RetrogeneDB ID: retro_olat_18

Retrocopy location

• Organism: Medaka (Oryzias latipes)
• Coordinates: 8:7212729..7215066(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSORLG00000004648
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: elfn1b
• Ensembl ID: ENSORLG00000009720
• Aliases: None
• Description: extracellular leucine-rich repeat and fibronectin type III domain containing 1b [Source:ZFIN;Acc:ZDB-GENE-080327-21]

Sequence

>retro_olat_18
AGCTCAGGCATGGTGATGAGTGCCTTGTTTTGGTCTGTAACTATTGTATATCTGACTCATGTTGGGAGAGTGAATGGAGA
CTGCTGGTTAATCGAGGGAGAAAAGGGCTTTGTCTGGCTTGCAATTTGTAGCCAAAACCAACCACCATTTGAGGCCATCC
CACAGCATATCAACAGCACCATCGTAGACCTTCGTCTTAACGAAAACAAAATAAAAAGTATCCATTATTCTGCCCTTAGC
CGCTTTGCCAACTTAACCTACCTGAACTTGACCAAGAATGAAATTTCCTACATAGAGGATGGGGCCTTCTCTGCTCAGTT
TAACCTACAAGTACTTCAAATGGGCTTCAACAAGCTACGGAACCTGACAGAGGGGATTCTCCGGGGTCTGGGAAAGCTGC
AGTACCTCTACCTCCAGGCAAACCTGATTGAGACTGTGACACCTAATGCCTTTTGGGAGTGCCCAAACATCGAGAACATC
GATCTCTCCATGAATCGCATCCAGCAGTTGGATGGGTCCACCTTTACCAGTTTAACTAAACTAACCACCTGTGAGCTGTA
CACCAACCCTTTCAACTGCTCCTGTGAGTTACTGGGATTTGTGAAATGGCTCTCAATTTTCCCAAACCGTACCAACGAGC
GAATGGTGTGCGACTCCCCACCTGGCGTCTCAGGATACAGTTTACTGAGCCAGAATCCCAACAACCCAACGTACCGAAAT
GCCCTCCACATGCTGAAAACTGTGTGTACCGATGACTATGTGACACCATTCATCTCTATTTCTATCGAGTCCACAACAAT
GCCACCCGACTCAACGCTTTGTGGGATGGATGAATGTCCGTCAGGCACCGAACCAGAGGACATTACTGTTAGTACCACGG
AAAACGAGGTGCAAGGAAAACTTAAGATGGAACTGAAGGAAATAACAAAAGCAGGGGCAACAATTACTATTCAGATTCCT
GATCCATACAAAAAGATGTACATCCTGGCTCTGTACAACAACAGCTTTTTCACAGATATTCAAAACCTGAAAGACAAAAA
GGAGGACATTGAGCTAAAAAACCTGAAACCACACATAAACTACACATACTGCATCGTTTCAATACGCAATTCTCTAAGAC
ACAATCACACCTGCCTAATTGTTTCTACAAACCCTCGGAATGGAAAAGAAAGAATTGTAAATCCTGCAACTGCTACTCAC
TACATTATGACAATTTTAGGTTGCCTCTTTAGTATGGTCATTTTTCTTGGGGTTGTTTATTACTGCCTGCGAAGAAAGCG
CCAGCAAGAAGAAAAGCACAAAAAAGAAGGCAGCCTAAAGAAAAATATAATGGAACTAAAGTATGGTCAAGAACTGGAAG
GTGGGACTATTTCTCGAATGTCGCAAAAGCAGTTATTGGCCGGGGAAAGCATGGGAAGAATGCCATACTTACCATCTACT
GGTGAAATGGAGCAGTATAAATTCCAGGAGATAAGTGAGACTCCGAAAATGATCAAGGGAAACTACATGGATGTCAGAAG
TATGGATCACCACGAGCGTAGAGAGTGTGATCTGGGAATGGCCGGGAACAGTCAAGGATCAGTAGCTGAAATTTCAACAA
TTGCAAAAGAGGTAGATAAAGTCAATCAGATCATTAACAACTGCATAGATGCCCTTAAGTCTGAATCCACTTCATTTCAG
GGGGTTAAATCTGGAGCTGTGTCTACCGCAGAACCTCAACTTGTCCTAATATCAGAGCACCCTCAGAATAAATCTGGTCT
TTTATCCCCAGTTTATAAAGATAGCTACCACCACTCTCTGCAGAGGCATCGAAGTTCCGATGTCTCTCCTAAGAGACCCA
GCACTGCCACAGGAGGACCCATGAGAAGTCCAAGGCCTTATCGCTCTGAATCCAAGTACATAGAAAAAGCTTCCCCAACT
GGAGAGACCATCCTCACTGTAACACCAGCTGCTGCCATCCTCAGGGCTGAGGCAGAGAAGATCCGCCAGTACGGTGAGCA
CAGGCACTCATACCCCGATGCTCAGATAGAAGAACTGGAAGGCCCCGACAGCCACAAGTTATTGGATCCTCTCACTCACT
CCCGCTCCAGAGACTTAGCATTTTCCCAAATGCCGTCTCAGTATCACAATCTAAGCTACTCCTCCAGTCCTGAATACTAC
TGCAAACCCTCACACAGCATCTGGGAGCGCTTCAGACTCCACCGAAAACGCCATAAAGATGAGGAGTACATGGCTGCTGG
CCATGCACTGCGAAAGAAAGTCCAGTTTGCAAAGGACGAGGACCTGCATGACATTTTAGACTACTGGAAAGGAGTTTCAG
CTCAAAATAAATCATAA

