RetrogeneDB ID: retro_onil_6

Retrocopy location

• Organism: Tilapia (Oreochromis niloticus)
• Coordinates: GL831149.1:3359638..3362011(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSONIG00000020933
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: elfn1b
• Ensembl ID: ENSONIG00000000160
• Aliases: None
• Description: extracellular leucine-rich repeat and fibronectin type III domain containing 1b [Source:ZFIN;Acc:ZDB-GENE-080327-21]

Sequence

>retro_onil_6
ATGACTCTCAAAGAAGCACCAATGGCCTGCAGCTTAGGCATGGTGATGAGTGCCTTGTTTTGGTCTGTAGCCATTGTATA
TTTGACTCATATTGGCAGAGTCAGTGGAGACTGCTGGTTAATTGAGGGTGAAAAGGGCTTTGTATGGCTCGCAATTTGTA
GTCAAAACCAGCCACCTTATGAGGCCATCCCACAGCATATCAACAGCACCATTGTGGACCTTCGTCTGAATGAAAACAAA
ATCAAAAGTATCCACTATTCTGCCCTTAGCCGCTTTGCCAACTTGACCTACCTGAACCTGACCAAGAATGAAATCTCCTA
CATAGAAGATGGGGCCTTTTCTGCTCAGTTTAACTTGCAAGTCCTTCAAATGGGCTTCAACAAGTTGCGGAACTTGACAG
AGGGGATCCTCAGGGGTTTAGGAAAGCTGCAGTACCTCTACCTCCAGGCAAACCTGATTGAGACTGTGACACCTAATGCC
TTTTGGGAATGCCCCAACTTAGAGAATATTGACCTCTCCATGAACCGAATCCAGCAGTTAGATGGGTCTACGTTTGCCAG
TTTAACTAAACTCACCACCTGTGAGTTGTACACAAACCCCTTCAACTGCTCATGTGAATTACTTGGTTTTGTCAAATGGC
TCTCAGTTTTCCCAAACAGGACAAATGAGCGAATGGTTTGCGACTCCCCACCCGGGGTCTCTGGTTATAGCTTACTGAGC
CAGATTCCTAACAATCCAAACTATCGAAATGCACTGTACATGCTTACCAAAGTGTGTACTGATGAATATGTAACACCATT
TATAACTGTGCCCATTGAGTCAACAACACTACCACCAGACTCAACACTTTGTGGAATGGAAGACTGTCCATCAGGCACAG
AACCAGAAGATACTACCATCAGTACACCTGAAAATGATGTTCAGGGAACCCCTCTGATGACAGTGAAGCAAGTAACACAC
ACAGGTGCTATCATCACAGTTCAGATTCCTCATCCCTATAAGAAGATGTACATCTTGGTTCTTTATAACAACAGTTTTTT
CACAGACATTCAAAACCTGAAAGATATAAAAGAGGACATTGAATTAAAAAACCTTAAACCCCACACCAACTACACATATT
GTGTTGCTTCAATACGCAATTCTCTTAGACACAACCATACATGTCTGACAGTCTCTACTGACCCTCAAAATGGAAAGGAT
GTAACTGTGAAAAAGCCGAGTGCTACTCACTACATTATGACAATTTTGGGCTGCCTATTCAGCATGGTTATATTTCTTGG
AGTTGTGTACTATTGCTTGCGAAGAAAGCGCCAACAAGATGAAAAGCACAAAAAAGCAGGAAGTTTAAAGAAAAACATAA
TGGAACTTAAATATGGACAAGAGCTTGAGGGTGGGACTATATCTCGAATGTCGCAGAAGCAGTTGTTGGCGGGAGAGAGC
ATGGCACGTATGCCATACTTACCATCTGCAAGTGAAATGGAGCAATACAAATTTCAAGAGATAAGTGATACTCCTAAGAT
GATGAAAGGAAATTACATGGAGGTGCGAAGTGTGGATCACCATGACCGCCGGGAGTGTGATATGGGAATGGCTGGGAATA
GTCAGGGATCAGTGGCAGAAATTTCCACAATTGCAAAAGAGGTGGATAAAGTCAATCAGATAATAAACAACTGCATAGAT
GCTTTAAAGTCAGAATCCACCTCTTTTCAAGGAGTGAAATCTGGAGCAGTATCCACTGCAGAGCCCCAGCTTGTACTAAT
ATCAGAACACCCACAGAATAAATCTGGCCTTCTGTCTCCAGTGTATAAGGACAGCTACCATCACTCTCTGCAGAGACATC
GGTCTTCTGATGTCTCTCCAAAGAGGCCCAGTACAGCCACAGGAGGACCCATGAGAAGCCCCAGGCCTTATCGCTCTGAA
TCCAAGTATATAGAGAAAACCTCCCCAACAGGAGAGACCATCCTCACTGTAACACCTGCTGCTGCCATCCTGAGGGCCGA
GGCAGAAAAGATCCGTCAGTACAGCGCCCACCGACACTCCTATCCCGACGCTCAGATAGAGGAGCTCGAAGGACCTGACA
GCCACAAGTCCTCCATGTTGGAGCCTCTCACTCACTCCCGCTCCAGAGACTTAGCATATTCGCAGATGTCCTCTCAGTAC
CACAATCTAAGCTATTCCTCCAGTCCTGAATACTACTGCAAACCTTCACATAGCATCTGGGAGCGTTTCAAACTCCATCG
GAAACGGCATAAAGATGAGGAGTACATGGCTGCAGGGCATGCACTGCGTAAGAAAGTCCAGTTTGCAAAGGATGAGGACC
TCCATGATATTTTAGACTACTGGAAAGGCGTATCATCCCAACATAAATCCTAA

