RetrogeneDB ID: retro_cjac_502

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:11996768..11997867(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000033945
• Aliases: None
• Description: None

Sequence

>retro_cjac_502
TTACGTCACCAGGAGTATGGAGAATTCCATAACAGCCACACTAATGACTGGGAAGACCACTTGGTAGTCAAGCAATTCTC
TATAGAAGATCAGCTGGAATTCAGGGAATTGCTATTCATCCTTCGTCAGGCTCCTTTTGACTTCTTTGAGAACAATAAGA
ATAAAGGCACCGTCAAACTCTATGTCCTTCATGTGTTCATCGTGCACTGCTGTGATGAGTTGATGCCGGAGGATCTCAAC
GTTATCTGTGGTATGGTTGACTCTGAGGATCCACCCCTGAACATTTGAGAAATGCTCCAGCAGAGCAAAATCTTGAAAGT
CATTCACAAAAACATTGTTAAGTAGTGCCTTGAGCTCTTCTCTGAGTTGTCAGAAGACAAAGAGAATTACAGAAAATTCT
ATGAGGCATTCTCTAAAAATCTAAAGTTTGGAATCTTCAAGGACTCCCCTAACTGGTGATACCTGTCTGAGCTGCTGCAC
TTTTACACCTCCCAGTCTGGAGACGGTATGACATCCATGTCAGAACATGTCTCTTGCATGAAGGAGACACAGAAATCTAT
CTACTGTATCACCGGTGAGAGCAATGAACAGGTGGCCAGCTCTGCTTTCGTGGAGTGAGTGCAGAAGCAGGGTTTTGAGG
TAGTATATAAGACAGAGCCCAGTGATGAGTACTGCATGCAGCACCTCAAGGAGTTTGATAGGAAAAGCCTATTCTCAGTT
ACCAGGGAGGGTCTGGAGCTACCTGAGGGTGAGGGGAGAAGAAGAAAATGGAGGAGTGCAAAGTGAATCTTGAGAACATC
TGCAAACTCATGAAAAAAATCTTGGATGAGAAGGTTGAGAAAATGACAGCTTCCAATAGGCTTGAGTCTTCACCTGCTGC
ATTGTGACCAGCATCTATGGCTGGACAGCCAATATGGAGCAGATCACAAAAGCCCAGGCACTTTGGGACAATTCTATGAT
GGCTTACATGATGGCCAAAGGGCACCTGGAGATCATTGTGACCACCCCATTGTGGAGATGCTGTGGCAGAAGGCTGAGGT
GGAAAAAGAACAAGGCTGTCAGGAACTGGGTGCTGCTGCTGTTGGGAACCAAGCTGCTC

Alignment

ORF - retro_cjac_502 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.64 %
• Parental protein coverage: 61.06 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ITNEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFVPRRAPFDLFENRKKKNNIKLYVRRVFIMDN
          ....EYGEF..S.TNDWEDHL.VK.FS.E.QLEFR.LLF..R.APFD.FEN.K.K...KLYV..VFI...
Retrocopy LRHQEYGEFHNSHTNDWEDHLVVKQFSIEDQLEFRELLFILRQAPFDFFENNKNKGTVKLYVLHVFIVHC

Parental  CEELIPEYYIYFIRGVVDSEDLPLNISREMLQQSKILKVIRKNLVKKCLELFTELAEDKENYKKFYEQFS
          C.EL.PE.....I.G.VDSED.PLNI..EMLQQSKILKVI.KN.VK.CLELF.EL.EDKENY.KFYE.FS
Retrocopy CDELMPED-LNVICGMVDSEDPPLNI*-EMLQQSKILKVIHKNIVK*CLELFSELSEDKENYRKFYEAFS

Parental  KNIKLGIHEDSQNRKKLSELLRYYTSASGDEMVSLKDYCTRMKENQKHIYYITGETKDQVANSAFVERLR
          KN.K.GI..DS.N...LSELL..YTS.SGD.M.S.......MKE.QK.IY.ITGE...QVA.SAFVE...
Retrocopy KNLKFGIFKDSPNW*YLSELLHFYTSQSGDGMTSMSEHVSCMKETQKSIYCITGESNEQVASSAFVE*VQ

Parental  KHGLEVIYMIEPIDEYCVQQLKEFEGKTLVSVTKEGLELPEDE-EEKKKQEEKKTKFENLCKIMKDILEK
          K.G.EV.Y..EP.DEYC.Q.LKEF..K.L.SVT.EGLELPE.E..EKKK.EE.K...EN.CK.MK.IL..
Retrocopy KQGFEVVYKTEPSDEYCMQHLKEFDRKSLFSVTREGLELPEGE<GEKKKMEECKVNLENICKLMKKILDE

Parental  KVEKVVVSNRLVTSP-CCIVTSTYGWTANMERIMKAQALRDNSTMGYMAAKKHLEI-NPDHSIIETLRQK
          KVEK...SNRL..SP.CCIVTS.YGWTANME.I.KAQAL.DNS.M.YM.AK.HLEI...DH.I.E.L.QK
Retrocopy KVEKMTASNRLESSP<CCIVTSIYGWTANMEQITKAQALWDNSMMAYMMAKGHLEI<HCDHPIVEMLWQK

Parental  AEADKNDKSVKDL-VILLYETALL
          AE..K.......L.V.LL..T.LL
Retrocopy AEVEK-EQGCQEL>VLLLLGTKLL

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	168.69 RPM
SRP051959_heart	0.02 RPM	217.01 RPM
SRP051959_kidney	0.00 RPM	145.21 RPM
SRP051959_liver	0.00 RPM	269.35 RPM
SRP051959_lung	0.00 RPM	194.35 RPM
SRP051959_lymph_node	0.00 RPM	189.24 RPM
SRP051959_skeletal_muscle	0.02 RPM	221.48 RPM
SRP051959_spleen	0.00 RPM	164.20 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_502 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_502 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_502 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006270	1 retrocopy	retro_btau_501,
Canis familiaris	ENSCAFG00000018036	1 retrocopy	retro_cfam_1094,
Callithrix jacchus	ENSCJAG00000033945	8 retrocopies	retro_cjac_1818, retro_cjac_2300, retro_cjac_2835, retro_cjac_3514, retro_cjac_3596, retro_cjac_3601, retro_cjac_3626, retro_cjac_502 ,
Cavia porcellus	ENSCPOG00000002015	1 retrocopy	retro_cpor_1372,
Homo sapiens	ENSG00000080824	2 retrocopies	retro_hsap_237, retro_hsap_859,
Macaca mulatta	ENSMMUG00000011073	2 retrocopies	retro_mmul_1526, retro_mmul_2313,
Monodelphis domestica	ENSMODG00000013302	3 retrocopies	retro_mdom_1653, retro_mdom_2010, retro_mdom_817,
Mus musculus	ENSMUSG00000021270	1 retrocopy	retro_mmus_2139,
Nomascus leucogenys	ENSNLEG00000015925	3 retrocopies	retro_nleu_714, retro_nleu_822, retro_nleu_854,
Pongo abelii	ENSPPYG00000006153	1 retrocopy	retro_pabe_1760,
Pan troglodytes	ENSPTRG00000006736	2 retrocopies	retro_ptro_207, retro_ptro_596,
Rattus norvegicus	ENSRNOG00000007219	1 retrocopy	retro_rnor_860,