RetrogeneDB ID: retro_lcha_83

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH127437.1:44382..46785(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLACG00000011124
• Aliases: None
• Description: None

Sequence

>retro_lcha_83
GTGAACTTCACAGTAAACCAGATCCATGAGATCATGGACAAAAGGTCCAACATCCATAACATGTCTGTGATTGCTCATGT
TGATCATGGCAAATCCACCATGACCAACTCACTGGTGAGCAAAGCTGGTATTATTGCCTCTGCCCGTGCTGGTGAAACCT
GCTTCACAGACATAAGAAAAGACAAACAAGAATGATGCATCACTATCAAATCAACTGCTATCTCTATGTACTACGAGCTC
ACTGAAAACAACTTGGCATTCATCAAACAGACCAAAGACGGTGTTGGCTTCCTCATTGACCTGATTGACTCCCCTGGGCA
CGTTGATTTTTCCTCTGAAGTACCAGCTGCACTCTGTGTCCCTGATGGTGCCTTGGTGATTATGGATTGTGTCTCAGGTG
TGTGCATGCAGACTGAGACTGTGCTGCATCAGGCTATCGTTGAGCATATCAAACCCATGCTGATGATGAACAAGATGGAC
CAAATTCTTCTGAAGCTGCAGCTTTGACCCAGAGGAGCTGTACCAGACCTTCCAGCATATCATGAAGAACGTCAACATCG
TCATCTCCACCTATGGCGAGGATGAAAATGGACCAATGGGAAACAACATGGTTGACCCAATGGTGGGTACAGTCGGTTTT
GGATCTGGTGTGCATGGATGGACTTTTACCCTGAAGCAGCTTGCTGGGATCTTACATTGCCAAGTTAAGTTTGCTGCTAA
GGGTGATTCCCAGCTCAGCTCTGCTGATAGATCCAAGAAAGTAGAAGACATGATGAAGAAGCTCTGGGGAGACCGATACT
TTGATCCATCTGCTGGCAAGTTCAGCAAAGTGGCACTAGCCCTGATGGCAGAAAACTTCCTCAGACTTTCTGTCAGCTCA
TTTTGGACCCAATCTTTAAGATATTTGATGCCATCATGAACTTCAAGAGGGAAGAGACAGCTAATCTGATTGAGAAACTG
GACATTAAGCTGGATAATGATGATAAGGACAAGGCAGGCAAACTCCTGCTGAAGGCTGTTATGTGCTGCTGGATCCCTGC
TGGCGAAGTTCTTCTTCAGCTGATTGCAATCCACTAGCCTTCTCCTGTTACAGCACAGAAATACCATTGCAAATTTCTGT
ATGAAGGCCCGGCTGATGCTTCTGCTGGTGCTCTGGGTGTCCGCAACTGTGACCCTAAGGGACCTCTTGCGATGTACGTC
TCTAAAATAGTGCCAACTTCTGATAAGAGCTGCTTCTACACTTTTGGTCGTGTCTTTTCTGGTATTGTGTCTACTGGCCT
AAAGGTCAGAATTATGGGACCAAACTACACTCCTGGCAAAAAGGAAGACTTATACCTCAAACCCATCCAGAGAACCATTT
TGATGATGGACCATTACATGGACTCATTGAAGACGTGCCTTGTGGTAACACTGTTGGCCTGGTTGGTGTCAACCAGTACC
TGGTGAAAACTGGCACCACCACCACCTATGAGCATGCCCACAACCTGAGGGTGATGAAGCTCAGTGTCAGCCCTGTTGTG
CATGTCACTGTTGAGGCCAAGAACCCAGCTGACCTCCCTAAACTGGTGGAGGGTCAGAAGTGTCTGGCAAAGTCTGACCC
TATGGCTCACTGTATCATTGAAGAGTCTAGAGAGCACATCATTTCTGGTGCTGGGGAGCTACATCTGGAGATCTGTCTGA
AAGATTTGGAGAAAGATCACGCCTGCATCCCTCTCAAGAAATCAGATCCTGTTGTGTCGTACTGTGAGACTATTTCAGAG
GAGTTGGAGCAGATTTATTTGTCCAAGTCTCCCAACAAGCACAACAGGCTGTACATGAAGGCCCGTCCCTTCCCAGATGG
TCTCACTGAAGATATTGGTAAGGATGAGTTCATGGTTTGTCAAGAGCTGAAACTCTGAGCTCGCTACCTGGCAGAAAAGA
ATGAGTGGGACATTACCGAAGCCCATAAGATCTGGTGCTTTGGACTGGATGGAACTGGTCCAAACATCTTAGTAGATGTC
ACCAAGGGGGTACAGTACCTGAATGAAATCAAGGACAGTGTGGTTGCTGGCTTCCAGTGGGCAACCAAAGAAGGCATGCT
GTATGAGAAGAACCTGTGTGCAGTCCATTTTGATATGTGTGATGTCACTCTGCACACAGATGTCACCCACAGAGGTGGCG
GCCAGATCATTCAGACTGCCAGAAGGTTAAAATGCCTGCCTGCTGACTGCAAAGCTTAGGCTCATGGAGCCAATGCTCTT
GGTTGAAATTCAGTGTCCAGAGCAGGTGGTTGGTGGAATCTGTGGCGTGCTGAACAGGAAACATGGGCATGTCTTTGAGG
AGTCCCAGATTGCTGACACACCCATGTTTGTAATTAATGCCTGCTTGCCTGTAGATGAATCTTTTGGTTTCACAGCTGAC
TTG

