RetrogeneDB ID: retro_cjac_4016

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL288442.1:8485..9232(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000035377
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000002838
• Aliases: None
• Description: None

Sequence

>retro_cjac_4016
ATGGAGGACGTCTTGGCCGGGCCCCTGCACCGGGCGGCGGCGGAGGCGGCCGAGGCATGAGCGCGGCCCGGGGTGACGCT
GCTGCCCTTAGTGCCCCTCACAGGGACTGCGGAGGCGGACGAGGGCGGCGGCCACTGGAGCTTCATTGACTGCGAGATGG
AGGAGGTGGACCTGCAGGACCTGCCCAGCGCCACCATCGCCTGCCACCCGGACCCGCCCTTGTTCGTGGATGGCCTGTGC
CGGGCCAAATTTGAGTCTGTCTTTAGGACATATGGCAAGGACATCGCCTTTCAGTATTTTAAGAGTTTCAAACGAGTCAG
AATAAACTTCAGCAACCTCTTCTCCGCAGCAGATGTCAGGCTCCAGCTGCATAAGACTGAGTTTCTGGGAAAGGAAATGA
AGTTATATTTTGCTCAGACCTTACACATAGGAAGCTCGCACCTGGCTCCGCCAAACCCCGACAAGCAGTTTCTGATCTCC
CCTCCCACCTCTCCACCAGTGGGGTGGAAACAAGTGGAAGACGCAACCCCAGTCATAAACTATGATCTCTTATATGCTAT
CTCCAAGCTGGGGCCAGGGGAAAAGTATGAATTGCATGCAGCGACTGACACCACTCCCAGCGCGGTAGTCCACGTATGTG
AGAGCGATGAAGAGGAGGAGGAAGAAGAGGAGATGGAGAGAATGAAGAGACCCAAGCCAAAAATTATCCAGACCAGGAAG
CCGGAGTACACACGGATCCACCTCAGC

Alignment

ORF - retro_cjac_4016 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.36 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEDGLAGPRHGAAAEATEARARPGATLRPFAPLSGTAEADEGGGDWSFIDCEMEEVDLQDLPSATIACHL
          MED.LAGP.H.AAAEA.EA.ARPG.TL.P..PL.GTAEADEGGG.WSFIDCEMEEVDLQDLPSATIACH.
Retrocopy MEDVLAGPLHRAAAEAAEA*ARPGVTLLPLVPLTGTAEADEGGGHWSFIDCEMEEVDLQDLPSATIACHP

Parental  DPRVFVDGLCRAKFESLFRTYDKDITFQYFKSFKRVRINFSNPFSAADARLQLHKTEFLGKEMKLYFAQT
          DP..FVDGLCRAKFES.FRTY.KDI.FQYFKSFKRVRINFSN.FSAAD.RLQLHKTEFLGKEMKLYFAQT
Retrocopy DPPLFVDGLCRAKFESVFRTYGKDIAFQYFKSFKRVRINFSNLFSAADVRLQLHKTEFLGKEMKLYFAQT

Parental  LHIGSSHLAPPNPDKQFLISPPASPPVGWKQVEDATPVINYDLLYAISKLGPGEKYELHAATDTTPSVVV
          LHIGSSHLAPPNPDKQFLISPP.SPPVGWKQVEDATPVINYDLLYAISKLGPGEKYELHAATDTTPS.VV
Retrocopy LHIGSSHLAPPNPDKQFLISPPTSPPVGWKQVEDATPVINYDLLYAISKLGPGEKYELHAATDTTPSAVV

Parental  HVCESDEEKEEEEEMERMKRPKPKIIQTRRPEYTPIHLS
          HVCESDEE.EEEEEMERMKRPKPKIIQTR.PEYT.IHLS
Retrocopy HVCESDEEEEEEEEMERMKRPKPKIIQTRKPEYTRIHLS

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	0.04 RPM	12.60 RPM
SRP051959_heart	0.11 RPM	31.59 RPM
SRP051959_kidney	0.20 RPM	110.18 RPM
SRP051959_liver	0.06 RPM	29.11 RPM
SRP051959_lung	0.02 RPM	14.32 RPM
SRP051959_lymph_node	0.07 RPM	10.96 RPM
SRP051959_skeletal_muscle	0.00 RPM	78.01 RPM
SRP051959_spleen	0.06 RPM	14.12 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4016 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4016 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4016 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002838	2 retrocopies	retro_cjac_4016 , retro_cjac_437,
Callithrix jacchus	ENSCJAG00000012084	1 retrocopy	retro_cjac_2149,
Cavia porcellus	ENSCPOG00000010683	1 retrocopy	retro_cpor_1267,
Tarsius syrichta	ENSTSYG00000006972	1 retrocopy	retro_tsyr_1913,