General information for g11954.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative MICAL-like protein 2.
Parent gene
- The parent gene g11954 is located on chr_1: 19775063..19776052 (+ 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_1 | g11954 | g11954.t1 | TSS | g11954.t1 | 19770721 | 19770721 |
| chr_1 | g11954 | g11954.t1 | isoform | g11954.t1 | 19771752 | 19776052 |
| chr_1 | g11954 | g11954.t1 | exon | g11954.t1.exon1 | 19771752 | 19771861 |
| chr_1 | g11954 | g11954.t1 | cds | g11954.t1.CDS1 | 19771752 | 19771861 |
| chr_1 | g11954 | g11954.t1 | exon | g11954.t1.exon2 | 19772519 | 19773751 |
| chr_1 | g11954 | g11954.t1 | cds | g11954.t1.CDS2 | 19772519 | 19773751 |
| chr_1 | g11954 | g11954.t1 | exon | g11954.t1.exon3 | 19774168 | 19774375 |
| chr_1 | g11954 | g11954.t1 | cds | g11954.t1.CDS3 | 19774168 | 19774375 |
| chr_1 | g11954 | g11954.t1 | exon | g11954.t1.exon4 | 19774594 | 19775437 |
| chr_1 | g11954 | g11954.t1 | cds | g11954.t1.CDS4 | 19774594 | 19775437 |
| chr_1 | g11954 | g11954.t1 | exon | g11954.t1.exon5 | 19775498 | 19775697 |
| chr_1 | g11954 | g11954.t1 | cds | g11954.t1.CDS5 | 19775498 | 19775697 |
| chr_1 | g11954 | g11954.t1 | exon | g11954.t1.exon6 | 19775762 | 19775908 |
| chr_1 | g11954 | g11954.t1 | cds | g11954.t1.CDS6 | 19775762 | 19775908 |
| chr_1 | g11954 | g11954.t1 | exon | g11954.t1.exon7 | 19775981 | 19776052 |
| chr_1 | g11954 | g11954.t1 | cds | g11954.t1.CDS7 | 19775981 | 19776052 |
| chr_1 | g11954 | g11954.t1 | TTS | g11954.t1 | NA | NA |
Sequences
>g11954.t1 Gene=g11954 Length=2814
ATGGCAAATGTTGTACCGAAAAGAGAACCTTGCGTAAAATGCAATAATCCTGTATTTTTT
GCTGAACGACTTGTTATCGAAAATCATCTCTATCATCGGACATGTTTTAGATGTGCACGA
TGTCATTCAGTATTAACATTGGGCAATTTCTACCAAACAGAAAAAGACAATGAATTTTGT
TGTGAAACATGTCCAGATGAGGAACTTAAGACCAAACGCAAGGTCGATGAGTCAAATCGT
TTATCAATTGCACAGCGAATTGCATTGTTTGAGAAAACAGAGACATCAAGTGTTCTCAAA
AAATCATTGAGTGATGAAGAGAAAACAAAAAGTCTGAATCGCCAATTGCCATCATCAACA
GCAGCAACATCTGTCAATTCCAATTCCAACGCGCTCAATAACTTTCTCACATCACAAATT
GTCGACGATGATGAAAAAACAAATGAGTCACAATCTTCAGAGTCGGAAAGCGATGACGAA
TTAGTGAATGATGACAAGAAGCTCTTTGAAACAAAAAGTGACCATAGTAATTCAATTAAT
AATGACAGCAACATTATTTCAACCAAAGAACTAACACAGACGACACAAGCGCATCAAAAT
GAATCTCAAGAGCAACTAAAGCAAATAGTTAACGATATAATCTTAGTAAGTTCCAATGAA
AATGTAGATGATATAGAATTGGAATTTGAGAAACTTGCTGAGGAAGCTGTAAACAATCCA
ATCCCATTGCTTGTATCACCTAACATAATAACAACAAAGCTATCAACACAAGCACAAGAA
ATTGTAGATAAAGAAAAAGAAGAGCCAACAATAATAATAGAAGAATCAATTGAGTCAAAA
AGTCAACCACAAGTATCAGTTCAAGAGAAAAATGAAGAGGAAAAAGTTGAGGTGATAAAA
ATAGAAGAACAAACTAAAGTAGAAGAAAATAAAACAGAATTAATTGAGGAAGAAAAGCTT
TCAGAAGAAATACTTAAAGAAAAACCAGTAACAATAGCAGCAGACATTTCAATTAGTTCA
CAAAAGACTCTCTATCCAGATGATTTGAATCCATTTGGTGATGATGATGAACAGAAAGAA