Alignment

ORF - retro_olat_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.61 %
• Parental protein coverage: 56.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ECWLIEGEKGFVWLAICSMNQPPYEAIPSHINSTIVDLRLNENKIRSIHYSSLSRFGNLTYLNLTKNDIS
          .CWLIEGEKGFVWLAICS.NQPP.EAIP.HINSTIVDLRLNENKI.SIHYS.LSRF.NLTYLNLTKN.IS
Retrocopy DCWLIEGEKGFVWLAICSQNQPPFEAIPQHINSTIVDLRLNENKIKSIHYSALSRFANLTYLNLTKNEIS

Parental  YVEDGAFSALFNLQVLQMGFNKLRNLTEGMLRGLGKLQYLYLQANVIETVTPNTFWECPNIENIDLSMNR
          Y.EDGAFSA.FNLQVLQMGFNKLRNLTEG.LRGLGKLQYLYLQAN.IETVTPN.FWECPNIENIDLSMNR
Retrocopy YIEDGAFSAQFNLQVLQMGFNKLRNLTEGILRGLGKLQYLYLQANLIETVTPNAFWECPNIENIDLSMNR

Parental  IQMLDGSLFSGLSKLTTCELYTNPFNCSCELLAFLRWLAAFPNRTTERMVCDSPPGFSGYNLLSQNPRMP
          IQ.LDGS.F..L.KLTTCELYTNPFNCSCELL.F..WL..FPNRT.ERMVCDSPPG.SGY.LLSQNP..P
Retrocopy IQQLDGSTFTSLTKLTTCELYTNPFNCSCELLGFVKWLSIFPNRTNERMVCDSPPGVSGYSLLSQNPNNP

Parental  TQRNALHVLSLVCTDDGSSVTPF--YILDSTTMSPD---CGLDDCASGIPPEDVT-NPSPTSSDPKLRMR
          T.RNALH.L..VCTDD...VTPF......STTM.PD...CG.D.C.SG..PED.T..........KL.M.
Retrocopy TYRNALHMLKTVCTDD--YVTPFISISIESTTMPPDSTLCGMDECPSGTEPEDITVSTTENEVQGKLKME

Parental  VKYVQHSSAVITVEIPHPYKKMYILMLYNNSFFTDIQNLKKQIEDVELKDLKPNTNYTYCVASIRNSLRF
          .K......A.IT..IP.PYKKMYIL.LYNNSFFTDIQNLK...ED.ELK.LKP..NYTYC..SIRNSLR.
Retrocopy LKEITKAGATITIQIPDPYKKMYILALYNNSFFTDIQNLKDKKEDIELKNLKPHINYTYCIVSIRNSLRH

Parental  NHTCLIVSTGRREGAEHLPNQFSATHYIMTIVGCLFGMLLFLGLIVHGLRKRKKMEEKEKKMSRIQRTLK
          NHTCLIVST..R.G.E...N...ATHYIMTI.GCLF.M..FLG.....LR.....EEK.KK.........
Retrocopy NHTCLIVSTNPRNGKERIVNPATATHYIMTILGCLFSMVIFLGVVYYCLRRKRQQEEKHKKEGSLKKNIM

Parental  ELKYGGEGDIEGGSGECVSQ-NLAGGDSMSRMPYLPQGAEIDPYKLQEVKETPGHKSAKLNYMDVRS
          ELKYG.E...EGG.....SQ..L..G.SM.RMPYLP...E...YK.QE..ETP..K..K.NYMDVRS
Retrocopy ELKYGQE--LEGGTISRMSQKQLLAGESMGRMPYLPSTGEMEQYKFQEISETP--KMIKGNYMDVRS

Legend:

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

Expression

RNA-Seq

Oryzias latipes was not studied using RNA-Seq expression data.

ChIP-Seq

Oryzias latipes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_olat_18 retrocopy.

TSS

Oryzias latipes was not studied using FANTOM5 data.

Lab

retro_olat_18 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_olat_18 has 3 orthologous retrocopies within teleost group .

Species	RetrogeneDB ID
Gasterosteus aculeatus	retro_gacu_19
Takifugu rubripes	retro_trub_13
Tetraodon nigroviridis	retro_tnig_5

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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,