Alignment

ORF - retro_lcha_83 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.14 %
• Parental protein coverage: 93.12 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VNFTVNQIREIMDKKSNIRNMSVIAHVDHGKSTLTDSLVSKAGIIASARAGETRFTDTRKDEQERCITIK
          VNFTVNQI.EIMDK.SNI.NMSVIAHVDHGKST.T.SLVSKAGIIASARAGET.FTD.RKD.QE.CITIK
Retrocopy VNFTVNQIHEIMDKRSNIHNMSVIAHVDHGKSTMTNSLVSKAGIIASARAGETCFTDIRKDKQE*CITIK

Parental  STAISMYYELSEADLAFIKQTKDGYGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVSGVCVQTET
          STAISMYYEL.E..LAFIKQTKDG.GFLI.LIDSPGHVDFSSEV.AAL.V.DGALV..DCVSGVC.QTET
Retrocopy STAISMYYELTENNLAFIKQTKDGVGFLIDLIDSPGHVDFSSEVPAALCVPDGALVIMDCVSGVCMQTET

Parental  VLRQAIAERIKPVLMMNKMDRALLELQL-DPEELYQTFQRIVENVNVIISTYGEDENGPMGNIMVDPMIG
          VL.QAI.E.IKP.LMMNKMD..LL.LQL.DPEELYQTFQ.I..NVN..ISTYGEDENGPMGN.MVDPM.G
Retrocopy VLHQAIVEHIKPMLMMNKMDQILLKLQL>DPEELYQTFQHIMKNVNIVISTYGEDENGPMGNNMVDPMVG

Parental  TVGFGSGLHGWAFTLKQFAEMY--VAKFAAKGDSQLSAADRCKKVEDMMKKLWGDRYFDPSAGKFSK-SA
          TVGFGSG.HGW.FTLKQ.A.......KFAAKGDSQLS.ADR.KKVEDMMKKLWGDRYFDPSAGKFSK.S.
Retrocopy TVGFGSGVHGWTFTLKQLAGILHCQVKFAAKGDSQLSSADRSKKVEDMMKKLWGDRYFDPSAGKFSK<SG

Parental  TSPDGRKLPRTFSQLILDPIFKIFDAIMNFKKEETAKLIEKLDIKLDSDDKDKEGKPLLKAVMRRWLPAG
          TSPDGRKLP.TF.QLILDPIFKIFDAIMNFK.EETA.LIEKLDIKLD.DDKDK.GK.LLKAVM..W.PAG
Retrocopy TSPDGRKLPQTFCQLILDPIFKIFDAIMNFKREETANLIEKLDIKLDNDDKDKAGKLLLKAVMCCWIPAG

