RetrogeneDB ID: retro_lcha_52

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH126973.1:37154..39067(-)
• Located in intron of: ENSLACG00000000959

Retrocopy information

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

Parental gene information

• Parental gene symbol: CXORF57
• Ensembl ID: ENSLACG00000010847
• Aliases: None
• Description: None

Sequence

>retro_lcha_52
AGTCAGAGGGTCATGGGTTCAAGTGTCCTGGCACCCCGGCCTTCTGCTTTACCATCTCAGCCCTGTGCCCTGGCATACAT
CTTACAGAGGGCCAATTCTGCGGTCGGGCTGAGTTATCTCCATAGACCACCCTGACTTTGTGGTTGTGGTGGCTATCGAG
AGGTGGTTACTTGAATCTCAGGGTAAACCAGATGGCCACTGCCCCCCGGCTCCTTGGTACTGCTATGATGTGACCCTCAC
CGACGGGGATTCATAGATAAAATGCCACTTTGCAGCTGAACTGAATTACCTGGTTCAGAAGAACATGCTGCGGTCTGGGC
GGGAGATACAAATCCAGCAGTGCTCTATTCGCTATGATGAGAAGAGATTGGGGGCCAAGGGGCTCTACATCCAGAAGGTG
GAATTGGGGGAGGATTTCTCCCCCCTCCTGTGGGACATAGTGAGCGGCGGCTTCCTGCCCTTGGAGGTATATCTGAAAGA
CATGCAGAACTATTACCTCTGTCTGTGGAATAGCGAGGATCCGTTTGGAGAAATGTGGAATGAAGAGGTGCAGTCCAAAT
TTAATGGGAACGTTTCCAAAGTGATCTCCCTCTCTACTTTGAATACGATGCAGAACGTATGCAACTGGCCGCTGCTGCTG
GGTAGAATAATGTTCAAATCCAGACTCCACTTCTTTGGGAAACCTGAGAAAAGGCTAATGATGCCTTACTAGGTGTATTT
GGAAGTAGCAGATCATTCAGGGATGATGTCGATGACACTGTGGGACTCTCTCTGCCCCAAGTGATACCAGACCCTGTATG
TTGGCACAGTGGTAATGCTTCAGGAGTATGTGGTCAAACCCAGCTTCCAATGGAGAACCAAACCCGTGTTTGCTGATTCA
GGAATTAGAAAATTTACATCATCAGGTATTAACCTGAACCCATGTGACCCCACTGCTTGTATCACTGTTATTCCTGAAGA
TGCAGTGAAGCTGAAATGGAGATTACCCCAAATAAAGTATCGCTTTATCACAAGGGCAGAGCTGGGCCACCTGCTGCACT
GTACTACTTGTGATGTGATTGGCTACGTCACCTTTGTGGGCAGGAGTAAACGACTTCGAGAGAGAAAGGAGGGCGAGGAT
TTCTGGGTGCATTGTTAGGTTCATGCTGTCGATAGAACCACAGAAGAACCGATTGTACTAGAGATCTTTGCAACTTCCCA
GCCCGAGATCTTTAATCGTATTCATCCACTGACGTACATTGTCTGCACCCAAATGAGAGTCATGCAGGCCAATCCCAAGA
CAGCACCCTACAAGTCTTACCTCACCACCTCCAATGAAAGTCAAATATTCATCACTGGTCAACACAGGGGTCAGCCATAC
ACAGTGCACCCCCGAGTCAGGGCCTTCGCTCAGTGGATGAACAGTACGTATACTGGAAAGGAATAGGACTGCCTGCAGAG
ATGTGTGATTGGAGGCCATTATTCCTACCCCCAATCCCTCCTACCTTATCGCTTTACTGGAAAATGGGAGCAACTTCATT
CGGTGGCAAGGAACAGACAGCGACAAATGAGCTGACAAAAGAAATGAGCAATCTTCACTACAGAGACCTCAGGCGTGTTG
CTGTACAGGGCATCATCATGGCTGTACGCTATGTTAGTCTCTCCCATGCACCCAAAGACACCGCTAATGTTGAGCTGATG
GAGGAAGGAGTTTTGGAGCCCACAGTCTTTCAGAATACAAGATCCATGGAGAAAAATAAAAGATGCTTCACAAAGGAGCA
GCTTCAGCAGGCATACTCCCAGCTCCTTCAGGATAAAGAGACCCCCCCACCCTATGTGGTTCAGTTGACCCCCAGATGAT
GTCATCTTCTCCCCTTACAAAGACCCCAAGACTCAACCAAAGAGTTCAATATCCTTATGCTTCAAAGGAGAAA

Alignment

ORF - retro_lcha_52 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.22 %
• Parental protein coverage: 74.59 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SAPVPRDSAPLPQPSPPAPQPSALAYILQRANSVVGVN-ISIDHPGFVAVVAIERWLLESQGKPGGRCPP
          S..V...S...P.PS....QP.ALAYILQRANS.VG...ISIDHP.FV.VVAIERWLLESQGKP.G.CPP
Retrocopy SQRVMGSSVLAPRPSALPSQPCALAYILQRANSAVGLS>ISIDHPDFVVVVAIERWLLESQGKPDGHCPP

