RetrogeneDB ID: retro_cjac_976

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:41077909..41078651(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WDR85
• Ensembl ID: ENSCJAG00000013422
• Aliases: None
• Description: None

Sequence

>retro_cjac_976
GCCTTCAATTGCTGGCATACAGAAATTATATATTCAGGGGGTGATGACTACTGGCCTACTGAGGGGCTGAGACAACAGGG
AACCTGGCAGATTTCTCTTCACCATCAAGAGATACTCCATGGGTGTGTGCAGTATCCAGAGCAGCCCCCATCGAGAGCAT
GTCCTGGCCACAGGAAGCTATGATGAGCACATCCTACTGTGGGATATATGAAACATGAAGCAATCATTGGCAGACACACC
TGTGCAGGGTGGGGTATGGAGAATCAAGTGGCACCCTTTCCACCACCACCTGCTTCTGGTCGCCTGTATGCACAGTGGCT
GTAAGATCCTCAACTGCCCAAAGGCAATGGAGGAGAAGCAGGAGGCGACGGTCCTGGCATATCACACATTGCCTAACTTG
CTGGTGTACGGAGCCGACTGGTCATAGCTGCTCTTTCATTCTCTGCAACTGGCCCTCTCGCGGCCCTGTCCTAGCAACCT
GGGAACCAAGACAGCAGACCTGAAGGGTACAAGCAAGTTGTCAGCACCCTGTCGTGAATGCATGGAGGATAATGATGGAG
AGGGCTGGGGAGTGAAGCCACTCACAGAGGACATGAGGAGGAATGGCACCTGGCTGTGGGCTACAGCAGCTGCCAAGCGT
GACTGTGGCCTGAGCCCAGAAGAAGCAGACTCAGCCTTCAGCCTCCTAGCCACCTGCTCTTTCTATCAGCATGCGCCCCA
CCTCTGGGAGTGGGAGGGGAGC

Alignment

ORF - retro_cjac_976 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.66 %
• Parental protein coverage: 55.03 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AFNYWHTEIVYS-GGD-DGLLRGWDTRAPGRFLFTSMSHCPGVCSIQSSPHREHVLATGSYDEHILLWDT
          AFN.WHTEI.YS.G.D..GLLRG.D.R.PGRFLFT......GVCSIQSSPHREHVLATGSYDEHILLWD.
Retrocopy AFNCWHTEIIYSGGDD>TGLLRG*DNREPGRFLFTIKRYSMGVCSIQSSPHREHVLATGSYDEHILLWDI

Parental  RNMKQPLADTPVQGGVWRIKWHPFHHHLLLAACMHSGFKILNCQKAMEEKQEATVLASHTLPNSLVYGAD
          .NMKQ.LADTPVQGGVWRIKWHPFHHHLLL.ACMHSG.KILNC.KAMEEKQEATVLA.HTLPN.LVYGAD
Retrocopy *NMKQSLADTPVQGGVWRIKWHPFHHHLLLVACMHSGCKILNCPKAMEEKQEATVLAYHTLPNLLVYGAD

Parental  WSWLLFHSLQLAPSRPCPSNLGTKTADLKGASELPGPSCECMEDNDGEGYGVKPLTEDSRENGTWLQATA
          WS.LLFHSLQLA.SRPCPSNLGTKTADLKG.S.L..P..ECMEDNDGEG.GVKPLTED.R.NGTWL.ATA
Retrocopy WS*LLFHSLQLALSRPCPSNLGTKTADLKGTSKLSAPCRECMEDNDGEGWGVKPLTEDMRRNGTWLWATA

Parental  TTMRDCGQSPEEANSAFSLLATCSFYDHALHLWEWEGN
          ...RDCG.SPEEA.SAFSLLATCSFY.HA.HLWEWEG.
Retrocopy AAKRDCGLSPEEADSAFSLLATCSFYQHAPHLWEWEGS

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	0.00 RPM	3.53 RPM
SRP051959_heart	0.00 RPM	4.17 RPM
SRP051959_kidney	0.00 RPM	4.30 RPM
SRP051959_liver	0.00 RPM	2.92 RPM
SRP051959_lung	0.00 RPM	4.41 RPM
SRP051959_lymph_node	0.00 RPM	4.82 RPM
SRP051959_skeletal_muscle	0.00 RPM	6.07 RPM
SRP051959_spleen	0.00 RPM	4.37 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_976 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_976 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_976 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013422	1 retrocopy	retro_cjac_976 ,