RetrogeneDB ID: | retro_trub_13 | ||
Retrocopy location | Organism: | Fugu rubripes (Takifugu rubripes) | |
| Coordinates: | scaffold_15:928301..930632(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSTRUG00000013856 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | elfn1b | ||
| Ensembl ID: | ENSTRUG00000015197 | ||
| Aliases: | None | ||
| Description: | extracellular leucine-rich repeat and fibronectin type III domain containing 1b [Source:ZFIN;Acc:ZDB-GENE-080327-21] |
Retrocopy-Parental alignment summary:
>retro_trub_13
GTGATGAGTGCCTTGTTTTGGTCTGTAGCCATTGTTTATTTGACTCAGATTGGCAGAGTGAGTGCAGACTGCTGGTTAAT
CGAGGGTGAAAAGGGCTTTGTATGGCTTGCAATCTGTAGCCAAAACCAACCACCTTACGAGGCCATCCCTCAGCATATCA
ACAGCACCATTGTGGACCTTCGTCTGAATGAAAACAAAATCAAAAGTATTCACTATTCTGCCCTTAGCCGCTTTGCCAAC
TTAACCTACCTAAACCTGACGAAGAATGAAATCTCCTACATCGAGGACGGGGCCTTTTCTGCTCAGTTTAACCTACAAGT
CCTTCAAATGGGCTTCAACAAGTTGAGAAACTTGACCGAAGGCATCCTCAGGGGTTTGGGAAAGCTGCAGTACCTCTACC
TCCAGGCAAATTTGATTGAGACTGTGACACCTAATGCCTTTTGGGAATGCCCCAACATTGAGAACATTGACCTCTCCATG
AACCGAATCCAGCAGTTAGATGGGTCCACATTCACCAGTTTGGCCAAACTGACCACCTGCGAGCTGTACACCAATCCTTT
TAACTGCTCCTGCGAGCTACTTGGATTTGTCAAATGGCTGTCGGTCTTCCCCAACAGAACAAACGAGCGGATGGTGTGCG
ACTCCCCATCTGGTGTCTCTGGTTATAGTTTACTCAGCCAGAATCCAAACAACCCAACATACAAAAATGCTCTTTATATG
CTCACCACCGTGTGTACTGATGACTACGTCACACCGTACACGCCAATCCCCACTGAGTCCATCACGCCCCCGCCAGACTC
AACACTGTGCGGTCTGGAGGATTGTCCCTCGGGGACAGAGCCGGAGGAGATCATCATCAGTACAACATATAACGATGTGG
AGGTAAACCCTGTCTTGAAGCTGAAACAGGTTACAAATACAGGCGCTACTATTACAGTTCAGATTCCGTATCCCTTCAAG
AAGATGTACATCCTGGTTCTGTACAACAACAGCTTTTTCACGGACATTCAAAACCTGAACAAAATAAAGGATGACATTGA
GCTGAAAAATCTCAATCCCCACACTAACTACACGTACTGTGTGGCTTCCATACGCAACTCCCTTCGCCATAATCACACTT
GTCTGACAATCACCACCGGCACCCGGAATGGGAAGGAAAGAAGCGTAAACAATGCAACTGCTACCCACTACATCATGACC
ATTTTAGGCTGCCTCTTCAGCATGGTCATCTTCCTCGGAGTTGTCTACTATTGTTTGCGGAGAAAGCGGCAACAAGATGA
AAAGCACAAAAAGTCAGGTAGCTTAAAGAAGAACATAATGGAGCTGAAATATGGACAGGAACTGGAAGGGGGGAATATTT
CTCGCATGTCACAGAAGCAGTTGTTGGCTGGGGACAGCATGGCACGCATGCCGTACCTACCACCTGCTGCCGAGATGGAG
CAGTACAAATTTCAAGAGATAGGTGACACCCCTAAAATGATGAAAGGGAACTACATGGAGGTGCGGAGCATGGACCACCA
CGACCGCAGGGAGTGCGAAATGGGAATGGCGGGGAATAGCCAGGGGTCGGTGGCCGAGATTTCCACCATAGCAAAAGAGG
TGGATAAAGTAAATCAGATTATTAACAACTGCATAGATGCGCTGAAGTCTGAATCCACCTCTTTTCAGGGCATGAAATCT
GGAGCGGTGTCCACCGCAGAGCCTCAGCTGGTGCTGATATCAGAGCACCCACAAGGTAAACCTGGCCTTCTGTCCCCCGC
ATATCAGGACAGCTACCACCACTCTCTGCAGAGGCATCGCTCGTCTGACATCTCGCCAAAGAGGCCCAGCACTGCCACAG
GAGGTCCAATGCGAAGCCCCAGGCCTTACCGCTCTGAATCCAAGTACATCGAGAAAACCTCCCCGACGGGAGAGACCATC
GTCACTGTAACGCCCACTGCAGCCATCCTGAGGGCTGAGGCGGACAAGATCCGCCAGTACAGCGACCATCGACACTCGTA
TCCCGACGCTCAGATTGAGGAGCTTGAAGGACCTGATGGCCACAAGTCATCCTTGTTAGAGCCTCTCACCCATTCCCGTT
CCAGAGACTTAGCGTACTCCCAACTGCCTTCCCAGTATCAAAATCTGAGCTACTCCTCCAGCCCCGAGTACTACTGCAAA
CCGCCACAGAGCATCTGGGGGCGATTCAAACTGCACCGGAAGCGGCACAAAGACGACGAGTACATGGCTGCCGGCCACGC
GCTGCGGAAGAAGGTCCAGTTTGCGAAGGACGAGGATCTGCACGACATTTTAGACTACTGGAAAGGTGTTTCAGCCCAGC
ATAAATCATAA
ORF - retro_trub_13 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 65.9 % |
