RetrogeneDB ID: retro_cjac_2835

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:106812660..106813843(-)
• 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_2835
CAGTTGGAATTCAGGGCATTGCTATTCATTCTCATCAGGCTCCCCTTTGACCTTTTGAGACAGATAAAAAGACATCAAAC
TCTATGTCTGTGTGTATCATCATGGACAGCTGTGATGAGTTAATACCAGAGTATCTCAACTTTATCTGTGGTGCAGTTGA
CTCTGAGGATTTGCCTCTGAACAGCTCCTGAGAAATGCTCCAGCAGAGCAAAATCCTGAAAGTCATTTGCAAAAACGTTG
TTAAGAAGTGCCTTGAGCTCTTCTCCAAGCTGGCGGAAGACAAGGAGAATTACAAGAAATTCTATGAGGCATTCTCTAAA
AATCTCAAGCTTGGAATTCACGAGGATTCCACTAACCAACGCCGCCTGTCTGAGCTGCTGCGCTATCACACCTCCCAGTC
TGGAAGTGAGATGACATCTCTGTCAGAGTATGTTTCTCTCATGAAGGAGACACAGAAGTCCATGTATTACATCACTGGTG
AGAGCAAAGAGCAGGTGGCCAACTCAGCTTTTATGGAGCGAGTGCGGAAGCGGGGCTTCGAGGTGGTATCTATGACTGAG
CCCATTGACAAATACTGTGTGCGGCAGCTAAAGGAGTTTGATGGGAAGAGCCTCGTCTCAGTTACCAAGGAGGGTCTGGA
GCTACTGGAGGATGAGTAGGAGAAGAAGAAAATGGAAGAGAGCAAGGCAAAGTTTCAGAACCTCTGCAAGCTCATGGAAG
AAATCTTAGACAAGGTTGAGAAGGTGACAATCTCCAATAGGCTTGTGTCTTCACCCTGCTGCATTGTGACCAGCACCTAC
AGCTGGACAGCCAATATGGAGCGGATCATGAAAGCCCAGGCACTTCAGGGCAACTCCACCAGGAGCTACATGATGGCCAA
AAAGCACCTGGAGATCAACCCTGACCACCCATTGGGGAGACACCGCGGCAGAAGGCTGAGGCAGGCAAGAATGACAAGGC
AGTCAAGGACCTTGTGGTGCTGCTGTTTGAAACCGCACTGCTCTCTTCTGGCTTTTACCTTGAGGATCCCCAGACCTACT
CCAACTGCATCTACCGCATGACCAAGTTAGGTCTAGGTATCTATGAAGATGAAGTGGCAGCAGAGGAGTCCAGTGCTGCA
GTTCCTGATGAGATCCCTCCTCCTGAGGGTGATGAGGATGCGTCTCGAATGGAAGTAGTAGAT

Alignment

ORF - retro_cjac_2835 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.46 %
• Parental protein coverage: 66.01 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QLEFRALLFVPRRAPFDL-FE-NRKKKNNIKLYVRRVFIMDNCEELIPEYYIYFIRGVVDSEDLPLNISR
          QLEFRALLF...R.PFDL.FE...K..N..........IMD.C.ELIPEY...FI.G.VDSEDLPLN.S.
Retrocopy QLEFRALLFILIRLPFDL<FETDKKTSNSMSVCI----IMDSCDELIPEY-LNFICGAVDSEDLPLNSS*

Parental  EMLQQSKILKVIRKNLVKKCLELFTELAEDKENYKKFYEQFSKNIKLGIHEDSQNRKKLSELLRYYTSAS
          EMLQQSKILKVI.KN.VKKCLELF..LAEDKENYKKFYE.FSKN.KLGIHEDS.N...LSELLRY.TS.S
Retrocopy EMLQQSKILKVICKNVVKKCLELFSKLAEDKENYKKFYEAFSKNLKLGIHEDSTNQRRLSELLRYHTSQS

Parental  GDEMVSLKDYCTRMKENQKHIYYITGETKDQVANSAFVERLRKHGLEVIYMIEPIDEYCVQQLKEFEGKT
          G.EM.SL..Y...MKE.QK..YYITGE.K.QVANSAF.ER.RK.G.EV..M.EPID.YCV.QLKEF.GK.
Retrocopy GSEMTSLSEYVSLMKETQKSMYYITGESKEQVANSAFMERVRKRGFEVVSMTEPIDKYCVRQLKEFDGKS

Parental  LVSVTKEGLELPEDEEEKKKQEEKKTKFENLCKIMKDILEKKVEKVVVSNRLVTSPCCIVTSTYGWTANM
          LVSVTKEGLEL.EDE.EKKK.EE.K.KF.NLCK.M..IL..KVEKV..SNRLV.SPCCIVTSTY.WTANM
Retrocopy LVSVTKEGLELLEDE*EKKKMEESKAKFQNLCKLMEEILD-KVEKVTISNRLVSSPCCIVTSTYSWTANM

Parental  ERIMKAQALRDNSTMGYMAAKKHLEINPDH-SIIETLRQKAEADKNDKSVKDLVILLYETALLSSGFSLE
          ERIMKAQAL..NST..YM.AKKHLEINPDH..I.ET.RQKAEA.KNDK.VKDLV.LL.ETALLSSGF.LE
Retrocopy ERIMKAQALQGNSTRSYMMAKKHLEINPDH<PIGETPRQKAEAGKNDKAVKDLVVLLFETALLSSGFYLE

Parental  DPQTHANRIYRMIKLGLGIDEDDPTADDTSAAVTEEMPPLEGDDDTSRMEEVD
          DPQT..N.IYRM.KLGLGI.ED...A...SAAV..E.PP.EGD.D.SRME.VD
Retrocopy DPQTYSNCIYRMTKLGLGIYEDEVAAEESSAAVPDEIPPPEGDEDASRMEVVD

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	0.09 RPM	168.69 RPM
SRP051959_heart	0.11 RPM	217.01 RPM
SRP051959_kidney	0.02 RPM	145.21 RPM
SRP051959_liver	0.11 RPM	269.35 RPM
SRP051959_lung	0.15 RPM	194.35 RPM
SRP051959_lymph_node	0.14 RPM	189.24 RPM
SRP051959_skeletal_muscle	0.15 RPM	221.48 RPM
SRP051959_spleen	0.08 RPM	164.20 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2835 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2835 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2835 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,