RetrogeneDB ID: retro_xmac_1

Retrocopy location

• Organism: Platyfish (Xiphophorus maculatus)
• Coordinates: JH556672.1:3441066..3443412(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSXMAG00000019743
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: elfn1b
• Ensembl ID: ENSXMAG00000014093
• Aliases: None
• Description: extracellular leucine-rich repeat and fibronectin type III domain containing 1b [Source:ZFIN;Acc:ZDB-GENE-080327-21]

Sequence

>retro_xmac_1
ATGGCCTGTAGATCAGACGGGGTGATGAGTGCCTTGTTTTGGTCTATAACTCTTATATGTTTGACTCACATTGGCAGAGT
AAGTGGTGACTGCTGGTTGATTGAGGGAGAAAAGGGCTTTGTGTGGCTTGCAATTTGCAGCCAAAATCAACCACCCTACG
AAGCCATCCCACAGCATATCAATAACACCATTGTTGACCTTCGTCTGAATGAAAACAAAATCAAAAGTATCCATTTTTCT
TCTCTCAGTCGCTTTGCCAACTTGACCTACCTGAACCTGACCAAGAATGAGATCTCATACATAGAAGACGGAGCCTTTTC
TGCTCAGTTTAACTTGCAAGTTCTCCAAATGGGCTTCAACAAGTTACGAAACCTGACAGAGGGGATTCTCCGGGGTTTAG
GAAAACTGCAGTACCTCTACCTCCAGGCGAACCTGATTGAAACTGTGATACATAATGCCTTTTGGGAATGCCCCAACATA
GAAAATATTGATCTCTCCATGAACCGAATCCAACAGTTAGATGGGTCCACGTTTACCAGCCTAAGTAAGCTCACCACTTG
TGAGCTGTATACAAACCCTTTCAATTGCTCATGTGAGTTGCTGGGGTTTGTGAAATGGCTTTCGACTTTCCCAAACCGGA
CAAATGAGCGGATGGTCTGTGACTCTCCTCGTGGTGTTGCCGGTTACAGCTTACTGAGCCAGAATCCTAACAACCCCACA
TACCGAAATGCACTTCACATGCTAACAACTGTGTGTACCGATGACTACGTGACCCCATTTATTACTGTCTCTATGGAGTC
CACAACACTACCACCTGACTCAACACTTTGTGGGCTGGAAGACTGTTCCTCAGGCACAGAACCAGATGACACAACCATTG
GTACAACTGAAAACGAGGTGCAGGGAACCCCTGTGATGAATCTAAAGGCAGTAACAAACACAGTTGCTACCGTTACAGTT
CAGTTTCCTGATCCCTTCAAGAAGCTGTATTTTCTGGTTCTTTACAACAACAACTTTTTCACAAACCTGGACAGGCTCTA
TAAAGTACAGGAAGATGTTGAGATTAAAAACCTTCAACCCCACTCCAACTACACAGTCTGTGTTACTTCAGAACGCAATT
CCCTTAAACAAAATCACACATGTCTGACATTCTCCACTGGCCCTTGGAATGGAAAAGACAGAGATGTAAACAATGCAACT
GCTACTCATTATATTATGACTATTTTGGGCTGCCTTTTTAGCATGGTGATTTTTCTGGGAATTGTGTATTATTGTTTGCG
AAGGAAGCGTCAACAAGATGAAAAGCAAAGAAAATCAGGAAGTCTTAAGAAAAACATAATGGAACTCAAGTATGGACAAG
AACTAGAAGGAGGGACTATTTCTCGAATGTCACAGAAGCAGCTGCTGGCTGGAGAGAACATGGCCCGTATGCCCTACCTG
CCATCTGCAAGTGAAATTGAACAGTACAAGTTTCAAGAGATAAGTGAGACTCCAAAAATGATGAAGGGGAACTACATGGA
TGTCCGGAGCATGGATCATCATGAGCGCAGAGAGTGTGATATGGGAATGGCTGGGAACAGTCAAGGATCAGTGGCAGAGA
TTTCCACAATTGCAAAAGAAGTTGATAAAGTCAATCAGATAATAAACAACTGTATAGATGCCCTAAAATCAGAATCAACT
TCTTTTCAAGGAGTTAAATCTGGAGCAGTGTCGACAGCAGAGCCCCAACTGGTGCTAATATCAGAGCACCCCCAAAGTAA
CCCTGGCCTTCTTTCCCCAGTGTATAAGGACAGCTACCATCACTCTCTTCAGAGGCATAGAAGCTCTGATGTCTCGCCAA
AGAGGCCCAGCACTGCCACAGGTGGGCCCATGCGAAGCCCAAGGCCTTATCGCTCCGACTCCAAGTACATAGAGAAAACC
TCCCCAACAGGAGAGAGCATCCTTACAGTAACACCTGCTGCAGCCATCTTGAGGGCGGAGGCAGATAAGATCCGCCAGTA
TAGTGACCACCGGCATTCATATCCCGATGCTCAGATAGAGGAGCTGGAAGGACCTGATAGCCACAAGCTGTTGGAACCCC
TTACGCACTCCCGGTCCAGAGACTTAGCCTACTCCCAGATGTCCTCGCAGTATCACAATCTAAGCTACTCATCCAGCCCT
GAATACTATTGCAAACCTTCACACAGCATCTGGGAGCGATTCAGACTCCACCGCAAGCGACATAAAGATGAGGAGTACAT
GGCTGCCGGCCATGCTCTGCGTAAGAAAGTTCAGTTTGCAAAGGATGAGGACCTGCATGACATATTAGACTACTGGAAAG
GCGTTTCAGCCCAACATAAATCATAA

