RetrogeneDB ID: retro_lcha_68

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH127181.1:222210..224317(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLACG00000003023
• Aliases: None
• Description: None

Sequence

>retro_lcha_68
GGGCACTGTTTCTCCACAACCTATTATGATATTACAACAAAGGCAGGAGTTAAATTAACATGTACTTGGCTTTGTTACTC
CAAGCTTGACAGTGCATATTGCGAGCCATGTTGGTTGTTTGCTGATCGTAGTGCACCTATATATAATGTGGCATGGGTTA
GAGGAGTTCAAGACTGGCATCACTTAAGCAGCAAAGTTTAATATCATGAAACATCAAAAATACATTTAGGTTCTTGTTTA
ATGTATGAGCAGTGGCAATTACATGGAACAATCGATGAAGATTTCGAAACTCAAATACAAAAGGAGAAAAACTTCTGGAG
GCAAGTTTTGGAATGTTTAATCAATGTGACTCTTACATTATCAATGTGCAATTTAGCTTTCAGGGGGCACAGAGAGGTTT
TAGGGCATGCTAATAGCGGGAATTTTCTTTCAATTGTGGAACTGTTAGCTAAGTATGATCCAGTGTTGAAGCAAGTCATT
TCTGTGCCCAGTGGTTCAATTCTGTACCTTAGTCATACTATACAGGATGAACTCATTGAAATTTTGTCGAAGCATATTGA
GGGAAATATTGTTGAAGAAATAAAGGCTGCACCTTTATTCTCTATAATAATGGATACCACCCAAGATATTTTGAAGACTG
ACCAATTGAATCAAATTTTTCGATATGTAACAATTGAAATGGATGAAAGGAATGTGGCTACTGGAGTGAAAATCAATGAA
TCTTTTCTGGGTTTTCAGGAAATTTGTGATCAGTCCTCCAGTGGACTTGAGAAGAAAATAATCAGCTGCATTGAACAGAA
AGGTTTAGATATATCTAAGTGTCATGGGCAGGGGTATGATGGGGCCTCTAATATGAGCGGTGTGTACTCAGGTGTGCAAG
AAAGAATATCCAAGAAGGAACTGAATGCTGAATATGTACATTGTGCTGCTCACAACTTAAATCTTACAATGACTGATTCT
GTTAGAGGAATACCAGAAGTGAAGCATTTTTGTGATGCGATTGAAACACTGTACACTTTTTTGGGCCACAACATAAAATG
CTGCGCCATGTTATCTTCATTAGCTTCTACTTCAGAGCTTTCCAGCAACATTACTTTGAAAAGGCTTTGCCCTACCCAAT
GGTCGTCCCGGTATGAATCACTCCTTGCTCTCAGGTTTCGGTATTTGGATATAATGAAGGCACTCACAAAAATAGTTCTT
CTGAGCAAAAAATGCTGATGAACACTGTGAGGCTTCAGCATCAAAGAAATTAATGGAAAATTTAAATTTTGTTTTTCTTT
TTGTGCTCCAAACAAAGATTCTAGAAGTGGTAAATGCTGTCTCAAAACTGCTGCAATCCAAAGACACAGACCTTTACAAA
GCAGAAAAATTACTTTGCAAAGCTACTGAAGATCTAGCTATGTTTCAAAATAATTTCAAAGAAGCCAAAAATTCAGGAAT
TAAATTATCAGAAAAATGGGGTGGACAAACCAAGTTTGAAGAAAAGCGCGTGAGGAAGGTGAAACGCCATTTTGACAAGC
TATGTGAAGATGAAAGACTTGCCAACTCAGAAAGTTTTTTCAAAGTGAATGTGTTTTATAGGTGTCTCAAAATAATAAAT
GCATAGCTTACCAATCGCTTTCAAAGCTTACAGGCAGTTGCTGATAAATTCAGTGTCATTCAGCCAAATATGCTCATTTC
TGCAAGTGATGAGGATCTGTATAAAGAAGCTGAAAAACTGGCCAATCATTTCAACAAAGACATTTCTCCTGTTTTTCCTG
GACAGTTGCTTTCATTCAGATCTTGTTTGAAATCTGAAATCTCTAAACAATCATTAGTGAAAGATTTGGCAAACATGTTA
ATTGTTGACAATAATGCATTAGCATCCAGTTTTTCAGAAGTTTGTACTGTACTTCTGCTGTTTCTCACCATCCCAGTAAC
AGTAGCAAGTGCTGAATGCTCATTTTCAAAACTAAAACTAATAAAGAACTATGTAAGGAGTACTATGGGACAAGAGAGAC
TTAGTGGATTGGGAATGTTATCCATTGAAAATGAGTGAGCCAGAAAAATTAAACTACAGCAGATAATTGATGAGTTTGCA
GAACGAAAGGCACACAAAATGCGATTC

Alignment

ORF - retro_lcha_68 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.93 %
• Parental protein coverage: 99.57 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GRCFSITYYDITTKAGVKLMCTWLCYSPKLDSAYCEPCWLFADCSAPAYNVAWVRGVRDWCHLSSKIEYH
          G.CFS.TYYDITTKAGVKL.CTWLCYS.KLDSAYCEPCWLFAD.SAP.YNVAWVRGV.DW.HLSSK..YH
Retrocopy GHCFSTTYYDITTKAGVKLTCTWLCYS-KLDSAYCEPCWLFADRSAPIYNVAWVRGVQDWHHLSSKV*YH

