RetrogeneDB ID: retro_lcha_20

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH127338.1:57567..58425(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLACG00000002724
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CAPZA1
• Ensembl ID: ENSLACG00000017963
• Aliases: None
• Description: None

Sequence

>retro_lcha_20
ATGGCAGACCAGTGCCTTCCCAGCAAAGAGCAGAAAGCCGAGATCATCGGCCGTTTGATCAGCCAGGCTCCCCCTGGGGA
ACTGACGGAAGTCTTAAGTGACGTCCGAATCTTGTTAAATGATGACGAGCTACTGTGTCAAGTAGCTGATAAAGCCTTTG
CCCAGTACAACATTGACCATTTTACTCCGGTCACGATTGATGGGAAGAAGGAGGAGGTCTTGATCACGCCTCACGGGAAA
CTGGGCAATGGCCGTTTCTTTGATCCGAACAGAAATCTATCATTTCGATGCGATCACTTGCGTAGAGAAGCTAGTGACCC
GCAGCCACATGAAAGGGATAAAGAGAAGGAAGTTTGGAGGAATGCGATCCAAACTGCTCTGGCGGCCTATGTGAAGCAAC
ACTATCCTACCGGAGTCTGCAGTGTGTATGAAAAAACTGAGGACAACCAACAACTGTATGTCGCTTGTGTTGAAGCCCAT
TTGTATCGGCCCAGATCTTTTTGGAATGGCTTGTGGAAGTCGGAATGGAGTTTACTCCTAACGTCACACCTCATACAGCT
TACTGGTAACATCAAAGTGGAAACCCACTACTTCGAAGATGGAAATGCCCATATAATGGTGAGTGAGGATTTTGCGGACG
CTTTCTGTGCAGCAAATGAAAGACAAGCAGCTCTAGCTTTTGTGGAAATTGTGGAAAAGGCAGATAACGAGCTTCAGACC
AGCCTGATGGAAGAAATTCAGGCACTATCAGACACGGCCTTCAAAGGTCTGAGAAGATCGCTTCCAGTTGTACGAACGTC
CATTGACTGGTGCAAAATTATCAAATCTCAGATTGTGGAAGTTGAGCCTGGATGCTAA

Alignment

ORF - retro_lcha_20 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.28 %
• Parental protein coverage: 94.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SEEQKVRIAATFITHAPPGEFNEVFNDVRLLLNNDNVLREGAAHAFAQYNMDQFTPAKIEGHDDQVLITE
          S.EQK..I....I..APPGE..EV..DVR.LLN.D..L...A..AFAQYN.D.FTP..I.G....VLIT.
Retrocopy SKEQKAEIIGRLISQAPPGELTEVLSDVRILLNDDELLCQVADKAFAQYNIDHFTPVTIDGKKEEVLITP

Parental  HGDLGNSRFLDPRNKLSFKFDHLRKEASDPQYHDVEAAVKPWRDACDSALRAYVKEHYPTGICTVYGKTI
          HG.LGN.RF.DP...LSF..DHLR.EASDPQ.H........WR.A...AL.AYVK.HYPTG.C.VY.KT.
Retrocopy HGKLGNGRFFDPNRNLSFRCDHLRREASDPQPHERDKEKEVWRNAIQTALAAYVKQHYPTGVCSVYEKTE

Parental  DGQQTVIACVESHQFQPKNFWNGRWRSEWKFTVTPPTAQVVGVLKIQVHYYEDGNVQLVSHKDIQESVTV
          D.QQ...ACVE.H...P..FWNG.W.SEW....T....Q..G..K...HY.EDGN.......D.......
Retrocopy DNQQLYVACVEAHLYRPRSFWNGLWKSEWSLLLTSHLIQLTGNIKVETHYFEDGNAHIMVSEDFADAFCA