GAAGAAAAAATAAAGAGACCAAGTCTTAATCCATTTGGAAGCTGTTCAGAGGATGAAGAG
GAAGATATAAAGTTCAGAAACTCAAATACTGGAACATTACACAAAATACAAAAGCCACCG
CGACCAAGTCGACCTCCACTCCCACGAGTTTCAATGACACTTAAGCCCGCTTCAACCAAT
CCATTTGGCAGCGATGATGAAGATGAAGAGTCAGCGTCACAAATTAACAACAAGACTCCA
GTTCCAACAACAAGAAAACAATTACATTCAATGACACCTGAGCCTGCACCACGTTTCAAT
AATTCTCCTGGCCATAGTTTAAATTTCAAAGGATCAAGCTCATCATTAGCGTCATCAACT
GATGGCATTACATCATTGAGAAGAAAAAAGAAAAAAGCACCAGCACCACCTGTTCCAGTT
CCCAAAATTGAATTGGAAAGTTCAACAGTTAAAAATGACAATGATGATAAATCAACGCAA
AGCACACCGAAGAAAAAAAGACAAGCGCCAACGCCTCCTTCTTCTACGTCATTCAAAGCA
CCTGAAAAAGCGTCAACAGAGGTTATAGAAAATACAGAAAATACTCTTAATGATGCAGCA
CTCTACGTGACACCATCAGAAACAATTAATGGAGAAAATCATGAAAATAATGTGAATGAA
AGCACCGATATCGACATTTCACTCAATGCCAGTAGCTTACAATCTGATGGTGATCAACGT
CGACTTATTCCACTTGAGGAATCGCTCATTGAAGAAGGTGCAAGCAGTAGTTCTATAAAT
AGTCGCAATGAAACGCAAGAAGTGACGTACAGGAGAAAAATTGTACCTCTTTCGCCCACA
TCACCAGATGATGACAGTTGCGAAAATTTGGAGCAAATAAAAGACCACAAAGAAGCGGAA
AATCGTCAACGTCAAAGTCAAAGCAGTCTTAAAGCGGACTCAACTGATTCGCTGCCATAT
CTCAACAAGTCATCACACGGAAAATGGAAAAGAAGAAAAGGCAAAGCACCAACTTTACCT
TTTGCTCTTCCACAGCGACGTGTTTTACAAATGTTGCCATTGCAAGAAATTCGTCATGAA
CTAGAAATCATCGAAGTGCAGCAGCAGGGATTAGAAAAGCAAGGTGTTCAGCTAGAAAAA
ATGATAAGAGAACGTTGTGAAGGCGATAATCGTACAACTGAAGAACTTTTAGAGCAATTA
CCCAATGCAAAGAATCCAAAGGAAGTTGAAGAACTCATATTACAATTATTTGAGTTAGTG
AATGAAAAAAATGAGCTATTTAGACGTCAAGCAGAGTTGATGTATTTAAGGAGAGCCCAT
CGTCTTGAAGAAGAACAAGCGGATGTTGAATATGAAATAAGAAAGTTAATGGCTCAACCT
GAACATAATAAGACTGACTCAGATAAAGCTAGAGAAGAAGCATTGATAGCGAGACTTGTG
GAAATTGTTCAATTAAGAAATGAAGTTGTTGATTGTCTAGAAATGGATCGATTGCGAGAA
GCAGAAGAAGATTTGAGTATTAAACAAAGAATGGAAAGTCACACAGCTAAACTTGACCAA
GAATATCTTAATCAAACACCAACAAAATTATCGAAGAAAGAAAAGAAGAAACTAAAAGAG
GCAAAAAAGATGAAAAACAAGAAACTCAATGATGCCGATAAAGATTTAGATACCAGTGAA
ATGAAAGCAGAAACGGGCGAAAAAAAGAAGAAGAAGAAAAAATTTTTGTTCTAA
>g11954.t1 Gene=g11954 Length=937
MANVVPKREPCVKCNNPVFFAERLVIENHLYHRTCFRCARCHSVLTLGNFYQTEKDNEFC
CETCPDEELKTKRKVDESNRLSIAQRIALFEKTETSSVLKKSLSDEEKTKSLNRQLPSST
AATSVNSNSNALNNFLTSQIVDDDEKTNESQSSESESDDELVNDDKKLFETKSDHSNSIN
NDSNIISTKELTQTTQAHQNESQEQLKQIVNDIILVSSNENVDDIELEFEKLAEEAVNNP
IPLLVSPNIITTKLSTQAQEIVDKEKEEPTIIIEESIESKSQPQVSVQEKNEEEKVEVIK
IEEQTKVEENKTELIEEEKLSEEILKEKPVTIAADISISSQKTLYPDDLNPFGDDDEQKE
EEKIKRPSLNPFGSCSEDEEEDIKFRNSNTGTLHKIQKPPRPSRPPLPRVSMTLKPASTN
PFGSDDEDEESASQINNKTPVPTTRKQLHSMTPEPAPRFNNSPGHSLNFKGSSSSLASST
DGITSLRRKKKKAPAPPVPVPKIELESSTVKNDNDDKSTQSTPKKKRQAPTPPSSTSFKA
PEKASTEVIENTENTLNDAALYVTPSETINGENHENNVNESTDIDISLNASSLQSDGDQR
RLIPLEESLIEEGASSSSINSRNETQEVTYRRKIVPLSPTSPDDDSCENLEQIKDHKEAE
NRQRQSQSSLKADSTDSLPYLNKSSHGKWKRRKGKAPTLPFALPQRRVLQMLPLQEIRHE
LEIIEVQQQGLEKQGVQLEKMIRERCEGDNRTTEELLEQLPNAKNPKEVEELILQLFELV
NEKNELFRRQAELMYLRRAHRLEEEQADVEYEIRKLMAQPEHNKTDSDKAREEALIARLV
