RetrogeneDB ID: retro_cjac_239

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:87805285..87806260(-)
• Located in intron of: ENSCJAG00000020148

Retrocopy information

• Ensembl ID: ENSCJAG00000020160
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000004677
• Aliases: None
• Description: None

Sequence

>retro_cjac_239
ATGATGTCTAGCAACTCCAGTGAAGCTGATGTGATAATAACAAGAATATCTACTTATGATGATGACAACACTGTTCTTCA
TGCATATGAAACAAAACATAAATTTGCAAATGAAACAAAAACTGAGCAGGAACCGATTACTGTAGCTGATGCATCCTGTA
ATACTGAAGAGCAACCGAAGTCAGTGTATGATGTCGTTACCTATTGCCAAGTTATATATGATACTATCCAAAACCTGGAT
AAGAAGATTGATGGCATTAGCAGAAAGGTTTCAAAAATCCAACGTTTCAATGCAAAAGCAGTGTGGACGAATCGCAAGCC
ATCTGGCTTTGGATATGGATATGCATACAGAAATTATTCTTGCCTGCTTGCTAAAAAGCTTAAACTCCAGAAAACGAAGA
AAAGTCAGGCTTACGAGACATTCTCCTACCCTCAAAGTTATAGTCCCACTTCACCAGTGGCAGTGCAGGCGGATAATTCC
CAGAGGAACAATCCAGCACCATCCTTTCACATGGAAGAAGAATACCAGCGAGCTGAGCCGGAGGAGGACCCAGTCCTCAG
CTGCACTCCGAGTCCAGTGCATCCCTCAGACCACTCTGAGCATGGTTTTCAACCATCTTATGCATCTGATGGTGCAATGC
CTGGCTCTTCAGGGCCCTACCGTGGCAGCGCTAGGGTTAACAGCAGCCAAGTTACAAGCATACCAATGGACAATGACCTG
TATTTAGAGGACAACTTCATTAAGCACCCTGCAACATGGTCGGTGGAAGCAGTGGGTTTATTTCTGAAGCAAACGGATCC
TAAGACATTATGCCCTCTTGTCGATCTCTTCAGAACCTATAAAACTGATGGGAAGGCTCTGCTCCTACTCACGAGCGACC
TGATGCTGAAGTACTTGGGTCGGAAGCTGGGAAGGGTCATGAAGCTATGCTACTACATTGAACAACTTAAACAAGGAAAA
TGCTTTGAAAATTAA

Alignment

ORF - retro_cjac_239 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.07 %
• Parental protein coverage: 67.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MMSSNTSEADVIKTRISTYDDDNTVVLHAYETKHKFANETKTE-EPITVADASCNTEEQPKSVYDVLTYC
          MMSSN.SEADVI.TRISTYDDDNTV.LHAYETKHKFANETKTE.EPITVADASCNTEEQPKSVYDV.TYC
Retrocopy MMSSNSSEADVIITRISTYDDDNTV-LHAYETKHKFANETKTEQEPITVADASCNTEEQPKSVYDVVTYC

Parental  QVIYDAIQNLDKKIDGISRKVSKIQRFNAKAGSTNRKPSGFGYGYAYRNYSCLLAKKLKLQKMKKSQAYE
          QVIYD.IQNLDKKIDGISRKVSKIQRFNAKA..TNRKPSGFGYGYAYRNYSCLLAKKLKLQK.KKSQAYE
Retrocopy QVIYDTIQNLDKKIDGISRKVSKIQRFNAKAVWTNRKPSGFGYGYAYRNYSCLLAKKLKLQKTKKSQAYE

Parental  TFSYSQSYSPTSPVAVRADDSQSNNPAPSFHM-EEYQRAEPEEDPVLSCTPSPVHPSDHSEHGFQPSYAS
          TFSY.QSYSPTSPVAV.AD.SQ.NNPAPSFHM.EEYQRAEPEEDPVLSCTPSPVHPSDHSEHGFQPSYAS
Retrocopy TFSYPQSYSPTSPVAVQADNSQRNNPAPSFHMEEEYQRAEPEEDPVLSCTPSPVHPSDHSEHGFQPSYAS

Parental  DGAMPGSSRPYRGSTRVNSSQ
          DGAMPGSS.PYRGS.RVNSSQ
Retrocopy DGAMPGSSGPYRGSARVNSSQ

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	0.09 RPM
SRP051959_heart	0.00 RPM	0.00 RPM
SRP051959_kidney	0.09 RPM	0.60 RPM
SRP051959_liver	0.00 RPM	0.00 RPM
SRP051959_lung	0.00 RPM	0.00 RPM
SRP051959_lymph_node	0.00 RPM	0.00 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.00 RPM
SRP051959_spleen	0.00 RPM	0.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_239 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_239 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_239 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
Callithrix jacchus	ENSCJAG00000004677	1 retrocopy	retro_cjac_239 ,
Vicugna pacos	ENSVPAG00000003425	1 retrocopy	retro_vpac_326,