Parental  EALLQMIAIHLPSPVTAQKYRCELLYEGPSDDDA-ALGIRNCDPKGPLVMYISKMVPTTDKGRFYAFGRV
          E.LLQ.IAIH.PSPVTAQKY.C..LYEGP.D..A.ALG.RNCDPKGPL.MY.SK.VPT.DK..FY.FGRV
Retrocopy EVLLQLIAIH*PSPVTAQKYHCKFLYEGPADASAGALGVRNCDPKGPLAMYVSKIVPTSDKSCFYTFGRV

Parental  FSGVVSTGLKVRIMGPNYTPGKKEDLYLKPIQRTILMMGRYVEP-IEDVPCGNIVGLVGVDQFLVKTGTI
          FSG.VSTGLKVRIMGPNYTPGKKEDLYLKPIQRTILMM..Y....IEDVPCGN.VGLVGV.Q.LVKTGT.
Retrocopy FSGIVSTGLKVRIMGPNYTPGKKEDLYLKPIQRTILMMDHYMDS<IEDVPCGNTVGLVGVNQYLVKTGTT

Parental  TTYEHAHNLRVMKFSVSPVVRVAVEAKNPGDLPKLVEGLKRLAKSDPMVQCIIEESGEHIIAGAGELHLE
          TTYEHAHNLRVMK.SVSPVV.V.VEAKNP.DLPKLVEG.K.LAKSDPM..CIIEES.EHII.GAGELHLE
Retrocopy TTYEHAHNLRVMKLSVSPVVHVTVEAKNPADLPKLVEGQKCLAKSDPMAHCIIEESREHIISGAGELHLE

Parental  ICLKDLEEDHACIPLKKSDPVVSYRETVSEESQQLCLSKSPNKHNRLYMKARPFPDGLAEDIDKGEVAAR
          ICLKDLE.DHACIPLKKSDPVVSY.ET.SEE..Q..LSKSPNKHNRLYMKARPFPDGL.EDI.K.E....
Retrocopy ICLKDLEKDHACIPLKKSDPVVSYCETISEELEQIYLSKSPNKHNRLYMKARPFPDGLTEDIGKDEFMVC

Parental  QELKLRARYLAEKYEWDVTEARKIWCFGPDGTGPNVLVDVTKGVQYLNEIKDSMIAGFQWATKEGVLCEE
          QELKL.ARYLAEK.EWD.TEA.KIWCFG.DGTGPN.LVDVTKGVQYLNEIKDS..AGFQWATKEG.L.E.
Retrocopy QELKL*ARYLAEKNEWDITEAHKIWCFGLDGTGPNILVDVTKGVQYLNEIKDSVVAGFQWATKEGMLYEK

Parental  NLRAVRFDVHDVTLHTDAIHRGGGQIIPTARRCLY-ACLLTASPRLMEPIYLVEIQCPEQVVGGIYGVLN
          NL.AV.FD..DVTLHTD..HR.GG..I....R.L..ACLLTA..RLMEP..LVEIQCPEQVVGGI.GVLN
Retrocopy NLCAVHFDMCDVTLHTDVTHR-GGGQIIQTARRLK>ACLLTAKLRLMEPMLLVEIQCPEQVVGGICGVLN

Parental  RKRGHVFEESQVTGTPMFVVKAYLPVNESFGFTADL
          RK.GHVFEESQ...TPMFV..A.LPV.ESFGFTADL
Retrocopy RKHGHVFEESQIADTPMFVINACLPVDESFGFTADL

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	884.19 RPM
DRP000627_kidney	0.00 RPM	755.03 RPM
DRP000627_pectoral_fin	0.00 RPM	1916.19 RPM
DRP000627_pelvic_fin	0.02 RPM	2833.29 RPM
DRP000627_pharynx	0.00 RPM	125.98 RPM
DRP000627_tail_muscle	0.00 RPM	106.12 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_83 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004258	2 retrocopies	retro_btau_1809, retro_btau_539,
Canis familiaris	ENSCAFG00000019158	1 retrocopy	retro_cfam_1503,
Latimeria chalumnae	ENSLACG00000011124	1 retrocopy	retro_lcha_83 ,
Macaca mulatta	ENSMMUG00000022767	1 retrocopy	retro_mmul_2026,
Monodelphis domestica	ENSMODG00000000750	1 retrocopy	retro_mdom_223,
Mus musculus	ENSMUSG00000034994	1 retrocopy	retro_mmus_2521,