Parental  APWYCYDVTLTDRDSQIKCHLAAELNYLVQKNILRPGREIQIQQCSIRYDEKRLGAKGLYIQKVELGEDF
          APWYCYDVTLTD.DS.IKCH.AAELNYLVQKN.LR.GREIQIQQCSIRYDEKRLGAKGLYIQKVELGEDF
Retrocopy APWYCYDVTLTDGDS*IKCHFAAELNYLVQKNMLRSGREIQIQQCSIRYDEKRLGAKGLYIQKVELGEDF

Parental  SCLLRDMASSGFPPLEVYLKDTQDFYLPLWNSEDPFGEMWNEEVQSEFNGNVSKVISLSTLNMMHNVWNW
          S.LL.D..S.GF.PLEVYLKD.Q..YL.LWNSEDPFGEMWNEEVQS.FNGNVSKVISLSTLN.M.NV.NW
Retrocopy SPLLWDIVSGGFLPLEVYLKDMQNYYLCLWNSEDPFGEMWNEEVQSKFNGNVSKVISLSTLNTMQNVCNW

Parental  PPLLVRIMFKSRLHYFGKPEKRLAMPYQVYLEVADHSGTMSVILWDCLCSKWYQTLHVGTVVMLQEYVVK
          P.LL.RIMFKSRLH.FGKPEKRL.MPY.VYLEVADHSG.MS..LWD.LC.K.YQTL.VGTVVMLQEYVVK
Retrocopy PLLLGRIMFKSRLHFFGKPEKRLMMPY*VYLEVADHSGMMSMTLWDSLCPK*YQTLYVGTVVMLQEYVVK

Parental  PSFKWRTKPVFADSGIRKFTSLDINLNPCDPTACITVIPEDAVKPEWRLPQIKYRFITRAELDHLPHTTT
          PSF.WRTKPVFADSGIRKFTS..INLNPCDPTACITVIPEDAVK..WRLPQIKYRFITRAEL.HL.H.TT
Retrocopy PSFQWRTKPVFADSGIRKFTSSGINLNPCDPTACITVIPEDAVKLKWRLPQIKYRFITRAELGHLLHCTT

Parental  CDVIGYVTFVGRSERLRKRKEGEDFWVYRWVHAVDGTTEEPIVLEIFATSQPEVFNRIHPLTYIVCTQMR
          CDVIGYVTFVGRS.RLR.RKEGEDFWV...VHAVD.TTEEPIVLEIFATSQPE.FNRIHPLTYIVCTQMR
Retrocopy CDVIGYVTFVGRSKRLRERKEGEDFWVHC*VHAVDRTTEEPIVLEIFATSQPEIFNRIHPLTYIVCTQMR

Parental  VMKANPETAPFKSYLTTSNESQIFITGQHRGQPYSAHPRVMAFAQWMNSTYTGKESDCLQRCVIGGHYSY
          VM.ANP.TAP.KSYLTTSNESQIFITGQHRGQPY..HPRV.AFAQWMNSTYTGKE.DCLQRCVIGGHYSY
Retrocopy VMQANPKTAPYKSYLTTSNESQIFITGQHRGQPYTVHPRVRAFAQWMNSTYTGKE*DCLQRCVIGGHYSY

Parental  P-PIPPTLSLYWKLGATSFGDKELTVTNELMKEMNNLHYRERRRVAVQGIIMAVRYVSLSHAPEDATNVE
          P.PIPPTLSLYWK.GATSFG.KE.T.TNEL.KEM.NLHYR..RRVAVQGIIMAVRYVSLSHAP.D..NVE
Retrocopy P<PIPPTLSLYWKMGATSFGGKEQTATNELTKEMSNLHYRDLRRVAVQGIIMAVRYVSLSHAPKDTANVE

Parental  LMEEGSLEPSVFQNTRSMEKNKRCFT-EEQLQQANSQLLQDE-ETPSLLGSADPQMMSPPPPAKTPGLNQ
          LMEEG.LEP.VFQNTRSMEKNKRCFT.E...Q.....L...E...P.L.GS.DPQMMS..P..KTP.LNQ
Retrocopy LMEEGVLEPTVFQNTRSMEKNKRCFTKEQLQQAYSQLLQDKE<DPPTLCGSVDPQMMSSSPLTKTPRLNQ

Parental  RVQYPRASKKK
          RVQYP.ASK.K
Retrocopy RVQYPYASKEK

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	8.56 RPM
DRP000627_kidney	0.00 RPM	6.86 RPM
DRP000627_pectoral_fin	0.00 RPM	11.24 RPM
DRP000627_pelvic_fin	0.00 RPM	12.85 RPM
DRP000627_pharynx	0.00 RPM	9.88 RPM
DRP000627_tail_muscle	0.00 RPM	11.21 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_52 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Latimeria chalumnae	ENSLACG00000010847	1 retrocopy	retro_lcha_52 ,