RetrogeneDB ID: retro_cjac_3626

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01190137.1:3535..4498(+)
• 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_3626
TCAGACGAGGAGGATGATAGTGGTAAGGATAAGAAGAAGGAAACTAAGAAGTTCAAAGAGAAATACATTGATCAGGAAGA
ACTAAACAAGACCAAGCCTATTTGGACTAGAAACCCTGATGCCATCATTGAAGAGGAGTATGGAGAATTCTACAAAAGCC
TCACCAATGACTGGGAAGACCACTTGGCAGTCAAGCACTTTTCTGTAGAAGGTCAGTTGGAATTCAGGGCATTGCTATTC
ATTCCTCGTCGGGCTCCCTTTGACCTTTTTGAGAACAAGAAGAACAACATCAAACTCTATGTCCATCGTGTATTCATCAT
GGATGGCTGTGATGAGCTGATACCAGAGTATCTCAGCTTTATCCGTGGTGTGGTTGACTCTGAGGGTTTGCCCCTGAACA
TCTCCCGAGAAATGCTCCAGCAGAGCAAAATCTTGAAAGTCATTCGCAAAAACATTGTTAAGAAGTGCCTTGAGCTCTTC
TCTGAGTTGGCAGAAGACAAGGAGAATTACAGGAAATTCTATGAGGCGTTCTGTAAAAATCTCAAGCTTGGAATTCACGA
GGATTCCACTAACCGACGCCGCCTGCCTGAGCTACTGCACTATCACACCTCCCAGTCTGGAGGTGAGATGACATCTCGGT
CAGAGTATGTTTCTCACATGAAGGAGACGCAGAAGTCCATCTATTACATCACTGGTGAGAGCAAAGAGCAGGTGGCCAAC
TCAGCTTTTGTGGCGCGAGTCCGGAAGCAGGGCTTCGAGGTGGTATATATGACTGAGCCCATTGACGGATACTCTGTGCA
GCAGCTAAAGCAGTTTGATGGGAAGAGCCTGGCCTCAGTTACCAAGGAGGGTCTGCAGCTACCAGAGGATGAGGAGGAGA
AGAAGAAAATGGAAGAGAGCAAGGCAAAGTTTGAGAACCTCTGCAAACTCATGAAAGAAATCTTAGATAAGAAGGTGAGA
AGG

Alignment

ORF - retro_cjac_3626 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.47 %
• Parental protein coverage: 53.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SDDEESEDKPEIEDVGSVKEKYIDQEELNKTKPIWTRNPDDITNEEYGEFYKSLTNDWEDHLAVKHFSVE
          SD.E....K.........KEKYIDQEELNKTKPIWTRNPD.I..EEYGEFYKSLTNDWEDHLAVKHFSVE
Retrocopy SDEEDDSGKDKKKETKKFKEKYIDQEELNKTKPIWTRNPDAIIEEEYGEFYKSLTNDWEDHLAVKHFSVE

Parental  GQLEFRALLFVPRRAPFDLFENRKKKNNIKLYVRRVFIMDNCEELIPEYYIYFIRGVVDSEDLPLNISRE
          GQLEFRALLF.PRRAPFDLFEN..KKNNIKLYV.RVFIMD.C.ELIPEY...FIRGVVDSE.LPLNISRE
Retrocopy GQLEFRALLFIPRRAPFDLFEN--KKNNIKLYVHRVFIMDGCDELIPEY-LSFIRGVVDSEGLPLNISRE

Parental  MLQQSKILKVIRKNLVKKCLELFTELAEDKENYKKFYEQFSKNIKLGIHEDSQNRKKLSELLRYYTSASG
          MLQQSKILKVIRKN.VKKCLELF.ELAEDKENY.KFYE.F.KN.KLGIHEDS.NR..L.ELL.Y.TS.SG
Retrocopy MLQQSKILKVIRKNIVKKCLELFSELAEDKENYRKFYEAFCKNLKLGIHEDSTNRRRLPELLHYHTSQSG

Parental  DEMVSLKDYCTRMKENQKHIYYITGETKDQVANSAFVERLRKHGLEVIYMIEPIDEYCVQQLKEFEGKTL
          .EM.S...Y...MKE.QK.IYYITGE.K.QVANSAFV.R.RK.G.EV.YM.EPID.Y.VQQLK.F.GK.L
Retrocopy GEMTSRSEYVSHMKETQKSIYYITGESKEQVANSAFVARVRKQGFEVVYMTEPIDGYSVQQLKQFDGKSL

Parental  VSVTKEGLELPEDEEEKKKQEEKKTKFENLCKIMKDILEKKVEK
          .SVTKEGL.LPEDEEEKKK.EE.K.KFENLCK.MK.IL.KKV..
Retrocopy ASVTKEGLQLPEDEEEKKKMEESKAKFENLCKLMKEILDKKVRR

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	2.09 RPM	168.69 RPM
SRP051959_heart	1.75 RPM	217.01 RPM
SRP051959_kidney	1.80 RPM	145.21 RPM
SRP051959_liver	2.97 RPM	269.35 RPM
SRP051959_lung	1.55 RPM	194.35 RPM
SRP051959_lymph_node	2.49 RPM	189.24 RPM
SRP051959_skeletal_muscle	3.47 RPM	221.48 RPM
SRP051959_spleen	1.89 RPM	164.20 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3626 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3626 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3626 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,