General information for g6297.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Structural maintenance of chromosomes protein 4.
Parent gene
- The parent gene g6297 is located on chr_2: 16023677..16025649 (+ 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 | g6297 | g6297.t1 | isoform | g6297.t1 | 16021289 | 16025649 |
| chr_2 | g6297 | g6297.t1 | exon | g6297.t1.exon1 | 16021289 | 16021400 |
| chr_2 | g6297 | g6297.t1 | cds | g6297.t1.CDS1 | 16021289 | 16021400 |
| chr_2 | g6297 | g6297.t1 | exon | g6297.t1.exon2 | 16021531 | 16021682 |
| chr_2 | g6297 | g6297.t1 | cds | g6297.t1.CDS2 | 16021531 | 16021682 |
| chr_2 | g6297 | g6297.t1 | exon | g6297.t1.exon3 | 16021738 | 16025157 |
| chr_2 | g6297 | g6297.t1 | cds | g6297.t1.CDS3 | 16021738 | 16025157 |
| chr_2 | g6297 | g6297.t1 | exon | g6297.t1.exon4 | 16025341 | 16025649 |
| chr_2 | g6297 | g6297.t1 | cds | g6297.t1.CDS4 | 16025341 | 16025649 |
| chr_2 | g6297 | g6297.t1 | TSS | g6297.t1 | NA | NA |
| chr_2 | g6297 | g6297.t1 | TTS | g6297.t1 | NA | NA |
Sequences
>g6297.t1 Gene=g6297 Length=3993
ATGTCTAATAAAAATTCCAGGAAAAAATCACTTCCTGAACAGCAGCAACAGAAAATTGTT
GAAGATGAAGCTCCAATTGATGAAGATATGGATATTTCAGAAGATGAAGAAGGAGGAACT
AGAGTTGGTGGTATTTATATTCCTCCGCCAGTTAAACCATATTGTTCGACAGAAAGCAAA
GGACCACGTCTGGTTATTACTCATATTGAAAATACTAATTTTAAAAGTTATGCAAACACA
GTTAGTGTAGGACCATTTCATCATCGATTCTCTTCTGTAATTGGTCCAAATGGAAGTGGT
AAAAGTAATGTCATTGATTCAATGTTATTTGTTTTTGGCTATCGAGCTCAACAACTTCGA
TCAAAGAAAATGTCTGTTCTTATTCACAATTCTTCGAAATATTCAAACGTTAATAGCTGC
AAAGTAGCAGTCCATTTCAAACAAATTCTTGATAAAGAAGATGGCACATTTGAATTCATT
CCAAATAGTGAAATTGTTATTGCAAGAGTCGCTCATAAAAACAATACTTCATATTACACA
CTCAATGGACGCGAAGTGAAATTTAAAGAAGTAGCAAAAGTTCTTGAAGCACATGGAATT
GACTTACTTCATAATCGTTTCTTAATTTTGCAAGGAGAAGTTGAATCTATTGCATTGATG
AAAGCAAAAGCACAGGCACCAAATGAGACAGGTTTGCTTGAATATCTTGAAGATATCATT
GGAACTGAGCGATACAAAAAACCACTTACACTTATTAATGAACGATTGGAAAAACTTAAT
GAAGAGAGAACTGAAAAGCATAATCGATGTCGTCTAGCAGAACGTGAAATGAAAGATTTA
GAGTTACCAATGACTCAAGCTGTCGAATATTTGAAAATCGAAAATAAGCTGTATCAGGCT
CAAAGTTTACATCTACAATTATATGTTTATCATAAGAAGATTCAGATTGCAAAACACGAA
GAGGAAAAAGCTGAAGCAGCACAAAATTTGAAAGATCACGATGATAAATATAATGAAATT
AAGAATCAGCGGATAGAGAAAGAGAAAATTGTTCAAGAAGAGATGAAGAAGCATGAAGAA
TTGCAAAATAAGTTGGAAGATTTTAAAGGAAAAGAGGCAAAAGCACGTGAAAATCATCAG
CGACTTGACGCAACAATGAAAGAAACAAATACTCGTCGTAAAGAACTCAAAAAGCAAAAT
