RetrogeneDB ID: retro_cjac_2522

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:61375352..61375967(+)
• Located in intron of: ENSCJAG00000001820

Retrocopy information

• Ensembl ID: ENSCJAG00000001830
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MCUR1
• Ensembl ID: ENSCJAG00000016050
• Aliases: None
• Description: mitochondrial calcium uniporter regulator 1 [Source:HGNC Symbol;Acc:21097]

Sequence

>retro_cjac_2522
GCACCCACACTTACTTCCTGGAGGAGAGAGCTAAGCCTGTCTACTGGATACCTGCAGTTGGAGCACAAAAGGAGAGATTT
CATCTCTTCTGGGAGTAGGAGGCTCTGTTTTGACACTCATACCTTAGTGTGCTTACTGGAAGACAGTGGATTTGCTACTA
AACAAGCAGAAATCATTGTGTCTACATTGGTCAAGATCTTGGAGGCCAACATGGACATCGTCTACAAAAATACGGTCACC
AAGATACAGCAGGAGATGACTCTTCAGCAGATAATGTCTCAGATTGTGAATGTGAAAAAGGATATGATTATTTTGGAGAA
GAGTGAATTTTCATCTCTCAGAACAGAAAATGAAAAAAATAAAACTTGAACTACATCAGCTAAAACAGCAAGTAATGGAT
GAAGTGATCAGAGTCCGGACAAATAACAAATTAGACTTCAACGTAGAAAAGAGCAGAGTAAAAGAATTGCATTCACTGAA
TGAAAGGAAGCTGTGGAATTGAGAACAGAAATAGTGACATTGCATGCCCAGCAAGATTGGTCCCTCACCCACACAGATAG
GAAGATGGAAACTGAGGTTGCTGGCCTCAAAACCATGCTCGAGGCCCACAAGCTT

Alignment

ORF - retro_cjac_2522 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.73 %
• Parental protein coverage: 56.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ALSLASCRRELSLSAGCLQLERRRRDFTSSGSRKLYFDTHALVCLLEDNGFATQQAEIIVSALVKILEAN
          A..L.S.RRELSLS.G.LQLE..RRDF.SSGSR.L.FDTH.LVCLLED.GFAT.QAEIIVS.LVKILEAN
Retrocopy APTLTSWRRELSLSTGYLQLEHKRRDFISSGSRRLCFDTHTLVCLLEDSGFATKQAEIIVSTLVKILEAN

Parental  MDIVYKDMVTKMQQEITLQQIMSQIANVKKDMIILEKSEFSALRAENE-KIKLELHQLKQQVMDEVIKVR
          MDIVYK..VTK.QQE.TLQQIMSQI.NVKKDMIILEKSEFS.LR.ENE.KIKLELHQLKQQVMDEVI.VR
Retrocopy MDIVYKNTVTKIQQEMTLQQIMSQIVNVKKDMIILEKSEFSSLRTENE>KIKLELHQLKQQVMDEVIRVR

Parental  TDTKLDFNLEKSRVKELYSLNEKKL-LELRTEIVALKHAQQDRALTQTDRKIETEVAGLKTMLESHKL
          T..KLDFN.EKSRVKEL.SLNE.KL..ELRTEIV.L.HAQQD..LT.TDRK.ETEVAGLKTMLE.HKL
Retrocopy TNNKLDFNVEKSRVKELHSLNERKL<VELRTEIVTL-HAQQDWSLTHTDRKMETEVAGLKTMLEAHKL

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	0.91 RPM	5.68 RPM
SRP051959_heart	0.79 RPM	5.05 RPM
SRP051959_kidney	0.62 RPM	8.74 RPM
SRP051959_liver	0.50 RPM	4.83 RPM
SRP051959_lung	1.15 RPM	5.32 RPM
SRP051959_lymph_node	1.37 RPM	6.69 RPM
SRP051959_skeletal_muscle	0.48 RPM	6.11 RPM
SRP051959_spleen	0.86 RPM	5.99 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2522 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2522 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2522 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1795
Pan troglodytes	retro_ptro_1200
Gorilla gorilla	retro_ggor_1320

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000395	2 retrocopies	retro_amel_1628, retro_amel_473,
Canis familiaris	ENSCAFG00000009857	3 retrocopies	retro_cfam_1018, retro_cfam_1556, retro_cfam_823,
Callithrix jacchus	ENSCJAG00000014547	1 retrocopy	retro_cjac_219,
Callithrix jacchus	ENSCJAG00000016050	1 retrocopy	retro_cjac_2522 ,
Cavia porcellus	ENSCPOG00000014899	1 retrocopy	retro_cpor_934,
Equus caballus	ENSECAG00000009150	2 retrocopies	retro_ecab_273, retro_ecab_469,
Felis catus	ENSFCAG00000005972	3 retrocopies	retro_fcat_1290, retro_fcat_1405, retro_fcat_1538,
Homo sapiens	ENSG00000050393	1 retrocopy	retro_hsap_1795,
Gorilla gorilla	ENSGGOG00000002632	1 retrocopy	retro_ggor_1320,
Loxodonta africana	ENSLAFG00000003287	2 retrocopies	retro_lafr_1252, retro_lafr_870,
Microcebus murinus	ENSMICG00000000183	2 retrocopies	retro_mmur_280, retro_mmur_580,
Myotis lucifugus	ENSMLUG00000010975	1 retrocopy	retro_mluc_1574,
Mustela putorius furo	ENSMPUG00000000698	1 retrocopy	retro_mputfur_640,
Nomascus leucogenys	ENSNLEG00000000914	1 retrocopy	retro_nleu_2768,
Otolemur garnettii	ENSOGAG00000013458	3 retrocopies	retro_ogar_1587, retro_ogar_1819, retro_ogar_3178,
Pan troglodytes	ENSPTRG00000017740	1 retrocopy	retro_ptro_1200,
Tarsius syrichta	ENSTSYG00000012562	1 retrocopy	retro_tsyr_810,
Tursiops truncatus	ENSTTRG00000012874	1 retrocopy	retro_ttru_1597,