RetrogeneDB ID: retro_cjac_164

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:1429589..1430714(+)
• Located in intron of: ENSCJAG00000001979

Retrocopy information

• Ensembl ID: ENSCJAG00000001999
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: LDHAL6A
• Ensembl ID: ENSCJAG00000007067
• Aliases: None
• Description: lactate dehydrogenase A-like 6A [Source:HGNC Symbol;Acc:28335]

Sequence

>retro_cjac_164
ATGAGTTGGACCTTGCCTGTGGTGCGGGCCACCCGGAGAGTGAGCTCGGCGGGGATGGATTTCCTGTGCCTGGGGATGGC
CCCGTTTCCCCGTCAGGGCACCCGGCTCTTCACCCCCACGAGCAAGATGGCGACTGTGAAGAGTGAGCTGATGGAGAGCT
TCACTTCCGGGAAGCTCGTTCCTCACAGTAAGGTCTCCATCATAGGTGCCGGGTCGGTGGGCATGGCCTGCGCCATCAGC
ATCTTACTAAAAGGCTTGACTGATGAACTTGCCCTTGTGGATCTCAATGAAGGGAAACTGAAGGGGGAGACCATGGACCT
TCAACACGGCAGCCCTTTCCTGAAAATGCCAAATATTGTCTGTAGCAGAGATTACCGTGTCACAGCAAACTCCAGCCTAG
TGATTATCACAGCAGGTGCACGCCAGGTAAAGGGAGAGACGCGCCTTAATTTAGTCCAGCGAAACGTGGCCATCTTCAAG
TCAATGATTTCCAGCATTGCCCAGTACAGCCCCCTCTGCAAACTGATTGTTGTTTCCAATCCAGTGGATATCCTGACTTA
CGTAGCCTGGAGACTGAGCGCATTTCCCAAAAATCGTGTTATTGGAAGCGGCTGTAATCTGGATACCGCTCGTTTTCGTT
TCTTGATCGGACAGAAGCTTGGTATCCACTCTGAGAGCTGCCACGGATGGATCCTCGGAGAGCATGGGGACTCAAGTGTT
CCTGTGTGGAGTGGAGTGAACATTGCTGGCGTCCCTCTGAAGGATCTGAACCCTGACATAGGAACTGATAAAGATCCTGA
GCAATGGAAAAATGTCCACAAAGAAGTGATTGCTAGTGCCTATGAGATTATTAAAATGAAAGGTTATACTTCTTGGGCTA
TTGGCCTATCTGTAGCTGATTTAACGGAAAGTATTTTGAAGAATCTCAGGAGAACACATCCAGTTTCCACCATAATTAAG
GGCCTCTATGGAATAGATGAAGAAGTGTTCCTCAGTATTCCTTGTATCCTGGGAGAGAACGGTATTACCAACCGAATAAA
GATAAAGCTGACCCCTGAAGAGGAGGCCCACCTGAAGAAGAGCGCAAAAACACTTTGGGAAATTCAGAAGGAGCTTAAGC
TTTAA

Alignment

ORF - retro_cjac_164 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.61 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATVKGELIKNVAEEKAIHHNKISIVGSGSVGVACAISILLKGLSDELVLVDDDEGKLKGETMDLQHGGP
          MATVK.EL.......K...H.K.SI.G.GSVG.ACAISILLKGL.DEL.LVD..EGKLKGETMDLQHG.P
Retrocopy MATVKSELMESFTSGKLVPHSKVSIIGAGSVGMACAISILLKGLTDELALVDLNEGKLKGETMDLQHGSP

Parental  FVKMPKIVSSKDYLVTANSNLVIITAGARQKKGETRLDLVQRNVSIFKLIIPSITQYSPHCKLLIVTNPV
          F.KMP.IV.S.DY.VTANS.LVIITAGARQ.KGETRL.LVQRNV.IFK..I.SI.QYSP.CKL..V.NPV
Retrocopy FLKMPNIVCSRDYRVTANSSLVIITAGARQVKGETRLNLVQRNVAIFKSMISSIAQYSPLCKLIVVSNPV

Parental  DILTYVAWKLSAFPKNRVIGSGCNLDSARFRYFIGQRLGIHSESCHGLVLGEHGNSSVPVWSGVNIAGVP
          DILTYVAW.LSAFPKNRVIGSGCNLD.ARFR..IGQ.LGIHSESCHG..LGEHG.SSVPVWSGVNIAGVP
Retrocopy DILTYVAWRLSAFPKNRVIGSGCNLDTARFRFLIGQKLGIHSESCHGWILGEHGDSSVPVWSGVNIAGVP

Parental  LKDLNPDIGTYKDPEQWENVHKKVVSSGYEMLKMKGYTSWGISLSVADLTESILKNLRRVHPVSTLSKGL
          LKDLNPDIGT.KDPEQW.NVHK.V..S.YE..KMKGYTSW.I.LSVADLTESILKNLRR.HPVST..KGL
Retrocopy LKDLNPDIGTDKDPEQWKNVHKEVIASAYEIIKMKGYTSWAIGLSVADLTESILKNLRRTHPVSTIIKGL

Parental  YGINEEIFLSVPCILGENGIADLIKVKLTLEEEACLQKSAEILWEIQKELKL
          YGI.EE.FLS.PCILGENGI...IK.KLT.EEEA.L.KSA..LWEIQKELKL
Retrocopy YGIDEEVFLSIPCILGENGITNRIKIKLTPEEEAHLKKSAKTLWEIQKELKL

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
SRP051959_colon	2.55 RPM	0.95 RPM
SRP051959_heart	0.91 RPM	0.70 RPM
SRP051959_kidney	0.82 RPM	0.58 RPM
SRP051959_liver	0.50 RPM	0.95 RPM
SRP051959_lung	0.46 RPM	1.29 RPM
SRP051959_lymph_node	0.66 RPM	1.07 RPM
SRP051959_skeletal_muscle	1.97 RPM	0.57 RPM
SRP051959_spleen	0.90 RPM	1.03 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_164 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_164 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_164 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_42
Pan troglodytes	retro_ptro_62
Pongo abelii	retro_pabe_203
Macaca mulatta	retro_mmul_261

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007067	2 retrocopies	retro_cjac_164 , retro_cjac_2180,
Callithrix jacchus	ENSCJAG00000007094	1 retrocopy	retro_cjac_2290,
Homo sapiens	ENSG00000166800	2 retrocopies	retro_hsap_42, retro_hsap_905,
Macaca mulatta	ENSMMUG00000014614	2 retrocopies	retro_mmul_1111, retro_mmul_261,
Nomascus leucogenys	ENSNLEG00000017780	2 retrocopies	retro_nleu_29, retro_nleu_378,
Otolemur garnettii	ENSOGAG00000009261	1 retrocopy	retro_ogar_2662,
Pongo abelii	ENSPPYG00000003435	2 retrocopies	retro_pabe_203, retro_pabe_779,
Pan troglodytes	ENSPTRG00000003423	1 retrocopy	retro_ptro_62,
Tarsius syrichta	ENSTSYG00000008062	4 retrocopies	retro_tsyr_1811, retro_tsyr_2064, retro_tsyr_2071, retro_tsyr_731,