RetrogeneDB ID: retro_cjac_1772

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:36069883..36070793(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000031894
• Aliases: None
• Description: None

Sequence

>retro_cjac_1772
TGCACAGACTCACCTAGGGAACCTCTGGGGACCCTGCTCCGCTACCACAACCCGAGTGAGGCCGGATCTCACACCCTCCA
GACGACCTATGGCTGCAACCTGGGGCCTGATGAGCACCTCCTCCATGGGTATTACCAACATGCCTTTGATGGCAAGGATT
ACATTGCCCTGAATGAGTACCTGTGCTCTTGGACAGAGGCTGACATGACTGCTCAAATCACCCAGCTCAAGTTGGAGGCC
GCGCATGCAGAAGGGCTCAGGGCCTACCTGGAGGGCATATACCTGAAGTGGCTCCACAGACACCTGGCCAAGGGGAAGGA
GACACTGCAGCATGCGGACCCCCCAAAGACACATGTGACCCATCACCCTGTCTCTGACCATGAGGCCACCCTGAGGTGCT
GGGCCCTGGCTTCTACCCTGCGGAGATCACACTGACCTGGCAGAGGGATGGGAAGGACCAAACTCAGGACACCGAGCTTG
TGGAGACCAGGCCAGCAGGGGATGGAAACTTCCAGAAGTGGGCAGCTGTGGTGGTGCCTTCTGGAGAAGAGCAGAGATAC
ACGTGCCATGTGCAGCATAAGGGATTGCCCGAGCCCCTCACCCTGAGGTGGGAGCCGTCTTCCCAGCCCACTGTCCCCAT
CGTGGGCATCATTGCTGACCTGGTTGTCTTTGGAGCTATGGCCATTGGAGCTGTGGTCACTGCTGTGATCTGGAGGAGGA
AGAGCTCAGGTGGAAAAGGAGGGAGCTACTCTCAGGCTGCATGCAGGGACAGTGCCCAGGGCTCTGATGTGTCTCTCACG
GCTTATAAAGCCTGAGACAGCTGCCTCGTGTGGGTTTGAGATGCAAGATTTCTTCACGCCTCACCTTTCTGACTTCAAGA
GCCTCTGGCATCTCTTTCTGTGAAGGCATC

Alignment

ORF - retro_cjac_1772 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.34 %
• Parental protein coverage: 76.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  CAQACRVSLRDIRGYYNQSEAGSHTLQVLFGCDLWPDGHLLLGYCRIAYDGKDHVALNEDLRSWTAADTV
          C....R..L.....Y.N.SEAGSHTLQ...GC.L.PD.HLL.GY...A.DGKD..ALNE.L.SWT.AD..
Retrocopy CTDSPREPLGTLLRYHNPSEAGSHTLQTTYGCNLGPDEHLLHGYYQHAFDGKDYIALNEYLCSWTEADMT

Parental  AEFTQRKLEAEKYAEQLRAQLEGECVEMLKRYLENGKETLQRAEPPKTHVTHHSISNQEVTLRCWAL-GF
          A..TQ.KLEA...AE.LRA.LEG.....L.R.L..GKETLQ.A.PPKTHVTHH..S..E.TLRCWAL.GF
Retrocopy AQITQLKLEAA-HAEGLRAYLEGIYLKWLHRHLAKGKETLQHADPPKTHVTHHPVSDHEATLRCWAL<GF

Parental  YPAEVTLTWQRDGEDQTQDTELVETRPAGDGNFQKWAAVVVPSGEEQRYTCHVQHEGLLEPLSLRWEPSS
          YPAE.TLTWQRDG.DQTQDTELVETRPAGDGNFQKWAAVVVPSGEEQRYTCHVQH.GL.EPL.LRWEPSS
Retrocopy YPAEITLTWQRDGKDQTQDTELVETRPAGDGNFQKWAAVVVPSGEEQRYTCHVQHKGLPEPLTLRWEPSS

Parental  QPTIPIMGIIAGLAVLGTVVIGAVVTAVIWRRK-SSGR-EGVRSGVWAVTVPRALMCLSGLVKPETAAC-
          QPT.PI.GIIA.L.V.G...IGAVVTAVIWRRK.S.G..EG......A.TVPRALMCLS.L.KPETAA..
Retrocopy QPTVPIVGIIADLVVFGAMAIGAVVTAVIWRRKSSGGK>EGATLRLHAGTVPRALMCLSRLIKPETAAS>

Parental  VGLRCRISSRLLFVTSRASGISFCKGI
          VGLRC.ISSRL.F.TSRASGISFC.GI
Retrocopy VGLRCKISSRLTFLTSRASGISFCEGI

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	0.02 RPM	1.91 RPM
SRP051959_heart	0.02 RPM	1.32 RPM
SRP051959_kidney	0.04 RPM	1.18 RPM
SRP051959_liver	0.06 RPM	0.43 RPM
SRP051959_lung	0.00 RPM	2.03 RPM
SRP051959_lymph_node	0.00 RPM	0.68 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.46 RPM
SRP051959_spleen	0.00 RPM	1.66 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1772 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1772 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1772 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000031894	1 retrocopy	retro_cjac_1772 ,