RetrogeneDB ID: retro_cjac_2712

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:38002615..38003346(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000004064
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CA5B
• Ensembl ID: ENSCJAG00000004353
• Aliases: None
• Description: None

Sequence

>retro_cjac_2712
AGAGGGAGTGTTTATGATCTGGGTTTCAAACTGCTCACAGTCTCTTAGGACCCAGCTACCTGCTGCCACATCTGGAATAA
CGGGTCCTCTTTCCTTATGAAATTTGAAAATTCTACAGATAAATCAGTGATCAAGGAAGGACCCCTGGAACACAACTACC
GATTGAAGCAGTTCCATTTTTGCTGGGAGGCCATCGATGCCTGGGGCTCTGAGCATACCATGGATATCAAAGGCTTCCCA
GAGCTGCACTTAGTGCATTGGAATGCATCGAATTAGGAAACTTTGAGGATGCAGCACTGGAAGAAAATGGTTTGGTTGTG
ATAGGAGTGTTTGTAAAGCTAGGCAAACATCATAAAGAGCTACAAAAATTAGTGGATACTTTGCTATCAATTAAGCACAA
GGACACCTTTGTGGAATTGGGGTCATTTGACCCTTCCTGCCTGATACCTACCTGCCTGGATTACTGGGCCTACTCAGGGT
CTCTGACTACCCCATCCCTCTCCGACTCTGTCACCTGGATCATTAAGAGGCAACAAGTAGAGGTTGATCATGATCATCTG
GAGCAATTTTGGACCCTGCTTTTCATTTCTGAGGGGCAGAAAGAGAAAAGAATTGTGGACAACTTCCACCCTCTTCAGCC
ACTGATGAATCGCACTGTCCATTCAACTTTCCGGCACGATGATGAGCTGAATGTACAAGTGAAACCCAAGCCGGCCACCA
GCCAAGCAACC

Alignment

ORF - retro_cjac_2712 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.49 %
• Parental protein coverage: 77.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RDSVYDPGLKPLTISYDPATCLHIWNNGYSFLVEFEDSTDKSVIKGGPLEHNYRLKQFHFHWGAIDAWGS
          R.SVYD.G.K.LT.S.DPATC.HIWNNG.SFL..FE.STDKSVIK.GPLEHNYRLKQFHF.W.AIDAWGS
Retrocopy RGSVYDLGFKLLTVS*DPATCCHIWNNGSSFLMKFENSTDKSVIKEGPLEHNYRLKQFHFCWEAIDAWGS

Parental  EHTVDSKCFPAELHLVHWNA-VKFENFEDAALEENGLAVIGVFLKLGKYHKELQKLVDTLPSIKHKDTLV
          EHT.D.K.FP.ELHLVHWNA.....NFEDAALEENGL.VIGVF.KLGK.HKELQKLVDTL.SIKHKDT.V
Retrocopy EHTMDIKGFP-ELHLVHWNA<IELGNFEDAALEENGLVVIGVFVKLGKHHKELQKLVDTLLSIKHKDTFV

Parental  EFGSFDPSCLMPTCPDYWTYSGSLTTPPLSESVTWIIKKQPVEVDHDQLEQFRTLLFTSEGEKEKRMVDN
          E.GSFDPSCL.PTC.DYW.YSGSLTTP.LS.SVTWIIK.Q.VEVDHD.LEQF.TLLF.SEG.KEKR.VDN
Retrocopy ELGSFDPSCLIPTCLDYWAYSGSLTTPSLSDSVTWIIKRQQVEVDHDHLEQFWTLLFISEGQKEKRIVDN

Parental  FRPLQPLMNRTVRSSFQHDYVLNVQAKPKPATSQAT
          F.PLQPLMNRTV.S.F.HD..LNVQ.KPKPATSQAT
Retrocopy FHPLQPLMNRTVHSTFRHDDELNVQVKPKPATSQAT

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	3.97 RPM
SRP051959_heart	0.00 RPM	14.07 RPM
SRP051959_kidney	0.00 RPM	11.54 RPM
SRP051959_liver	0.00 RPM	2.17 RPM
SRP051959_lung	0.00 RPM	13.03 RPM
SRP051959_lymph_node	0.00 RPM	12.03 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.38 RPM
SRP051959_spleen	0.00 RPM	10.32 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2712 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2712 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2712 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012150	1 retrocopy	retro_cfam_1201,
Callithrix jacchus	ENSCJAG00000004353	1 retrocopy	retro_cjac_2712 ,