RetrogeneDB ID: retro_cjac_1166

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:83788954..83789968(-)
• Located in intron of: ENSCJAG00000008457

Retrocopy information

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

Parental gene information

• Parental gene symbol: WDR77
• Ensembl ID: ENSCJAG00000013344
• Aliases: None
• Description: None

Sequence

>retro_cjac_1166
ATGTGAAAGGAAATCCCGCCTTCCCTAGTGCCCCCGTCGGCCTGGGAGTGGAACCTTCCCCCTAATGTGCCCGCTTGCAT
GGAACGGCAGTTGGAGGCTGCACGGTACCAGTCCGATGGGGCGCTTCTCCTTGGGGCCTCCAGCCTGAGTGGCCGCTGCT
GGGCCGGCTCCCTCTGGCTTTTTAAGGACCCTGTGCCGCCCCAACAAAGGCTTCTGCTCCACCAGAGTCCAAACGGAGGC
TGGAGTGGCAGACCTCACTTGGGCTGGGGAGAGAGGTATTGTAGTGGCCTCAGGTGCTGTTGAATTGTGGGAACTAGATG
AGAATGAGACAGTTACAGTCAGCAAGTTCTGCAAGTATGAGCATGATGACATTGTGTCTACAGTCAGTGTCCTGAGCTCT
GGCGCACAAGCTGTCGGTGTAGCAAAGACTTCTGCATCAAGGTTTGGGACCTTGGTCAGCAGATGGTACTGAATTCATAC
CGAGCTCATGCTGCGCAGGTCACCTGTATTGCTGCTTCTCCCCACGAGGATTCTGTTTCTTTCATGCAGTGAGGACAATA
AAATTTTATTTGGGATACCCGCTGCCCCAAGCCAGCAACACGGATTGGCTGCAGTGCCTCTGGCTGCCTTTCTACCTCAC
TGGCTTGGCATCCTCAGCAAAGTGAAGTCTTTGTTTTTGGTGATGAAAATGGGATGGTCTCCCTTGTTGACACCAAGAGT
ACAAGCTGTGTCCCAAGCTCAGCTGTCCACTCCCAGTGTGTCACTGGGCTGCTGTTCTCCCCACACCGTGTTCCTTTCCT
GGCCTCTCTCAGTGAAGACTGCTCACTTGCCTTGCTGGACTCAAGCCTTGCTAAGGTGGCTAGAAGCAGAGCCCACAGAG
ACTTTGTGAGAGATGCTACTTGGTCCCTGCTCAATCACTCACTGCTTATCACAGTGGGTCGGGACCATCAGGTTGTCCAC
CACATTGTGCCCACAGAACCTCTCCTAGCCCCTGGACCTGCGAGTGTTGCTGAA

Alignment

ORF - retro_cjac_1166 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.97 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MRKETPPPLVPPAAREWNLPPNAPACMERQLEAARYRSDGALLLGASSLSGRCWAGSLWLFKDP-CAA-P
          M.KE.PP.LVPP.A.EWNLPPN.PACMERQLEAARY.SDGALLLGASSLSGRCWAGSLWLFKDP.CAA.P
Retrocopy M*KEIPPSLVPPSAWEWNLPPNVPACMERQLEAARYQSDGALLLGASSLSGRCWAGSLWLFKDP<CAA<P

Parental  NEGFCSAGVQTEAGVADLTWVGERGILVASDSGAVELWELDENETLIVSKFCKYEHDDIVSTVSVLSSGT
          N.GFCS..VQTEAGVADLTW.GERGI.VA..SGAVELWELDENET..VSKFCKYEHDDIVSTVSVLSSG.
Retrocopy NKGFCSTRVQTEAGVADLTWAGERGIVVA--SGAVELWELDENETVTVSKFCKYEHDDIVSTVSVLSSGA

Parental  QAVS-GSKDFCIKVWDLAQQVVLNSYRAHAAQVTCVAASPHKDSV-FLSCSEDNRILLWDTRCPKPASHI
          QAV...SKDFCIKVWDL.QQ.VLNSYRAHAAQVTC.AASPH.DSV.F......N....WDTRCPKPA..I
Retrocopy QAVG<CSKDFCIKVWDLGQQMVLNSYRAHAAQVTCIAASPHEDSVSFMQ*GQ*N--FIWDTRCPKPATRI

Parental  GCSASGSLPTSLAWHPQQSEVFVFGDENGMVSLVDTKSTSCVLSSAVHSQCVTGLVFSPHSVPFLASLSE
          GCSASG.L.TSLAWHPQQSEVFVFGDENGMVSLVDTKSTSCV.SSAVHSQCVTGL.FSPH.VPFLASLSE
Retrocopy GCSASGCLSTSLAWHPQQSEVFVFGDENGMVSLVDTKSTSCVPSSAVHSQCVTGLLFSPHRVPFLASLSE

Parental  DCSLAVLDSSLSEVFRSRAHRDFVRDATWSPLNHSLLTTVGWDHQVVHHIVPTEPLPAPGPASVAE
          DCSLA.LDSSL..V.RSRAHRDFVRDATWS.LNHSLL.TVG.DHQVVHHIVPTEPL.APGPASVAE
Retrocopy DCSLALLDSSLAKVARSRAHRDFVRDATWSLLNHSLLITVGRDHQVVHHIVPTEPLLAPGPASVAE

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	0.51 RPM	5.28 RPM
SRP051959_heart	0.46 RPM	4.86 RPM
SRP051959_kidney	0.93 RPM	7.61 RPM
SRP051959_liver	0.37 RPM	7.43 RPM
SRP051959_lung	0.57 RPM	4.41 RPM
SRP051959_lymph_node	0.46 RPM	4.31 RPM
SRP051959_skeletal_muscle	0.44 RPM	10.22 RPM
SRP051959_spleen	1.81 RPM	3.74 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1166 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1166 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1166 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014102	1 retrocopy	retro_btau_1342,
Choloepus hoffmanni	ENSCHOG00000013829	1 retrocopy	retro_chof_2618,
Callithrix jacchus	ENSCJAG00000013344	2 retrocopies	retro_cjac_1166 , retro_cjac_3063,
Dasypus novemcinctus	ENSDNOG00000006521	1 retrocopy	retro_dnov_695,
Homo sapiens	ENSG00000116455	1 retrocopy	retro_hsap_2995,
Gorilla gorilla	ENSGGOG00000005208	1 retrocopy	retro_ggor_2076,
Macaca mulatta	ENSMMUG00000003311	1 retrocopy	retro_mmul_1917,
Mus musculus	ENSMUSG00000000561	1 retrocopy	retro_mmus_1120,
Nomascus leucogenys	ENSNLEG00000003918	1 retrocopy	retro_nleu_746,
Oryctolagus cuniculus	ENSOCUG00000007801	1 retrocopy	retro_ocun_535,
Pongo abelii	ENSPPYG00000001033	1 retrocopy	retro_pabe_2482,
Pan troglodytes	ENSPTRG00000001098	1 retrocopy	retro_ptro_2026,
Tupaia belangeri	ENSTBEG00000010325	1 retrocopy	retro_tbel_2253,