| Parental protein coverage: | 61.06 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | VLSTFLCWLVVLSVMRLPVVTADCWLIEGEKGFVWLAICSMNQPPYESIPAHINSTIVDLRLNENKIRSV |
| V.S................V.ADCWLIEGEKGFVWLAICS.NQPPYE.IP.HINSTIVDLRLNENKI.S. | |
| Retrocopy | VMSALFWSVAIVYLTQIGRVSADCWLIEGEKGFVWLAICSQNQPPYEAIPQHINSTIVDLRLNENKIKSI |
| Parental | HYSSLSRFGNLTYLNLTKNDISYVEDGAFSAQFNLQVLQMGFNKLRNLTEGMLRGLGKLQYLYLQANLIE |
| HYS.LSRF.NLTYLNLTKN.ISY.EDGAFSAQFNLQVLQMGFNKLRNLTEG.LRGLGKLQYLYLQANLIE | |
| Retrocopy | HYSALSRFANLTYLNLTKNEISYIEDGAFSAQFNLQVLQMGFNKLRNLTEGILRGLGKLQYLYLQANLIE |
| Parental | TVTPNTFWECPNIENIDLSMNKIQVLDGSLFSGLSKLTTCELYTNPFNCSCELLGFLRWLSTFPNRTSER |
| TVTPN.FWECPNIENIDLSMN.IQ.LDGS.F..L.KLTTCELYTNPFNCSCELLGF..WLS.FPNRT.ER | |
| Retrocopy | TVTPNAFWECPNIENIDLSMNRIQQLDGSTFTSLAKLTTCELYTNPFNCSCELLGFVKWLSVFPNRTNER |
| Parental | MVCDSPQGFFGYSLLSQNLRMSSQGNALHMLSVVCTDVDSSVTSFNGIGMVDFTTMLPDFASPCGLDDCA |
| MVCDSP.G..GYSLLSQN.......NAL.ML..VCT..D..VT....I.....T...P.....CGL.DC. | |
| Retrocopy | MVCDSPSGVSGYSLLSQNPNNPTYKNALYMLTTVCT--DDYVTPYTPIPTESITP--PPDSTLCGLEDCP |
| Parental | SGTPPDEVINFSPIFSD--TNPIMTLKQVQHSSAVITVQLPHPYKKMYILALYNNSFFMDIQNLRRQRED |
| SGT.P.E.I..S....D...NP...LKQV....A.ITVQ.P.P.KKMYIL.LYNNSFF.DIQNL.....D | |
| Retrocopy | SGTEPEEII-ISTTYNDVEVNPVLKLKQVTNTGATITVQIPYPFKKMYILVLYNNSFFTDIQNLNKIKDD |
| Parental | IELKNLKPNTNYTYCVASIRNSLRFNHTCLTISTGRQSGVERAVNKSSATHYIMTILGCLFGMLLFLGLI |
| IELKNL.P.TNYTYCVASIRNSLR.NHTCLTI.TG...G.ER.VN...ATHYIMTILGCLF.M..FLG.. | |
| Retrocopy | IELKNLNPHTNYTYCVASIRNSLRHNHTCLTITTGTRNGKERSVNNATATHYIMTILGCLFSMVIFLGVV |
| Parental | VHCLRKRRLMEEKERKMSRIQRTLIELKYGGDDDIEGGGVGPVSQK-LSAGDSLSRIPYLPQGGEIDPYK |
| ..CLR..R...EK..K.........ELKYG.....EGG.....SQK.L.AGDS..R.PYLP...E...YK | |
| Retrocopy | YYCLRRKRQQDEKHKKSGSLKKNIMELKYG--QELEGGNISRMSQKQLLAGDSMARMPYLPPAAEMEQYK |
| Parental | LQEVIETPPHKPAKPNYMEVRGSGIERERERE |
| .QE...TP..K..K.NYMEVR.......RE.E | |
| Retrocopy | FQEIGDTP--KMMKGNYMEVRSMDHHDRRECE |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Takifugu rubripes was not studied using RNA-Seq expression data.
Takifugu rubripes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_trub_13 retrocopy.
Takifugu rubripes was not studied using FANTOM5 data.
retro_trub_13 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_trub_13 has 3 orthologous retrocopies within teleost group .| Species | RetrogeneDB ID |
|---|---|
| Gasterosteus aculeatus | retro_gacu_19 |
| Oryzias latipes | retro_olat_18 |
| Tetraodon nigroviridis | retro_tnig_5 |
Parental genes homology:
Parental genes homology involve 6 parental genes, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Gasterosteus aculeatus | ENSGACG00000016502 | 1 retrocopy | |
| Oreochromis niloticus | ENSONIG00000000160 | 1 retrocopy | |
| Oryzias latipes | ENSORLG00000009720 | 1 retrocopy | |
| Tetraodon nigroviridis | ENSTNIG00000008254 | 1 retrocopy | |
| Takifugu rubripes | ENSTRUG00000015197 | 1 retrocopy |
retro_trub_13 ,
|
| Xiphophorus maculatus | ENSXMAG00000014093 | 1 retrocopy |