General information for g6007.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Embryonic polarity protein dorsal.
Parent gene
- The parent gene g6007 is located on chr_2: 13471516..13483139 (- 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 | g6007 | g6007.t1 | isoform | g6007.t1 | 13468514 | 13480170 |
| chr_2 | g6007 | g6007.t1 | exon | g6007.t1.exon1 | 13468514 | 13470400 |
| chr_2 | g6007 | g6007.t1 | cds | g6007.t1.CDS1 | 13468514 | 13470400 |
| chr_2 | g6007 | g6007.t1 | exon | g6007.t1.exon2 | 13470467 | 13470511 |
| chr_2 | g6007 | g6007.t1 | cds | g6007.t1.CDS2 | 13470467 | 13470511 |
| chr_2 | g6007 | g6007.t1 | exon | g6007.t1.exon3 | 13470576 | 13470808 |
| chr_2 | g6007 | g6007.t1 | cds | g6007.t1.CDS3 | 13470576 | 13470808 |
| chr_2 | g6007 | g6007.t1 | exon | g6007.t1.exon4 | 13470928 | 13471106 |
| chr_2 | g6007 | g6007.t1 | cds | g6007.t1.CDS4 | 13470928 | 13471106 |
| chr_2 | g6007 | g6007.t1 | exon | g6007.t1.exon5 | 13471196 | 13471523 |
| chr_2 | g6007 | g6007.t1 | cds | g6007.t1.CDS5 | 13471196 | 13471523 |
| chr_2 | g6007 | g6007.t1 | exon | g6007.t1.exon6 | 13473778 | 13473822 |
| chr_2 | g6007 | g6007.t1 | cds | g6007.t1.CDS6 | 13473778 | 13473822 |
| chr_2 | g6007 | g6007.t1 | exon | g6007.t1.exon7 | 13480128 | 13480170 |
| chr_2 | g6007 | g6007.t1 | cds | g6007.t1.CDS7 | 13480128 | 13480170 |
| chr_2 | g6007 | g6007.t1 | TSS | g6007.t1 | NA | NA |
| chr_2 | g6007 | g6007.t1 | TTS | g6007.t1 | NA | NA |
Sequences
>g6007.t1 Gene=g6007 Length=2760
ATGGACGATCATAATTTTGGTGTCAACCCAAATGAAATCCAAGCAGTTGACGAGGTTTCA
GACTTATCGATTCACATAAGTGATGTCATTGCAGTAATTGAAAGTACAGATCCAATGTTT
CCAATTGATTTAAATTCAATGGCACCTGTAGTAAACGGAAATATGCAAACAAATATGGCA
CCACAACAGCAACAACAACAATCACCACAAGAAGCAATACCTTATGTCGCAATATTAGAG
CAACCAGCATCAAAAGCACTTCGTTTTCGCTATGAATGCGAAGGTAGAAGTGCAGGATCA
ATTCCTGGAGCAAATAGCACAGCAGATAATAAAACATACCCAACAATACAGATCAAAAAT
TATGTTGGAAAAGCAGTTGTAGTTGTATCATGCGTTACCAAAGATTTTCCCTACAAACCC
CATCCACATAATTTGGTCGGAAAAGAAGGTTGCAAGAAGGGTGTGTGCACATTGGAAATC
AATTCTGATGACATGAAAATGGTCTTTAGTAATTTGGGCATTCAATGTGTTAAACGTCGC
GATATTGAAGAAGCTTTAAGAATTCGTGAAGAAATTCGTGTTGATCCGTACAGAACTGGT
TACACACATCGCAATCAGCCATCGAGTATTGATTTGAATGCAGTTCGTTTATGCTTTCAA
GTATTTTTGGAAGGTCCACAAAGAGGCAGATTCACACAACCACTGAAACCAGTCGTGTCA
GAACCGATTTTCGATAAAAAGTCAATGTCAGATTTGGTGATAACAAAATTGAGCCATTGT
AATGCTTTCTGCAATGGTGGACAGGAAATAATATTATTATGTGAAAAGGTGGCAAAAGAG
GACATTCAGATTAGATTTTATGAGGAGAGCATGATGCCTGAACAAGAACCATGGGAAGGA
TATGGAGAGTTTCAGCATTCGCAAGTGCACAAACAAGTTGCAATTTCTTTCAGAACACCG
CGTTATAAGTCGATCAACTTGACAGATCCAGTAAAAGTGAAGGTGCAGCTTAGAAGACCG
