RetrogeneDB ID: retro_cjac_3601

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01187446.1:2835..4256(-)
• 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_3601
TCAGATGAGGAGGATGATAGCAGTAAGAATAAGAAGAAGAAAACTAAGAAGATCAAAGAGAAATACATTGATCAGGAAGA
ACTAAACAAGACTGAGCCTCTTTGGACCAGAAACCCTGATGACATCATTCAAGAAGAGTATGGAGAATTCTACAAAAGCC
TCACCAATGACTGGGAAGACCACTTGGCAGTCAAGCACTTTTCTGTAGAAGGTCAGTTGGAATTCAGGGCATTGCTATTC
ATTCCTCATTGGGCTTCCTTTGAACTTTTTGAGAACAAGAAGAAAAAGAACAACATCAAACTCTATGCCCACCATGTATT
TATCATGGACAGCTGTGATGAGCTGATACCAGAGTATCTCAACTTTAATCGTGGTATGGTTGACTCTGAGAATTTGCCTC
TGAACATCTCCAGAGAAATGCTCCAGCAGAGCAAAATCTTGAAAGTCATTCGCAAAAACATTGTTAAGAAGTGCGTTGAG
CTCTTCTCTGAGCTGGCAGAAGACAAGGAGAATTACAAAAAATTCTATGAGGCATTCTCTAAAACTCTCAAGCTTGGAAT
TCATGAGGATTCCACTAACCAACGCCGCCTTTCTGAGCTGCTGCACTATCACACCAGCTGCTGCACTATCACACCTGGAG
ATGAGATGACATCTCTGTCAGAGTATGTTTCTCGCAAGAAAGAGACACGGAAGTCCATCTATTACATCACTGGTGAGAGC
AAAGAGCAGGTGGCCAACTCAGCTTTTGTGCAGTGAGTGCAGAAGTGGGGCTTCGAGGTGGTATATATGACTGAGCCCAT
CGATGAATACTGTGTGCAGCAGCTAAAGGAGTTTGATGGGAAGAGCCTGGTCTCAGTTACCAAGGAGGATCTGGAGCTAC
CGGTGGATGAGGAAGAGAAGAAGAAAATGGAAGGGAGCAAGGCAAAGTTTGAGAACCTCTGCAAGCTCATGAAAGAAATC
TTAGATAAGAAGGTTGAGAAGGTGACAATCTCCAATAGGCTTGTGTCTTCACTCTGCTGCATTGTGACCAGCACCTATGG
CTGGATAGCCAATATGGAATAAATCATGAGAGCCCAGGCACTTTGGGACAACTCCACCATGGGCTACATGATGGACAAAA
AGCACCTGGAGATCAACCCTGACCACCCTCTTGTGGAGACGCTGTGGCAGAAGGCTGAGGCAGACAAGAAAGACAAGACA
GTCAACGACCTTGTGGTGCTGCTGTTTGAAACCACCCTGCTCTCTTCTGGCTTTTCCCTTGAGGATCCCCAGACCCACTC
CAACCACATCTACTGTATGACCAAGCAAGGTCTACGTATCAATGAAGATGAAGTGGCAGCAGAGGAACTCAGTGCTATAG
TTCTGGATGAGATCCCCCCCTTGAGGGTGATGAGGATGCATCTCACGTGGAAGAAGTAGAT

Alignment

ORF - retro_cjac_3601 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.74 %
• Parental protein coverage: 77.72 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SDDEESEDKPEIEDVGSVKEKYIDQEELNKTKPIWTRNPDDITNEEYGEFYKSLTNDWEDHLAVKHFSVE
          SD.E....K.........KEKYIDQEELNKT.P.WTRNPDDI..EEYGEFYKSLTNDWEDHLAVKHFSVE
Retrocopy SDEEDDSSKNKKKKTKKIKEKYIDQEELNKTEPLWTRNPDDIIQEEYGEFYKSLTNDWEDHLAVKHFSVE

Parental  GQLEFRALLFVPRRAPFDLFENRKKKNNIKLYVRRVFIMDNCEELIPEYYIYFIRGVVDSEDLPLNISRE
          GQLEFRALLF.P..A.F.LFEN.KKKNNIKLY...VFIMD.C.ELIPE.Y..F.RG.VDSE.LPLNISRE
Retrocopy GQLEFRALLFIPHWASFELFENKKKKNNIKLYAHHVFIMDSCDELIPE-YLNFNRGMVDSENLPLNISRE

Parental  MLQQSKILKVIRKNLVKKCLELFTELAEDKENYKKFYEQFSKNIKLGIHEDSQNRKKLSELLRYYTS---
          MLQQSKILKVIRKN.VKKC.ELF.ELAEDKENYKKFYE.FSK..KLGIHEDS.N...LSELL.Y.TS...
Retrocopy MLQQSKILKVIRKNIVKKCVELFSELAEDKENYKKFYEAFSKTLKLGIHEDSTNQRRLSELLHYHTSCCT

Parental  -ASGDEMVSLKDYCTRMKENQKHIYYITGETKDQVANSAFVERLRKHGLEVIYMIEPIDEYCVQQLKEFE
          ...GDEM.SL..Y..R.KE..K.IYYITGE.K.QVANSAFV....K.G.EV.YM.EPIDEYCVQQLKEF.
Retrocopy ITPGDEMTSLSEYVSRKKETRKSIYYITGESKEQVANSAFVQ*VQKWGFEVVYMTEPIDEYCVQQLKEFD

Parental  GKTLVSVTKEGLELPEDEEEKKKQEEKKTKFENLCKIMKDILEKKVEKVVVSNRLVTSPCCIVTSTYGWT
          GK.LVSVTKE.LELP.DEEEKKK.E..K.KFENLCK.MK.IL.KKVEKV..SNRLV.S.CCIVTSTYGW.
Retrocopy GKSLVSVTKEDLELPVDEEEKKKMEGSKAKFENLCKLMKEILDKKVEKVTISNRLVSSLCCIVTSTYGWI

Parental  ANMERIMKAQALRDNSTMGYMAAKKHLEINPDHSIIETLRQKAEADKNDKSVKDLVILLYETALLSSGFS
          ANME.IM.AQAL.DNSTMGYM..KKHLEINPDH...ETL.QKAEADK.DK.V.DLV.LL.ET.LLSSGFS
Retrocopy ANME*IMRAQALWDNSTMGYMMDKKHLEINPDHPLVETLWQKAEADKKDKTVNDLVVLLFETTLLSSGFS

Parental  LEDPQTHANRIYRMIKLGLGIDEDDPTADDTSAAVTEEM-PPLEGDDDTSRMEEVD
          LEDPQTH.N.IY.M.K.GL.I.ED...A...SA.V..E..PPLEGD.D.S..EEVD
Retrocopy LEDPQTHSNHIYCMTKQGLRINEDEVAAEELSAIVLDEI<PPLEGDEDASHVEEVD

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	0.04 RPM	168.69 RPM
SRP051959_heart	0.12 RPM	217.01 RPM
SRP051959_kidney	0.07 RPM	145.21 RPM
SRP051959_liver	0.15 RPM	269.35 RPM
SRP051959_lung	0.05 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_3601 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3601 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3601 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,