GATGCAGAACAGAAGAAACTCGATCAACTAAGAACTTTGCCTGAACGAAATAAACAAGAA
ATTGAAGAGAGTGAAAAAATTATGGAGCGTCATGCAAAAGAGAAGAATGAATTGGAAACC
AAATTAGAGGAAAATACCAAAAGTTTGAAAAATGATACAAAACCATTGCAAGATGAAAAG
GAACCACTTGAGAAAGAGCTTAGTGTACTAAAATCTTCACTCGATAAATTGAAAGCAGAC
TATACTGAAGCAGAGAAAGAACTTGAGATTATTAAGAAAGATGAAACAACAGAAATTCGC
AAATATGAGTCATTACGAAATTCATTTGAAGATACTAAAAAGCAATTGGAAGAATATCAA
GAAAAAGCTGAAACATTAAAAGTTGAAATTCCACAAATGAAAGAGCAAATTGTCGTTAAA
CAAAATGAAATAAAGAAACTTAATGAAGAAGAGCAAGAAGTAACAGCTGATTTACGTAAA
GTTCGAATGAAATTGGAAGAAAGTCGTGTTAATATGCAAACAGCTCAAAGTAATAACAAA
GTTCTCAATGCTTTAATGAAAGAGAAACAAAAAGGGAACATACCTGGTATTCTTGGTCGT
CTTGGTGATTTAGGTGGAATTGATAAGCAATATGATGTTGCTATTTCAACATGCTGTGGT
AGATTAGATAATATTGTTGTCACAGATGTTAATACTGCTCAAAAGTGCATTCAATTTTTA
AAAGATCACAATGTTGGTCGTGCCTCATTCATTGCCTTAGAGAAAGTTGCTCATTATATG
AATGATTACAGACGTAAACGACAATATCCTCAAAATGTGCCTCGTTTAGTTGATCTCATT
CGTGTTGAAGATGAAAGAGTTTTACCAGCATTTTATTTCTCCTTGCATGAGACATTAGTA
GCAAGAGATATGCAGCAGGCTCGTGAGATTGCATATGGTGCACAGCGTTATCGTGTTGTA
ACACTCAATGGTGAAGTGATCGAACTCGCAGGTACAATGTCGGGTGGTGGTAGGACTAAA
ATCAGTGGTCGAATGGGTCAAAAAGTTCAAACTAAATCGGCTCCATCACGTCATTCAATG
TCTGAACGTGATATACAGCAATTGTCAGAAGCAGCACAAGTGATGCAAGGAAAAATTAAT
GACTTTCAGCATCAACAAGGTATTTTGGAAGAGGAAATTAAAAAATTAAATATTTCCATT
CAACAGAAAGAACAAGAATTGAAGCGACTTTCACTCAATATAAAAAGTTATTCTGAACAA
ATTCCTCGATTGGAAGATCAACTTAACAAACAGAAAAAGAAAGCTGATTCAACAAAATCA
GATGCAGCAAAAGTTGCTGATTTAGAGAAAAAAGTGACAAAATGCAAAACTGAATTTGAG
AAGAAGGATAAAGAAGTTGAAGAAATTCAAAATAAAGTCACTGCCATTAATAGAAAAATT
AAAGAAATTTCTGATAAAAAAATCAAAGAAGTGCAAATGAGTATCAACAAAATAACAACG
CAAATCGATAAACTCAAAACTAATATCAATAAATTAACTGTTGAAATTCGCACAACAGAC
CGGAATATACAAAAATGTGAAGAGCGAATCGAACAGAATAAGAATGAAATAACAGCTGCA
GAAACATCACTAACACGCATGGCTGGTGAACGAACACAATTTCTTGAAGAGAGTGAAGAA
ATGGCAAAACGTATTGAGGAAGCAAAGAAAGAAATAGAAGAAGCAACGAGTGATTCATCG
ACAATTAGAAAAGAAATTACAAAATTACAAAAGGATGAAGCTGATGGTAAAATGAAACGA
CTGGAGCTTGAAGATCAACTTAAAACACTTGAGAAAACATTGAAAGAACAGTCTGCGAAG
ATTCCTGCTTGGGAAAAGAAACAACAAGCACTGAAATTGCATGCAATTCCTAATGAGCAA
ATGCCTGATCCACCATTTAAGATCTATACAGATGATGAATTGAAGCAACGTGATGTCAAT
GACACTCAATATGAAATAACATCGCTGGAAGAAAAGTTAAGAATAAATAAACCTAATTTG
GGTGTTATTGAGGAATACAATAAGAAACGAGAAGCTTATTTAGAGAGAATAAATATACTT
GAAGATGTTACACTTCGCAGAAATGAAATGCGTGAAGCACTTGACAGTGTGAAAAAGAAA
CGTTTCCATGAATTCACAGAAGGATTTCAAATCATCAGTCGAAAACTGAAAGAAATGTAT