AGTGATGGTGCCACGAGTGATCCATTGGACTTTGAGATGCTTCCACTTAATGAAGGTAGG
CGAAGTTATTGGAATTTACAACGAGAATTGAAAAAGAGATCAGCTGAAACTGATCTATTT
CAACAATTACTCGACGTTGATAATGAAGAGCAGAAGGTCGATATTGTTAATTTTACAAAC
GTCAATTCACTGCCGTTGCAAAGCAATAATAATGCTATTGAGCAAACTGAGGTTGTTATT
TTGGACACACCGATTGATGATAATGCGAAACCAATTGAAGATGACAAGACAATGCTCTGG
CTTGAAAATGCAGAATTCATAATTGATGGTAATAATAATAATGAAAACAATCAGAATGTT
ATTAATCAATCGGATGATGACAAGACTTTAAGCGATTTGCTGGAACAAGTTGCTGAATTG
GATGTTATTTATCAAGATCATCAAGTACGTAAAGAGATACAAGCAATGCAAGATGAGTTG
AATGATATGGATCAATGTTTACCGCAGGAAGGTGAGCAAATGGAAACAGATTTTGATGAT
GCTGCCACTTATTCGAGCTTACAAAAAGCTTTCAAGCATCCAATTGTGTTCACTGATGCT
CCACCAGTTCCACCAAAACCTGGCCATGTTTTTTCGAATTCATCATTTGAGTTGATTTTA
CCACCTATAGTTATTAATCCAGCAACACCTGATATTTATATGAAGGAAGAAAAATTACCG
CCATTGCCTCCGAAAAGAGCAAAAAAGATTTCAGAATCTGGTGACAAGGAAAATATTAAT
GAACAAATGCAACAACAAAATGTAGAACAACAGCAAGCACAACGAGATGAAAACACTTTA
GTTCGAAATAATTCAACACGTAGTCTTACACCACGACCACCACAACAACCGATTGTTATC
AAATCAGCAGATTTACGACGAAGTCCTTCACATAAATTGCCTCCAAAATCGCCCACAAAA
TCAACAACATCGACTACATCATCACAAACAAATACAAACACATTGCCCAAGCAAAAGAAA
CCGGGTTTCTTTTCAAAAATCTTTTCAAGACGAAAGAGCAAGTCAGATATTGATTCAAGC
ATTGGTGGCGATAGTGCCTCAATAAAGATTGAGAGCGAGATGGAGAATGAAAATGTAGAT
GAATCAATTGATGATGTAGAGAATCAATTTGAGCCCGAAGATCAAAATCGTAGTCCAATG
CGCAGTACAAAGTCATTGAGATCTCCCAAGAAACAAAAATATGGAAAGCCAGTTGGTCGT
AGTGTATCAAGTGTAAGTGGAAAACGTCCACATCTTACGCCAGATATAATTCATATTCCA
CTCAAAGGAGATAGCTCAAATTCATTGCCATTACATCAGAGTGGCAGCGCAACTCATCTT
TCATTGCCAGGAAATGATTTTTATGAGCGAGCATCGACAGCATCGCTTCATCCGATTGAT
AGAAAAACAATGAGTGCATTACAATTGGCAGATGTTCCAATTCAAGATGGTGATATGGAA
TTGGTTGCAATTGCTGATGCACAAAGTCTTCGAAATTTATGTGAAAATGGTGAACATGGA
ATAATTTTAGATCCAAGTGTTGATCTCACCGAAGCAGAGCATTATGCATTATATACAACC
TTAGCACCGCATGCAACGCAAAGTGAATTTGACGAGACCTCGTGTTACTATCAGCCTGTT
GAGGCAGGTCAAATTTTAACACCAGCTGAAGTTGCTCGACGAATGAACGATAATTTTTAA
>g6007.t1 Gene=g6007 Length=919
MDDHNFGVNPNEIQAVDEVSDLSIHISDVIAVIESTDPMFPIDLNSMAPVVNGNMQTNMA
PQQQQQQSPQEAIPYVAILEQPASKALRFRYECEGRSAGSIPGANSTADNKTYPTIQIKN
YVGKAVVVVSCVTKDFPYKPHPHNLVGKEGCKKGVCTLEINSDDMKMVFSNLGIQCVKRR
DIEEALRIREEIRVDPYRTGYTHRNQPSSIDLNAVRLCFQVFLEGPQRGRFTQPLKPVVS
EPIFDKKSMSDLVITKLSHCNAFCNGGQEIILLCEKVAKEDIQIRFYEESMMPEQEPWEG
YGEFQHSQVHKQVAISFRTPRYKSINLTDPVKVKVQLRRPSDGATSDPLDFEMLPLNEGR
RSYWNLQRELKKRSAETDLFQQLLDVDNEEQKVDIVNFTNVNSLPLQSNNNAIEQTEVVI
LDTPIDDNAKPIEDDKTMLWLENAEFIIDGNNNNENNQNVINQSDDDKTLSDLLEQVAEL
DVIYQDHQVRKEIQAMQDELNDMDQCLPQEGEQMETDFDDAATYSSLQKAFKHPIVFTDA
PPVPPKPGHVFSNSSFELILPPIVINPATPDIYMKEEKLPPLPPKRAKKISESGDKENIN
EQMQQQNVEQQQAQRDENTLVRNNSTRSLTPRPPQQPIVIKSADLRRSPSHKLPPKSPTK
STTSTTSSQTNTNTLPKQKKPGFFSKIFSRRKSKSDIDSSIGGDSASIKIESEMENENVD