Alignment

ORF - retro_xmac_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.43 %
• Parental protein coverage: 64.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LALLSLLRLPAVTADCWLIEGEKGFVWLAICSMNQPPYEAIPSHINSTIVDLRLNENKIRSVHYSSLSRF
          ..L..L.....V..DCWLIEGEKGFVWLAICS.NQPPYEAIP.HIN.TIVDLRLNENKI.S.H.SSLSRF
Retrocopy ITLICLTHIGRVSGDCWLIEGEKGFVWLAICSQNQPPYEAIPQHINNTIVDLRLNENKIKSIHFSSLSRF

Parental  GNLTYLNLTKNDISYVEDGAFSAQFNLQVLQMGFNKLRNLTEGMLRGLGKLQYLYLQANLIETVTTNTFW
          .NLTYLNLTKN.ISY.EDGAFSAQFNLQVLQMGFNKLRNLTEG.LRGLGKLQYLYLQANLIETV..N.FW
Retrocopy ANLTYLNLTKNEISYIEDGAFSAQFNLQVLQMGFNKLRNLTEGILRGLGKLQYLYLQANLIETVIHNAFW

Parental  ECPNLENIDLSMNRIQVLDGSLFSGLSKLTTCELYTNPFNCSCELLGFLRWLAVFPNRTSERMVCDSPQG
          ECPN.ENIDLSMNRIQ.LDGS.F..LSKLTTCELYTNPFNCSCELLGF..WL..FPNRT.ERMVCDSP.G
Retrocopy ECPNIENIDLSMNRIQQLDGSTFTSLSKLTTCELYTNPFNCSCELLGFVKWLSTFPNRTNERMVCDSPRG

Parental  FSGYNLLSQNPRMPAQRNALHVLNLVCTDDGSSVTPFY-IFDSTTQLPDIASPCGLDDCASGTAPEE-VI
          ..GY.LLSQNP..P..RNALH.L..VCTDD...VTPF.......T.LP.....CGL.DC.SGT.P....I
Retrocopy VAGYSLLSQNPNNPTYRNALHMLTTVCTDD--YVTPFITVSMESTTLPPDSTLCGLEDCSSGTEPDDTTI

Parental  SNSPNLIDSKPVMTIKKVEHSSAVITVQIPYLFKKLYILILYNNSFFTEIKTLNKNSEDIELKNLTPNTD
          ....N.....PVM..K.V....A..TVQ.P..FKKLY.L.LYNN.FFT....L.K..ED.E.KNL.P...
Retrocopy GTTENEVQGTPVMNLKAVTNTVATVTVQFPDPFKKLYFLVLYNNNFFTNLDRLYKVQEDVEIKNLQPHSN

Parental  YTYCVASTRYSLRFNHTCLTFSTGRRAGADRIRNQSSATHYIMTILGCLFGMLLFLGLVVHCLRKKRIME
          YT.CV.S.R.SL..NHTCLTFSTG...G.DR..N...ATHYIMTILGCLF.M..FLG.V..CLR.KR...
Retrocopy YTVCVTSERNSLKQNHTCLTFSTGPWNGKDRDVNNATATHYIMTILGCLFSMVIFLGIVYYCLRRKRQQD

Parental  EKERKMNRIQRTLIELKYGGEGDIEGGSGGSVSQK-LAVGESLSRMPYLPQGGEIDPYKLQEVIETPGHK
          EK.RK.........ELKYG.E...EGG.....SQK.L..GE...RMPYLP...EI..YK.QE..ETP..K
Retrocopy EKQRKSGSLKKNIMELKYGQE--LEGGTISRMSQKQLLAGENMARMPYLPSASEIEQYKFQEISETP--K

Parental  SAKLNYMEVRGSGIEKEREREREREMSPQANPQGSVAEISTIAKEVDKVNQIINNCIDALKSESTSFQQG
          ..K.NYM.VR...........RE..M....N.QGSVAEISTIAKEVDKVNQIINNCIDALKSESTSF.QG
Retrocopy MMKGNYMDVR----SMDHHERRECDMGMAGNSQGSVAEISTIAKEVDKVNQIINNCIDALKSESTSF-QG

Parental  IKS
          .KS
Retrocopy VKS

Legend:

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

Expression

RNA-Seq

Xiphophorus maculatus was not studied using RNA-Seq expression data.

ChIP-Seq

Xiphophorus maculatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xmac_1 retrocopy.

TSS

Xiphophorus maculatus was not studied using FANTOM5 data.

Lab

retro_xmac_1 was not experimentally validated.

Homology

Retrocopy orthology:

Xiphophorus maculatus 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.

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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 ,