RetrogeneDB ID: retro_lcha_84

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH127486.1:566293..567428(+)
• Located in intron of: ENSLACG00000010216

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLACG00000007580
• Aliases: None
• Description: None

Sequence

>retro_lcha_84
TGCCTTTCCATGGTGACAAGATTCTTTTTTTTACCGCAAAATGGCAACTTTCTGGGATGTCTTGAACTCATCAGTTGCTT
TGATCCACTTTTATCAGATCATCTCACCAAATTTGCAAATGCTGGCAAAGGAATGCCTAATTACTTGCCTTCCATGATTT
GTGATTAATTCATTCAGCTGAAGTCTGATAAAATTCTGAGTACCATTGTCAGCGAAATTAAATGTTCCAAGTACTATTCT
ATTATTGTGGCTTCTGCTCCTGACCTAACTCATATTGACCAGCTTACTTTTATGACCAGATATGTGCAGAAGAATGGAGA
ACCTATCAAGCATTTTTTGAAATTCATACCAATTCATGGCCACCATGCTGAACATCTGGAGAGAACCATCATGTAGTTGC
TACAAGAACTTGATATTGATATTAGTGAGTGTCATGGTCAGAATTACAACAATGCTAGCAACATATCTGGCAAATATTCA
GGGCTTCAGGCAAGGATTAAAAATCTAAACCCTCTTGTTGAATATGTTCCGTGTTCTGCACATTCACTGAACTTGGTTTG
TTCAAGTGCTGCAGAATGCTGTTTGGCTGCGGTTTCATTTTTTTGGCTTTATTGAAAGTCTGTACAACTTTTCTGCATCA
GCACATCATTGGGAAGTTCTGACATCAGAGCTTGAAAAATGTAGCAACAAAGGTCTTACACCAAAAACTCTATCTGCAAC
TAGATGGTCTGCAAGAGCTGATGCAACAAAGGCTTTACAATTTGGTTACAATATCATTCAGAATGCTTTGATTGAAATAT
CTGCCTATAATGAACAGCCAAAAGCCACACAGCATGAAGCTTGCCAGTTAAGGGCCACAATGGTCAAACTGGAAACTGCA
GTAATGACTGTTGTGTGGGCTGTCATCTTTCAAAGAATGAATGCTACTAGTAAAGCTTTACAGGAAGTGAAGATGCATCT
GGGTTCAATCTCTGTGCTGTATGATTCACTTATTGACTTTATCGGACAGGTCAGAAATGACTTTGAAATGTACGAAACTG
AGGCAAAAATGCTTACAAATACTGAGGGGTACAAAGTGGAATCACAATGGAGTAGGACTAGGAAAAAAATATTTGGGGAA
TCAGTAACTCCAGAT

Alignment

ORF - retro_lcha_84 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.41 %
• Parental protein coverage: 93.33 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CLSMVTRFFFSLQNGNFLGCLELLGHFDPLLSDHLTTFADAGKGTPNYLSSAICDVFIQLMSDKVLSAIV
          CLSMVTRF....QNGNFLGCLEL...FDPLLSDHLT.FA.AGKG.PNYL.S.ICD.FIQL.SDK.LS.IV
Retrocopy CLSMVTRFXXXPQNGNFLGCLELISCFDPLLSDHLTKFANAGKGMPNYLPSMICD*FIQLKSDKILSTIV

Parental  SEIKCSKYYSIIIVDSAPDLTHIDLLTIMLRYVQKNGEPTERFLKLIPTHGHCTEHLERTITSLLQELAI
          SEIKCSKYYSII...SAPDLTHID.LT.M.RYVQKNGEP...FLK.IP.HGH..EHLERTI..LLQEL.I
Retrocopy SEIKCSKYYSIIVA-SAPDLTHIDQLTFMTRYVQKNGEPIKHFLKFIPIHGHHAEHLERTIM*LLQELDI

Parental  DISDCCGQSYDSASNLSGKYAGLRARINNRNP----VPCSARSLNLVGSCAAECCLAAVSFF-SFVQSLY
          DIS.C.GQ.Y..ASN.SGKY.GL.ARI.N.NP....VPCSA.SLNLV.S.AAECCLAAVSFF..F..SLY
Retrocopy DISECHGQNYNNASNISGKYSGLQARIKNLNPLVEYVPCSAHSLNLVCSSAAECCLAAVSFF>GFIESLY

Parental  NFFSASARRWEVLTSHLXKSLRFGCNVILDALTEISEPARDDAVKSLRFGCNVILDALTEISDDNDQPKA
          NF.SASA..WEVLTS.L.K....G........T..S..AR.DA.K.L.FG.N.I..AL.EIS..N.QPKA
Retrocopy NF-SASAHHWEVLTSELEKCSNKGLTPKTLSATRWS--ARADATKALQFGYNIIQNALIEISAYNEQPKA

Parental  AQREACQFRAAMAKLELQCYCDCWDVILQRVNVTSKTLQQAKTDLGSVSVLYDSLIDFIRQVRNDFETYE
          .Q.EACQ.RA.M.KLE.......W.VI.QR.N.TSK.LQ..K..LGS.SVLYDSLIDFI.QVRNDFE.YE
Retrocopy TQHEACQLRATMVKLETAVMTVVWAVIFQRMNATSKALQEVKMHLGSISVLYDSLIDFIGQVRNDFEMYE

Parental  TEAKTLPNTEGYKAESEQCRARKRIFVESATPE
          TEAK.L.NTEGYK.ES...R.RK.IF.ES.TP.
Retrocopy TEAKMLTNTEGYKVESQWSRTRKKIFGESVTPD

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	0.00 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	0.00 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_84 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 ,