE
RCDLRQTPNTYRECTNESKCHGDWFIGPWSTCQGDCFNASRWRTVVCIKDDGFAEESECD
LKSKPATFEDCTPDEMKDCKPKWHFSEWTECSKPCGNGIQKRTVKCLEIEKNEKVLKESK
NCKYSERPNAMKYCNTQDCSETTTTYDPRVDLLQNDDPTCTDEFPNCEIILKASLCGYHY
YNENCCKSCRSFSNELYL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 18 | g5579.t1 | Gene3D | G3DSA:2.20.100.10 | - | 221 | 285 | 3.3E-10 |
| 15 | g5579.t1 | Gene3D | G3DSA:2.60.120.830 | - | 388 | 532 | 5.5E-15 |
| 16 | g5579.t1 | Gene3D | G3DSA:2.20.100.10 | - | 570 | 629 | 9.4E-7 |
| 19 | g5579.t1 | Gene3D | G3DSA:2.20.100.10 | - | 740 | 800 | 3.6E-5 |
| 17 | g5579.t1 | Gene3D | G3DSA:2.20.100.10 | - | 857 | 919 | 3.7E-10 |
| 26 | g5579.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 698 | 737 | - |
| 25 | g5579.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 704 | 723 | - |
| 9 | g5579.t1 | PANTHER | PTHR13723 | ADAMTS A DISINTEGRIN AND METALLOPROTEASE WITH THROMBOSPONDIN MOTIFS PROTEASE | 213 | 794 | 2.8E-93 |
| 8 | g5579.t1 | PANTHER | PTHR13723 | ADAMTS A DISINTEGRIN AND METALLOPROTEASE WITH THROMBOSPONDIN MOTIFS PROTEASE | 708 | 940 | 2.8E-93 |
| 10 | g5579.t1 | PRINTS | PR01857 | ADAM-TS family signature | 231 | 249 | 4.6E-5 |
| 11 | g5579.t1 | PRINTS | PR01857 | ADAM-TS family signature | 356 | 375 | 4.6E-5 |
| 6 | g5579.t1 | Pfam | PF00090 | Thrombospondin type 1 domain | 227 | 285 | 2.3E-6 |
| 7 | g5579.t1 | Pfam | PF05986 | ADAM-TS Spacer 1 | 397 | 521 | 1.4E-29 |
| 3 | g5579.t1 | Pfam | PF19030 | Thrombospondin type 1 domain | 571 | 628 | 7.5E-8 |
| 1 | g5579.t1 | Pfam | PF19030 | Thrombospondin type 1 domain | 743 | 800 | 1.1E-7 |
| 4 | g5579.t1 | Pfam | PF19030 | Thrombospondin type 1 domain | 804 | 852 | 4.3E-7 |
| 2 | g5579.t1 | Pfam | PF19030 | Thrombospondin type 1 domain | 863 | 919 | 2.0E-13 |
| 5 | g5579.t1 | Pfam | PF08686 | PLAC (protease and lacunin) domain | 940 | 970 | 3.6E-10 |
| 28 | g5579.t1 | ProSiteProfiles | PS50092 | Thrombospondin type-1 (TSP1) repeat profile. | 222 | 286 | 10.701 |
| 30 | g5579.t1 | ProSiteProfiles | PS50092 | Thrombospondin type-1 (TSP1) repeat profile. | 739 | 801 | 9.179 |
| 29 | g5579.t1 | ProSiteProfiles | PS50092 | Thrombospondin type-1 (TSP1) repeat profile. | 859 | 920 | 11.105 |
| 31 | g5579.t1 | ProSiteProfiles | PS50900 | PLAC domain profile. | 936 | 973 | 11.002 |
| 27 | g5579.t1 | ProSiteProfiles | PS51670 | ShKT domain profile. | 940 | 973 | 7.881 |
| 23 | g5579.t1 | SMART | SM00209 | TSP1_2 | 225 | 286 | 2.5E-9 |
| 24 | g5579.t1 | SMART | SM00209 | TSP1_2 | 571 | 629 | 2.2 |
| 22 | g5579.t1 | SMART | SM00209 | TSP1_2 | 742 | 801 | 0.029 |
| 21 | g5579.t1 | SMART | SM00209 | TSP1_2 | 803 | 860 | 0.58 |
| 20 | g5579.t1 | SMART | SM00209 | TSP1_2 | 862 | 920 | 5.9E-7 |
| 14 | g5579.t1 | SUPERFAMILY | SSF82895 | TSP-1 type 1 repeat | 223 | 285 | 2.18E-8 |
| 13 | g5579.t1 | SUPERFAMILY | SSF82895 | TSP-1 type 1 repeat | 796 | 853 | 1.09E-5 |
| 12 | g5579.t1 | SUPERFAMILY | SSF82895 | TSP-1 type 1 repeat | 862 | 919 | 3.27E-10 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5579/g5579.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5579.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K23377 (thrombospondin type-1 domain-containing protein 4)
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. There were no conditions that were differentially expressed