Parental  ETSKIHLDSCLVYEQWRLHGTIDEDFETQIQKEKNFWRQVLECLINVTFTLSMCNLAFRGHREVLGHANS
          ETSKIHL.SCL.YEQW.LHGTIDEDFETQIQKEKNFWRQVLECLINVT.TLSMCNLAFRGHREVLGHANS
Retrocopy ETSKIHLGSCLMYEQWQLHGTIDEDFETQIQKEKNFWRQVLECLINVTLTLSMCNLAFRGHREVLGHANS

Parental  GNFLSIVELLAMYDPMLKQVISMPSGSILYLSHNIQDELIEILSKHIEGNIVEEIKAAPFFSIIVDTTQD
          GNFLSIVELLA.YDP.LKQVIS.PSGSILYLSH.IQDELIEILSKHIEGNIVEEIKAAP.FSII.DTTQD
Retrocopy GNFLSIVELLAKYDPVLKQVISVPSGSILYLSHTIQDELIEILSKHIEGNIVEEIKAAPLFSIIMDTTQD

Parental  ILKTDQLNQIFQYVTIETDERNVAIGVKINESFLGFQEICDQSSSGLEKKIISCIEQKGLDISKCRGQGY
          ILKTDQLNQIF.YVTIE.DERNVA.GVKINESFLGFQEICDQSSSGLEKKIISCIEQKGLDISKC.GQGY
Retrocopy ILKTDQLNQIFRYVTIEMDERNVATGVKINESFLGFQEICDQSSSGLEKKIISCIEQKGLDISKCHGQGY

Parental  DGASNMSGMYSGVQARISKKEPNAEYVHCAAHNFNLTMNDSVRGIPEVKYFYDVIETLYTFFGHSIKCWT
          DGASNMSG.YSGVQ.RISKKE.NAEYVHCAAHN.NLTM.DSVRGIPEVK.F.D.IETLYTF.GH.IKC..
Retrocopy DGASNMSGVYSGVQERISKKELNAEYVHCAAHNLNLTMTDSVRGIPEVKHFCDAIETLYTFLGHNIKCCA

Parental  MLSSFASTSELSSNLTLKRLCPTRWSSQYESLLALRFRYLDIMKALTKIVLLS-KNADEHCEASALKKLM
          MLSS.ASTSELSSN.TLKRLCPT.WSS.YESLLALRFRYLDIMKALTKIVLLS.KNADEHCEASA.KKLM
Retrocopy MLSSLASTSELSSNITLKRLCPTQWSSRYESLLALRFRYLDIMKALTKIVLLS>KNADEHCEASASKKLM

Parental  ENLNFVFL-VLQTKILEVVNAVSKLLQSKDTDLYKAAKLLCKVTEDLAMFQNNFKEAKSSAIKLLEKWGG
          ENLNFVFL.VLQTKILEVVNAVSKLLQSKDTDLYKA.KLLCK.TEDLAMFQNNFKEAK.S.IKL.EKWGG
Retrocopy ENLNFVFLFVLQTKILEVVNAVSKLLQSKDTDLYKAEKLLCKATEDLAMFQNNFKEAKNSGIKLSEKWGG

Parental  QTKFEEKRVRKVKRHFDELCEDERLANSESFFKVNVFYRCLNKL----TNHFQSLQAVADKFSVIQPNML
          QTKFEEKRVRKVKRHFD.LCEDERLANSESFFKVNVFYRCL.......TN.FQSLQAVADKFSVIQPNML
Retrocopy QTKFEEKRVRKVKRHFDKLCEDERLANSESFFKVNVFYRCLKIINA*LTNRFQSLQAVADKFSVIQPNML

Parental  ISASDEDLYKEAEKLANHFNKDISLVFPGQLLSFSFCLKSEISKQSLVKDLANMLIVD-NALASSFSDVC
          ISASDEDLYKEAEKLANHFNKDIS.VFPGQLLSF..CLKSEISKQSLVKDLANMLIVD.NALASSFS.VC
Retrocopy ISASDEDLYKEAEKLANHFNKDISPVFPGQLLSFRSCLKSEISKQSLVKDLANMLIVDNNALASSFSEVC

Parental  TVLLLFLTIPVTVASAERSFSKLKLIKNYPRSTTGQERLCGLGMLSIENDWIGMVDVYKITSDIADTNAC
          TVLLLFLTIPVTVASAE.SFSKLKLIKNY.RST.GQERL.GLGMLSIEN..........I....A...A.
Retrocopy TVLLLFLTIPVTVASAECSFSKLKLIKNYVRSTMGQERLSGLGMLSIENE*ARKIKLQQIIDEFAERKAH

Parental  KMFF
          KM.F
Retrocopy KMRF

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
DRP000627_gill	0.00 RPM	0.02 RPM
DRP000627_kidney	0.00 RPM	0.00 RPM
DRP000627_pectoral_fin	0.00 RPM	0.00 RPM
DRP000627_pelvic_fin	0.00 RPM	0.00 RPM
DRP000627_pharynx	0.00 RPM	0.00 RPM
DRP000627_tail_muscle	0.02 RPM	0.00 RPM

ChIP-Seq

Latimeria chalumnae was not studied using ChIP-Seq data.

EST

Latimeria chalumnae was not studied using EST data.

TSS

Latimeria chalumnae was not studied using FANTOM5 data.

Lab

retro_lcha_68 was not experimentally validated.

Homology

Retrocopy orthology:

Latimeria chalumnae 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Latimeria chalumnae	ENSLACG00000003023	2 retrocopies	retro_lcha_120, retro_lcha_68 ,
Latimeria chalumnae	ENSLACG00000007580	1 retrocopy	retro_lcha_84,