RetrogeneDB ID: retro_cjac_3263

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:11504642..11505193(-)
• Located in intron of: ENSCJAG00000006840

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000035426
• Aliases: None
• Description: None

Sequence

>retro_cjac_3263
ATGGTGGTCCTGGCACCTCTGATTGCTCTGGTGTATTCTGTGCCGTGACTTTCACCATGGCTGGCCCAACCTTACTACCT
CCTGTCAGCCCTGCTCTCTGCTCCCTTCCTACTCGTGAGGAAACTGCTACCGCTCTGCAACGGTCTGCCCACCCAATGCA
AAGACAGCAACCTGCGTGACTTTGACTGGAGAGAAGTAGAGATCCTGATGTTCCTCAGTGCCATTGTGATGATAAAGAAC
CGCTGATCCATCACCGTGGAGCAATACATAGGCAACATTTTCATGTTTAGTAAAGTGGCCAATGCAATTCTTTTCTTCCG
CTTGGATATTTGCATGGGCCTTTTTACATCACACCCTGTGTAGTGTTGCTGATGATGTGCAAACCCCCACTATATATGGG
CCCTGAGAATATCAAGTACTTCAATGATAAAGCCATTGATGAGGAACTAGAACAGGACAAGAGGGTCACTTGGATTGTGA
AGTTCTTTGCCAATTGGCCTGATGACTGCCAATCATTTGCTCCTATCTATGCTGACCTCTCCCTCAAGTAC

Alignment

ORF - retro_cjac_3263 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.95 %
• Parental protein coverage: 62.16 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAILAPLIALVYSVPRLSRWLAQPYYLLSALLSAAFLLVRKLPPLCNGLPTQREDGNPCDFDWREVEILM
          M..LAPLIALVYSVP.LS.WLAQPYYLLSALLSA.FLLVRKL.PLCNGLPTQ..D.N..DFDWREVEILM
Retrocopy MVVLAPLIALVYSVP*LSPWLAQPYYLLSALLSAPFLLVRKLLPLCNGLPTQCKDSNLRDFDWREVEILM

Parental  FLSAIVMMKNRRSITVEQHIGNIFMFSKVANAILFFRLDIRMGL-LYITLCIVFLMTCKPPLYMGPENIK
          FLSAIVM.KNR.SITVEQ.IGNIFMFSKVANAILFFRLDI.MGL..YIT.C.V.LM.CKPPLYMGPENIK
Retrocopy FLSAIVMIKNR*SITVEQYIGNIFMFSKVANAILFFRLDICMGL<FYITPCVVLLMMCKPPLYMGPENIK

Parental  YFNDKTIDEELERDKRVTWIVEFFANWSNDCQSFAPIYADLSLKY
          YFNDK.IDEELE.DKRVTWIV.FFANW..DCQSFAPIYADLSLKY
Retrocopy YFNDKAIDEELEQDKRVTWIVKFFANWPDDCQSFAPIYADLSLKY

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	10.92 RPM
SRP051959_heart	0.04 RPM	8.74 RPM
SRP051959_kidney	0.91 RPM	13.78 RPM
SRP051959_liver	0.09 RPM	10.96 RPM
SRP051959_lung	0.03 RPM	7.71 RPM
SRP051959_lymph_node	0.00 RPM	7.92 RPM
SRP051959_skeletal_muscle	0.09 RPM	7.62 RPM
SRP051959_spleen	0.00 RPM	7.27 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3263 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3263 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3263 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000035426	1 retrocopy	retro_cjac_3263 ,
Homo sapiens	ENSG00000213593	1 retrocopy	retro_hsap_4158,
Gorilla gorilla	ENSGGOG00000001519	1 retrocopy	retro_ggor_2792,
Monodelphis domestica	ENSMODG00000020112	1 retrocopy	retro_mdom_924,
Mus musculus	ENSMUSG00000050043	1 retrocopy	retro_mmus_154,
Pan troglodytes	ENSPTRG00000033702	1 retrocopy	retro_ptro_2827,