ESIDDVENQFEPEDQNRSPMRSTKSLRSPKKQKYGKPVGRSVSSVSGKRPHLTPDIIHIP
LKGDSSNSLPLHQSGSATHLSLPGNDFYERASTASLHPIDRKTMSALQLADVPIQDGDME
LVAIADAQSLRNLCENGEHGIILDPSVDLTEAEHYALYTTLAPHATQSEFDETSCYYQPV
EAGQILTPAEVARRMNDNF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g6007.t1 | CDD | cd07887 | RHD-n_Dorsal_Dif | 74 | 247 | 6.66892E-102 |
| 15 | g6007.t1 | CDD | cd01177 | IPT_NFkappaB | 252 | 355 | 6.90211E-47 |
| 14 | g6007.t1 | Coils | Coil | Coil | 596 | 616 | - |
| 13 | g6007.t1 | Coils | Coil | Coil | 709 | 729 | - |
| 12 | g6007.t1 | Gene3D | G3DSA:2.60.40.340 | - | 74 | 247 | 1.1E-70 |
| 11 | g6007.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 249 | 369 | 8.5E-42 |
| 19 | g6007.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 602 | 773 | - |
| 20 | g6007.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 602 | 635 | - |
| 21 | g6007.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 654 | 679 | - |
| 3 | g6007.t1 | PANTHER | PTHR24169 | NUCLEAR FACTOR NF-KAPPA-B PROTEIN | 57 | 649 | 4.6E-118 |
| 4 | g6007.t1 | PRINTS | PR00057 | Transcription factor NF-KB signature | 80 | 97 | 4.7E-32 |
| 7 | g6007.t1 | PRINTS | PR00057 | Transcription factor NF-KB signature | 235 | 249 | 4.7E-32 |
| 5 | g6007.t1 | PRINTS | PR00057 | Transcription factor NF-KB signature | 266 | 286 | 4.7E-32 |
| 8 | g6007.t1 | PRINTS | PR00057 | Transcription factor NF-KB signature | 304 | 322 | 4.7E-32 |
| 6 | g6007.t1 | PRINTS | PR00057 | Transcription factor NF-KB signature | 345 | 359 | 4.7E-32 |
| 2 | g6007.t1 | Pfam | PF00554 | Rel homology DNA-binding domain | 76 | 246 | 4.9E-68 |
| 1 | g6007.t1 | Pfam | PF16179 | Rel homology dimerisation domain | 254 | 356 | 1.4E-35 |
| 18 | g6007.t1 | ProSitePatterns | PS01204 | NF-kappa-B/Rel/dorsal domain signature. | 89 | 95 | - |
| 22 | g6007.t1 | ProSiteProfiles | PS50254 | NF-kappa-B/Rel/dorsal domain profile. | 71 | 250 | 76.35 |
| 17 | g6007.t1 | SMART | SM00429 | iptmega2 | 251 | 354 | 1.6E-11 |
| 10 | g6007.t1 | SUPERFAMILY | SSF49417 | p53-like transcription factors | 74 | 254 | 8.7E-72 |
| 9 | g6007.t1 | SUPERFAMILY | SSF81296 | E set domains | 249 | 367 | 5.37E-38 |
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:0003677 | DNA binding | MF |
| GO:0006355 | regulation of transcription, DNA-templated | BP |
| GO:0005737 | cytoplasm | CC |
| GO:0003700 | DNA-binding transcription factor activity | MF |
KEGG
Orthology
- This transcript has been annotated with K09254 (c-Rel proto-oncogene protein)
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.