EIVQLRNEVVDCLEMDRLREAEEDLSIKQRMESHTAKLDQEYLNQTPTKLSKKEKKKLKE
AKKMKNKKLNDADKDLDTSEMKAETGEKKKKKKKFLF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g11954.t1 | CDD | cd09400 | LIM_like_1 | 7 | 68 | 1.66513E-31 |
| 9 | g11954.t1 | Coils | Coil | Coil | 215 | 235 | - |
| 8 | g11954.t1 | Coils | Coil | Coil | 647 | 667 | - |
| 10 | g11954.t1 | Coils | Coil | Coil | 714 | 734 | - |
| 11 | g11954.t1 | Coils | Coil | Coil | 799 | 819 | - |
| 7 | g11954.t1 | Coils | Coil | Coil | 895 | 915 | - |
| 6 | g11954.t1 | Gene3D | G3DSA:2.10.110.10 | Cysteine Rich Protein | 7 | 128 | 3.3E-14 |
| 19 | g11954.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 100 | 127 | - |
| 18 | g11954.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 113 | 127 | - |
| 22 | g11954.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 139 | 163 | - |
| 23 | g11954.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 336 | 576 | - |
| 25 | g11954.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 434 | 483 | - |
| 21 | g11954.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 508 | 523 | - |
| 27 | g11954.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 524 | 576 | - |
| 20 | g11954.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 612 | 696 | - |
| 17 | g11954.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 647 | 664 | - |
| 16 | g11954.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 665 | 682 | - |
| 26 | g11954.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 878 | 937 | - |
| 24 | g11954.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 904 | 931 | - |
| 3 | g11954.t1 | PANTHER | PTHR23167:SF59 | MICAL-LIKE 1A-RELATED | 7 | 913 | 6.2E-92 |
| 4 | g11954.t1 | PANTHER | PTHR23167 | CALPONIN HOMOLOGY DOMAIN-CONTAINING PROTEIN DDB_G0272472-RELATED | 7 | 913 | 6.2E-92 |
| 2 | g11954.t1 | Pfam | PF00412 | LIM domain | 11 | 64 | 1.7E-7 |
| 1 | g11954.t1 | Pfam | PF12130 | Bivalent Mical/EHBP Rab binding domain | 717 | 867 | 1.7E-47 |
| 15 | g11954.t1 | ProSitePatterns | PS00478 | LIM zinc-binding domain signature. | 11 | 45 | - |
| 29 | g11954.t1 | ProSiteProfiles | PS50023 | LIM domain profile. | 9 | 71 | 11.355 |
| 28 | g11954.t1 | ProSiteProfiles | PS51848 | bMERB domain profile. | 701 | 869 | 49.542 |
| 14 | g11954.t1 | SMART | SM00132 | lim_4 | 10 | 64 | 1.6E-8 |
| 13 | g11954.t1 | SMART | SM01203 | DUF3585_4 | 711 | 869 | 3.3E-64 |
| 5 | g11954.t1 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 5 | 36 | 1.66E-6 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K19948 (MICAL-like protein 1)
Pathway
This gene does not belong to any 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.