Parental  SNEAQTAKEFIKIIENAENEYQTAISENYQAMSDTTFKALRRQLPITRSKVDWHKILNYQIAK
          .NE.Q.A..F..I.E.A.NE.QT...E..QA.SDT.FK.LRR.LP..R...DW.KI...QI..
Retrocopy ANERQAALAFVEIVEKADNELQTSLMEEIQALSDTAFKGLRRSLPVVRTSIDWCKIIKSQIVE

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	0.02 RPM	67.00 RPM
DRP000627_kidney	0.00 RPM	47.76 RPM
DRP000627_pectoral_fin	0.00 RPM	15.00 RPM
DRP000627_pelvic_fin	0.08 RPM	25.29 RPM
DRP000627_pharynx	0.01 RPM	141.14 RPM
DRP000627_tail_muscle	0.02 RPM	140.94 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_20 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 24 parental genes, and 56 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003570	1 retrocopy	retro_amel_219,
Choloepus hoffmanni	ENSCHOG00000004131	8 retrocopies	retro_chof_1008, retro_chof_1419, retro_chof_1499, retro_chof_1704, retro_chof_1861, retro_chof_2129, retro_chof_625, retro_chof_711,
Callithrix jacchus	ENSCJAG00000013548	3 retrocopies	retro_cjac_2259, retro_cjac_2850, retro_cjac_4125,
Cavia porcellus	ENSCPOG00000014532	1 retrocopy	retro_cpor_1155,
Dipodomys ordii	ENSDORG00000000671	3 retrocopies	retro_dord_224, retro_dord_265, retro_dord_44,
Felis catus	ENSFCAG00000013303	2 retrocopies	retro_fcat_700, retro_fcat_746,
Homo sapiens	ENSG00000116489	2 retrocopies	retro_hsap_2338, retro_hsap_4871,
Gorilla gorilla	ENSGGOG00000023677	1 retrocopy	retro_ggor_1216,
Latimeria chalumnae	ENSLACG00000017963	1 retrocopy	retro_lcha_20 ,
Myotis lucifugus	ENSMLUG00000009796	1 retrocopy	retro_mluc_2483,
Macaca mulatta	ENSMMUG00000015668	2 retrocopies	retro_mmul_2612, retro_mmul_942,
Mustela putorius furo	ENSMPUG00000004977	1 retrocopy	retro_mputfur_616,
Mus musculus	ENSMUSG00000070372	4 retrocopies	retro_mmus_179, retro_mmus_1828, retro_mmus_3370, retro_mmus_349,
Nomascus leucogenys	ENSNLEG00000004191	1 retrocopy	retro_nleu_1689,
Oryctolagus cuniculus	ENSOCUG00000000270	6 retrocopies	retro_ocun_1315, retro_ocun_1417, retro_ocun_1787, retro_ocun_301, retro_ocun_527, retro_ocun_555,
Otolemur garnettii	ENSOGAG00000014074	4 retrocopies	retro_ogar_1640, retro_ogar_2159, retro_ogar_3217, retro_ogar_845,
Pongo abelii	ENSPPYG00000001021	2 retrocopies	retro_pabe_2116, retro_pabe_3789,
Pan troglodytes	ENSPTRG00000001110	2 retrocopies	retro_ptro_1710, retro_ptro_3245,
Rattus norvegicus	ENSRNOG00000013538	1 retrocopy	retro_rnor_77,
Sorex araneus	ENSSARG00000001278	1 retrocopy	retro_sara_166,
Ictidomys tridecemlineatus	ENSSTOG00000015956	1 retrocopy	retro_itri_1044,
Tupaia belangeri	ENSTBEG00000001727	5 retrocopies	retro_tbel_1870, retro_tbel_3525, retro_tbel_4327, retro_tbel_638, retro_tbel_868,
Tarsius syrichta	ENSTSYG00000006259	2 retrocopies	retro_tsyr_179, retro_tsyr_471,
Vicugna pacos	ENSVPAG00000005361	1 retrocopy	retro_vpac_579,