CAAATGATTACGCTTGGTGGTGATGCTGAACTTGAATTAGTCGATTCAATGGATCCGTTT
AGTGAGGGAATTGTCTTCTCTGTTCGTCCACCGAAAAAGAGCTGGAAAGTGATTACTAAT
TTATCGGGAGGTGAAAAAACACTTTCATCACTTGCTCTTGTTTTTGCATTGCATTATTAC
AAACCAAGTCCTCTCTACTTTATGGATGAAATTGATGCCGCTCTCGACTTCAAAAACGTT
TCAATCGTTGCTAATTATATCAATGAACGTACAAAAAATGCTCAATTCATTATTATCTCA
TTACGATCGAACATGTTTGAATTAGCTGATTATCTAGTAGGAATATATAAAGTCGAGGAT
TGCACACATTCAGTTACTATACAAAACTATGATAAACAGCGTGTAATGGGTCTCGGTGAG
AAAGAGAATGAAAAAGAAAATCAAGATGAAAATAAATATGAAGAATCAACTATTAACTCA
CAATCATCTAAATCTATTATGAAAAATGACACTCTTATATCACAAGTAATAGATCAAGAA
AATGAAATTTCCCAAAATCAATCAGTACAATAA
>g6297.t1 Gene=g6297 Length=1330
MSNKNSRKKSLPEQQQQKIVEDEAPIDEDMDISEDEEGGTRVGGIYIPPPVKPYCSTESK
GPRLVITHIENTNFKSYANTVSVGPFHHRFSSVIGPNGSGKSNVIDSMLFVFGYRAQQLR
SKKMSVLIHNSSKYSNVNSCKVAVHFKQILDKEDGTFEFIPNSEIVIARVAHKNNTSYYT
LNGREVKFKEVAKVLEAHGIDLLHNRFLILQGEVESIALMKAKAQAPNETGLLEYLEDII
GTERYKKPLTLINERLEKLNEERTEKHNRCRLAEREMKDLELPMTQAVEYLKIENKLYQA
QSLHLQLYVYHKKIQIAKHEEEKAEAAQNLKDHDDKYNEIKNQRIEKEKIVQEEMKKHEE
LQNKLEDFKGKEAKARENHQRLDATMKETNTRRKELKKQNDAEQKKLDQLRTLPERNKQE
IEESEKIMERHAKEKNELETKLEENTKSLKNDTKPLQDEKEPLEKELSVLKSSLDKLKAD
YTEAEKELEIIKKDETTEIRKYESLRNSFEDTKKQLEEYQEKAETLKVEIPQMKEQIVVK
QNEIKKLNEEEQEVTADLRKVRMKLEESRVNMQTAQSNNKVLNALMKEKQKGNIPGILGR
LGDLGGIDKQYDVAISTCCGRLDNIVVTDVNTAQKCIQFLKDHNVGRASFIALEKVAHYM
NDYRRKRQYPQNVPRLVDLIRVEDERVLPAFYFSLHETLVARDMQQAREIAYGAQRYRVV
TLNGEVIELAGTMSGGGRTKISGRMGQKVQTKSAPSRHSMSERDIQQLSEAAQVMQGKIN
DFQHQQGILEEEIKKLNISIQQKEQELKRLSLNIKSYSEQIPRLEDQLNKQKKKADSTKS
DAAKVADLEKKVTKCKTEFEKKDKEVEEIQNKVTAINRKIKEISDKKIKEVQMSINKITT
QIDKLKTNINKLTVEIRTTDRNIQKCEERIEQNKNEITAAETSLTRMAGERTQFLEESEE
MAKRIEEAKKEIEEATSDSSTIRKEITKLQKDEADGKMKRLELEDQLKTLEKTLKEQSAK
IPAWEKKQQALKLHAIPNEQMPDPPFKIYTDDELKQRDVNDTQYEITSLEEKLRINKPNL
GVIEEYNKKREAYLERINILEDVTLRRNEMREALDSVKKKRFHEFTEGFQIISRKLKEMY
QMITLGGDAELELVDSMDPFSEGIVFSVRPPKKSWKVITNLSGGEKTLSSLALVFALHYY
KPSPLYFMDEIDAALDFKNVSIVANYINERTKNAQFIIISLRSNMFELADYLVGIYKVED
CTHSVTIQNYDKQRVMGLGEKENEKENQDENKYEESTINSQSSKSIMKNDTLISQVIDQE
NEISQNQSVQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 23 | g6297.t1 | CDD | cd03274 | ABC_SMC4_euk | 1171 | 1265 | 3.28313E-65 |
| 16 | g6297.t1 | Coils | Coil | Coil | 249 | 276 | - |
| 20 | g6297.t1 | Coils | Coil | Coil | 316 | 413 | - |
| 13 | g6297.t1 | Coils | Coil | Coil | 421 | 452 | - |
| 19 | g6297.t1 | Coils | Coil | Coil | 460 | 494 | - |
