RetrogeneDB ID: retro_cjac_3514

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01182568.1:5168..6557(+)
• 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_3514
TCAGATGAAGAGGATGATAGTGGTAAGGATAAGAAGAAAAAAACAAAGAAGATCAAAGAGGAATACATTGATCAGAAAGA
ACTAAACAAGACCAAACCTATTTGGACCAGAAACCCTGATGCCATCATTGAAGAGGAGTATGGAGAATTCTACAAAAGCC
TCACCAATGACTGGGAAGACAACTTGGCAGTCAAGCACCTTTCTGTAGAAGGTCAGTTGGAATTCAGGGCATTGCTATTC
ATTCCTCATCGGGCTCCCTTCGACCTTTTTGATAAGAAGAAGAAGAAAAAGAACAACATCAAACTCTATGTCCATCGTGT
ATTTATCATGGACAGCTGTGATGAGCTGATACCAGAGTATCTCAACTTTATTCATGGTGTGGTTGACTCTGAGGATTTGC
CTCTGAACATCTCCAGAGAAATGCTCCAGCAGAGAAAAGTCTTGAAAGTCATTCACAAAAACATTGTTAAGAAGTGCCTT
GAGCTCTTCTCTGAGCTGGCAGAATACAAGAAGAATTACAAGAAATTCTATGAGGCATTCTCTAAAAATCTCAAGCTTGA
AATTCACAAGGATTCCACTAACCAACACCGCCTGTCTGAGCTGCTGCATTATCACACCTCCCAGTCTGGAGATGAGATGA
CATCTCTGTCAGAGTATGTTTCTCGCATGAAGAAGACACAGAAGTCCATCTATTACATCACTGGTGAGAGCAAACAGCAG
GTGTCCAACTCAGCTTTTATAAAGCGAGTGCAGAAGCAGGGCTTCGAGGTGGTATATATGACTGAGCCCATTGATGAATA
CTGTGTGCAGCAGCTAAAGGAGTTTGATGGGAAGAGCCTGGTCTCAGTTACCAAGGAGGGTCTAGAGCTACCAGAGGATG
AGGAGGAGAAGAAGAAAATGGAAGAGAGCAAGGCAAAGTTTGAGAATCTCTGCAAGCTCATGAAAGAAATCTTAGATAAG
AAGGTTGAGAAAGTGACAATCACCAATAGGCTTGTGTCTTCACCCTGCTGCATTGTGACCAGCACCTATGGCTGGATAGC
CAATATGGAATAAGTCATGAGAGCCCAGGCACTTTGGGACAACTCCACCATGGGCTACATGATGGACAAAAAGTACCTGG
AGATCAACCCTGACCACCCTCTTGTGGAGACACTGTGGCAGAAGGCTGAGGCAGACAAGAATGACAAGACAGTCAACGAC
CTTGTGGTGCTGCTGTTTGAAACCGCCCTGCTCTCTTCTGGCTTTTCCCTTGAGGATCCCCAGACCCACTCCAACCACAT
CTACTGCATGATCAAGCTAGGTCTACGTATCAACGAAGATGAAGTGGCAGCAGAGGAACCCAGTGCTGCAGTTCCTGAGG
AGATCCCCCCTCTTGAGGGTGATGAGGAT

Alignment

ORF - retro_cjac_3514 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.65 %
• Parental protein coverage: 76.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SDDEESEDKPEIEDVGSVKEKYIDQEELNKTKPIWTRNPDDITNEEYGEFYKSLTNDWEDHLAVKHFSVE
          SD.E....K.........KE.YIDQ.ELNKTKPIWTRNPD.I..EEYGEFYKSLTNDWED.LAVKH.SVE
Retrocopy SDEEDDSGKDKKKKTKKIKEEYIDQKELNKTKPIWTRNPDAIIEEEYGEFYKSLTNDWEDNLAVKHLSVE

Parental  GQLEFRALLFVPRRAPFDLFE-NRKKKNNIKLYVRRVFIMDNCEELIPEYYIYFIRGVVDSEDLPLNISR
          GQLEFRALLF.P.RAPFDLF....KKKNNIKLYV.RVFIMD.C.ELIPE.Y..FI.GVVDSEDLPLNISR
Retrocopy GQLEFRALLFIPHRAPFDLFDKKKKKKNNIKLYVHRVFIMDSCDELIPE-YLNFIHGVVDSEDLPLNISR

Parental  EMLQQSKILKVIRKNLVKKCLELFTELAEDKENYKKFYEQFSKNIKLGIHEDSQNRKKLSELLRYYTSAS
          EMLQQ.K.LKVI.KN.VKKCLELF.ELAE.K.NYKKFYE.FSKN.KL.IH.DS.N...LSELL.Y.TS.S
Retrocopy EMLQQRKVLKVIHKNIVKKCLELFSELAEYKKNYKKFYEAFSKNLKLEIHKDSTNQHRLSELLHYHTSQS

Parental  GDEMVSLKDYCTRMKENQKHIYYITGETKDQVANSAFVERLRKHGLEVIYMIEPIDEYCVQQLKEFEGKT
          GDEM.SL..Y..RMK..QK.IYYITGE.K.QV.NSAF..R..K.G.EV.YM.EPIDEYCVQQLKEF.GK.
Retrocopy GDEMTSLSEYVSRMKKTQKSIYYITGESKQQVSNSAFIKRVQKQGFEVVYMTEPIDEYCVQQLKEFDGKS

Parental  LVSVTKEGLELPEDEEEKKKQEEKKTKFENLCKIMKDILEKKVEKVVVSNRLVTSPCCIVTSTYGWTANM
          LVSVTKEGLELPEDEEEKKK.EE.K.KFENLCK.MK.IL.KKVEKV...NRLV.SPCCIVTSTYGW.ANM
Retrocopy LVSVTKEGLELPEDEEEKKKMEESKAKFENLCKLMKEILDKKVEKVTITNRLVSSPCCIVTSTYGWIANM

Parental  ERIMKAQALRDNSTMGYMAAKKHLEINPDHSIIETLRQKAEADKNDKSVKDLVILLYETALLSSGFSLED
          E..M.AQAL.DNSTMGYM..KK.LEINPDH...ETL.QKAEADKNDK.V.DLV.LL.ETALLSSGFSLED
Retrocopy E*VMRAQALWDNSTMGYMMDKKYLEINPDHPLVETLWQKAEADKNDKTVNDLVVLLFETALLSSGFSLED

Parental  PQTHANRIYRMIKLGLGIDEDDPTADDTSAAVTEEMPPLEGDDD
          PQTH.N.IY.MIKLGL.I.ED...A...SAAV.EE.PPLEGD.D
Retrocopy PQTHSNHIYCMIKLGLRINEDEVAAEEPSAAVPEEIPPLEGDED

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	0.11 RPM	168.69 RPM
SRP051959_heart	0.21 RPM	217.01 RPM
SRP051959_kidney	0.16 RPM	145.21 RPM
SRP051959_liver	0.26 RPM	269.35 RPM
SRP051959_lung	0.13 RPM	194.35 RPM
SRP051959_lymph_node	0.27 RPM	189.24 RPM
SRP051959_skeletal_muscle	0.37 RPM	221.48 RPM
SRP051959_spleen	0.27 RPM	164.20 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3514 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3514 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3514 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,