Alignment

ORF - retro_onil_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.54 %
• Parental protein coverage: 63.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SSFFCFLALLSVMRLPVVKADCWLIEGEKGFVWLAICSMNQPPYEAIPSHINSTIVDLRLNENKIRAVHY
          S..F...A.........V..DCWLIEGEKGFVWLAICS.NQPPYEAIP.HINSTIVDLRLNENKI...HY
Retrocopy SALFWSVAIVYLTHIGRVSGDCWLIEGEKGFVWLAICSQNQPPYEAIPQHINSTIVDLRLNENKIKSIHY

Parental  SSLSRFSNLTYLNLTKNDISYVEDGAFSAQFNLQVLQMGFNKLRNLTEGMLRGLGKLQYLYLQANLIETV
          S.LSRF.NLTYLNLTKN.ISY.EDGAFSAQFNLQVLQMGFNKLRNLTEG.LRGLGKLQYLYLQANLIETV
Retrocopy SALSRFANLTYLNLTKNEISYIEDGAFSAQFNLQVLQMGFNKLRNLTEGILRGLGKLQYLYLQANLIETV

Parental  TPNTFWECPNIENIDLSMNRIQVLDGSLFSGLSKLTTCELYTNPFNCSCELLGFLRWLAAFPNRTSERMV
          TPN.FWECPN.ENIDLSMNRIQ.LDGS.F..L.KLTTCELYTNPFNCSCELLGF..WL..FPNRT.ERMV
Retrocopy TPNAFWECPNLENIDLSMNRIQQLDGSTFASLTKLTTCELYTNPFNCSCELLGFVKWLSVFPNRTNERMV

Parental  CDSPHGFSGYNLLNQNPRMLNQRSALYALSHVCTDDSSSATSFYGIDSTTPPPDFASPCGLDDCASGTPP
          CDSP.G.SGY.LL.Q.P...N.R.ALY.L..VCTD..........I.STT.PPD....CG..DC.SGT.P
Retrocopy CDSPPGVSGYSLLSQIPNNPNYRNALYMLTKVCTDEYVTPFITVPIESTTLPPD-STLCGMEDCPSGTEP

Parental  DGGEVISLSPIFPDAKPIMTVKQVLPSSAVITVQIPDPYKKMYILMLYNNSFFTDIQNLKDKREDIELKN
          .....IS.........P.MTVKQV....A.ITVQIP.PYKKMYIL.LYNNSFFTDIQNLKD..EDIELKN
Retrocopy E-DTTISTPENDVQGTPLMTVKQVTHTGAIITVQIPHPYKKMYILVLYNNSFFTDIQNLKDIKEDIELKN

Parental  LKPNTDYTYCVASIRNSLRFNHTCLTISTGHRVGTEKVPRPPSVTHYIMTILGCLFGMLVFLGFVVHCLR
          LKP.T.YTYCVASIRNSLR.NHTCLT.ST....G.......PS.THYIMTILGCLF.M..FLG.V..CLR
Retrocopy LKPHTNYTYCVASIRNSLRHNHTCLTVSTDPQNGKDVTVKKPSATHYIMTILGCLFSMVIFLGVVYYCLR

Parental  RKRIMEEKERKMSRIQRTLIELKYGGEGDIEGGSGGSVSQK-LGAGDSLSRMPYLPQGGEIDPYKLQEVI
          RKR...EK..K.........ELKYG.E...EGG.....SQK.L.AG.S..RMPYLP...E...YK.QE..
Retrocopy RKRQQDEKHKKAGSLKKNIMELKYGQE--LEGGTISRMSQKQLLAGESMARMPYLPSASEMEQYKFQEIS

Parental  ETPAHKPPKLNYMEVRGSDIEREREREREREMSPQANPQGSVAEISTIAKEVDKVNQIINNCIDALKSES
          .TP..K..K.NYMEVR..D....RE......M....N.QGSVAEISTIAKEVDKVNQIINNCIDALKSES
Retrocopy DTP--KMMKGNYMEVRSVDHHDRRECD----MGMAGNSQGSVAEISTIAKEVDKVNQIINNCIDALKSES

Parental  TSFQQGIKS
          TSF.QG.KS
Retrocopy TSF-QGVKS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Oreochromis niloticus was not studied using RNA-Seq expression data.

ChIP-Seq

Oreochromis niloticus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_onil_6 retrocopy.

TSS

Oreochromis niloticus was not studied using FANTOM5 data.

Lab

retro_onil_6 was not experimentally validated.

Homology

Retrocopy orthology:

Oreochromis niloticus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Gasterosteus aculeatus	ENSGACG00000016502	1 retrocopy	retro_gacu_19,
Oreochromis niloticus	ENSONIG00000000160	1 retrocopy	retro_onil_6 ,
Oryzias latipes	ENSORLG00000009720	1 retrocopy	retro_olat_18,
Tetraodon nigroviridis	ENSTNIG00000008254	1 retrocopy	retro_tnig_5,
Takifugu rubripes	ENSTRUG00000015197	1 retrocopy	retro_trub_13,
Xiphophorus maculatus	ENSXMAG00000014093	1 retrocopy	retro_xmac_1,