| 21 | g6297.t1 | Coils | Coil | Coil | 499 | 578 | - |
| 12 | g6297.t1 | Coils | Coil | Coil | 765 | 841 | - |
| 17 | g6297.t1 | Coils | Coil | Coil | 845 | 886 | - |
| 11 | g6297.t1 | Coils | Coil | Coil | 888 | 943 | - |
| 15 | g6297.t1 | Coils | Coil | Coil | 951 | 1027 | - |
| 18 | g6297.t1 | Coils | Coil | Coil | 1083 | 1120 | - |
| 14 | g6297.t1 | Coils | Coil | Coil | 1329 | 1330 | - |
| 8 | g6297.t1 | Gene3D | G3DSA:3.40.50.300 | - | 65 | 250 | 4.2E-40 |
| 9 | g6297.t1 | Gene3D | G3DSA:1.20.1060.20 | - | 576 | 750 | 6.9E-41 |
| 10 | g6297.t1 | Gene3D | G3DSA:3.30.70.1620 | - | 654 | 739 | 6.9E-41 |
| 7 | g6297.t1 | Gene3D | G3DSA:3.40.50.300 | - | 1117 | 1290 | 3.8E-48 |
| 29 | g6297.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 41 | - |
| 27 | g6297.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 370 | 462 | - |
| 26 | g6297.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 740 | 761 | - |
| 25 | g6297.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 744 | 761 | - |
| 28 | g6297.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1278 | 1293 | - |
| 30 | g6297.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1278 | 1306 | - |
| 3 | g6297.t1 | PANTHER | PTHR43939 | - | 60 | 1257 | 7.3E-233 |
| 4 | g6297.t1 | PANTHER | PTHR43939:SF1 | STRUCTURAL MAINTENANCE OF CHROMOSOMES PROTEIN 4 | 60 | 1257 | 7.3E-233 |
| 22 | g6297.t1 | PIRSF | PIRSF005719 | SMC | 63 | 1276 | 2.9E-293 |
| 2 | g6297.t1 | Pfam | PF02463 | RecF/RecN/SMC N terminal domain | 66 | 1262 | 3.1E-61 |
| 1 | g6297.t1 | Pfam | PF06470 | SMC proteins Flexible Hinge Domain | 595 | 711 | 4.7E-24 |
| 24 | g6297.t1 | SMART | SM00968 | SMC_hinge_2 | 595 | 711 | 1.2E-33 |
| 5 | g6297.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 64 | 1255 | 8.99E-40 |
| 6 | g6297.t1 | SUPERFAMILY | SSF75553 | Smc hinge domain | 557 | 752 | 1.83E-49 |
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:0005524 | ATP binding | MF |
| GO:0005515 | protein binding | MF |
| GO:0051276 | chromosome organization | BP |
| GO:0005694 | chromosome | CC |
| GO:0016887 | ATP hydrolysis activity | MF |
KEGG
Orthology
- This transcript has been annotated with K06675 (structural maintenance of chromosome 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.
