RetrogeneDB ID: retro_cjac_173

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:85972845..85973442(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022900
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000014351
• Aliases: None
• Description: None

Sequence

>retro_cjac_173
ATGGACAAGACCTGTGAAATGAAACGCACCACGCTGGACAGCCCTTTGCGGAAGCTGGAGCTGTCCTGTTGTGAGCAAGG
TCTGCACGAAATCAGCTTCCTGGGCCGGGGGACGCCCGCAGCTGATGCCATGGAGGTCCCAGCCCCAGCTGGGGTTCTCA
GAGGTCCCGAGCCCCTGAAGCAGTGCGCAGCCTGGCTCAACGCCTATTTCCAGCAGCCCGAGGCCATCGAGGAGCTCCCC
GTGCCGACTCTTCACCACCCCGTTTTCCAGCAAGAGTCGTGTACCAGGCAGGTGTTATGGGAGCTGCTGAAGGCTGTGAA
ATTCGGAGAAGTGGTTTCTTACCAACAATTAGCAGCCCTGGCAGGCAACCCCAAAGCCACGCGAGCAGTGGGAGGAGCAA
TGAGAAGCAACCCTGTCCCCATCCTCATCCCGTGCCACAGAGTGGTCTGCAGCAGCGGAACCATGGGCAACTACTCCGGA
GGACTGGCGGTGAAGGAATGGCTTCTGGTCTACGAAGGCCACCGGGTGGGGAAGCCAGCCTTGGGAGGGAGCTCGAGTCG
GGCAGGGGCCTGGCTCAGGGCAGTGGGGACCACCTAG

Alignment

ORF - retro_cjac_173 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.43 %
• Parental protein coverage: 95.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDKTCEMKRTTLDSPLGKLELSGCEQGLHKISFLGQGTPAADAMEVPAPAEVLRGPEPLKQCAAWLNAYF
          MDKTCEMKRTTLDSPL.KLELS.CEQGLH.ISFLG.GTPAADAMEVPAPA.VLRGPEPLKQCAAWLNAYF
Retrocopy MDKTCEMKRTTLDSPLRKLELSCCEQGLHEISFLGRGTPAADAMEVPAPAGVLRGPEPLKQCAAWLNAYF

Parental  QQPEAIEELPVPALHHPVFQQESFTRQVLWELLKAVKFGEVVSYQQLAALAGNPKAARAVGGAMRSNPVP
          QQPEAIEELPVP.LHHPVFQQES.TRQVLWELLKAVKFGEVVSYQQLAALAGNPKA.RAVGGAMRSNPVP
Retrocopy QQPEAIEELPVPTLHHPVFQQESCTRQVLWELLKAVKFGEVVSYQQLAALAGNPKATRAVGGAMRSNPVP

Parental  ILIPCHRVVCSSGAMGNYSGGLAVKEWLLVHEGHRVGKPALGRSSRRAGAWLRAVGPT
          ILIPCHRVVCSSG.MGNYSGGLAVKEWLLV.EGHRVGKPALG.SS.RAGAWLRAVG.T
Retrocopy ILIPCHRVVCSSGTMGNYSGGLAVKEWLLVYEGHRVGKPALGGSSSRAGAWLRAVGTT

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	0.00 RPM	2.24 RPM
SRP051959_heart	0.00 RPM	1.54 RPM
SRP051959_kidney	0.00 RPM	1.00 RPM
SRP051959_liver	0.00 RPM	3.03 RPM
SRP051959_lung	0.00 RPM	2.67 RPM
SRP051959_lymph_node	0.00 RPM	2.26 RPM
SRP051959_skeletal_muscle	0.02 RPM	0.76 RPM
SRP051959_spleen	0.00 RPM	1.30 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_173 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_173 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_173 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	ENSCJAG00000014351	1 retrocopy	retro_cjac_173 ,