RetrogeneDB ID: retro_cjac_4012

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL288279.1:13542..14835(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000033660
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CSTF1
• Ensembl ID: ENSCJAG00000011281
• Aliases: None
• Description: None

Sequence

>retro_cjac_4012
ATGTATAGAACCAAAGTGGGCTTGAAGGACCGCCAGCAGCTCTACAAGCTGATCATTAGCCAGCTGCTGTATGACGGCTA
CATCAGCATCGCCAATGGACTCATCAATGAAATCAAGCCTCAGTCTGTCTGTGCACCCTCGGAGCAGCTCCTGCATCTCA
TCAAACTAGGAATGGAAAATGATGACACCGCAGTGCAGTATGCAATTGGTCGTTCAGATACTGTTGCCCCTGGCACAGGA
ATTGACCTGGAATTTGATGCAGATGTCCAGACTATGTCCCCAGAGGCTTCTGAGTATGAAACATGCTATGTCACATCACA
TAAGGGACCATGCCGTGTAGCTACCTATAGTAGAGATGGACAGTTAATAGCTACTGGGTCTGCTGATGCTTCGATAAAGA
TACTTGACACAGAGAGGATGTTAGCCAAAAGTGCCATGCCAATAGAGGTCATGATGAATGAGACCGCACAACAAAATATG
GAAAACCACCCAGTGATTCGAACTCTTTATGACCATGTGGATGAAGTCACATGCCTCGCTTTCCACCCAACAGAACAGAT
TCTGGCTTCTGGTTCAAGGGATTATACTCTTAAATTATTTGATTATTCCAAACCATCAGCAAAAAGAGCCTTCAAATACA
TTCAGGAAGCTGAAATGTTACGCTCCATCTCTTTTCATCCTTCTGGAGACTTTATACTTGTTGGAACTCAGCATCCTACT
CTTCGTCTATATGATATCAACACCTTTCAATGTTTTGTCTCTTGCAATCCTCAAGATCAACACACCGATGCTATATGTTC
CGTTAATTACAATTCTAGTGCCAATATGTACGTAACTGGAAGCAAGGACGGCTGCATCAAATTATGGGATGGTGTTTCAA
ATCGATGCATCACAACTTTTGAAAAAGCACACGATGGGGCTGAAGTTTGTTCTGCCATTTTTTCCAAAAATTCTAAATAC
ATTCTCTCAAGTGGAAAAGACTCTGTAGCTAAACTTTGGGAAATATCAACAGGACGAACACTGGTCAGATACACGGGTGC
GGGTCTGAGTGGACGCCAGGTGCACCGGACACAGGCTATGTTTAACCACACCGAGGACTATGTGTTGCTGCCCGACGAGA
GGACTATCAGTCTCTGCTGCTGGGACTCTACGACGGCCGAGCGGAGAAACCTGCTCTCCTTGGGGCACAACAACATTGTA
CGCTGCATAGTGCACTCACCCACCAACCCTGGGTTCATGACGTGCAGCGATGACTTCAGAGCGCGATTTTGGTACCGGAG
ATCCACCACCGAC

Alignment

ORF - retro_cjac_4012 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.54 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MYRTKVGLKDRQQLYKLIISQLLYDGYISIANGLINEIKPQSVCAPSEQLLHLIKLGMENDDTAVQYAIG
          MYRTKVGLKDRQQLYKLIISQLLYDGYISIANGLINEIKPQSVCAPSEQLLHLIKLGMENDDTAVQYAIG
Retrocopy MYRTKVGLKDRQQLYKLIISQLLYDGYISIANGLINEIKPQSVCAPSEQLLHLIKLGMENDDTAVQYAIG

Parental  RSDTVAPGTGIDLEFDADVQTMSPEASEYETCYVTSHKGPCRVATYSRDGQLIATGSADASIKILDTERM
          RSDTVAPGTGIDLEFDADVQTMSPEASEYETCYVTSHKGPCRVATYSRDGQLIATGSADASIKILDTERM
Retrocopy RSDTVAPGTGIDLEFDADVQTMSPEASEYETCYVTSHKGPCRVATYSRDGQLIATGSADASIKILDTERM

Parental  LAKSAMPIEVMMNETAQQNMENHPVIRTLYDHVDEVTCLAFHPTEQILASGSRDYTLKLFDYSKPSAKRA
          LAKSAMPIEVMMNETAQQNMENHPVIRTLYDHVDEVTCLAFHPTEQILASGSRDYTLKLFDYSKPSAKRA
Retrocopy LAKSAMPIEVMMNETAQQNMENHPVIRTLYDHVDEVTCLAFHPTEQILASGSRDYTLKLFDYSKPSAKRA

Parental  FKYIQEAEMLRSISFHPSGDFILVGTQHPTLRLYDINTFQCFVSCNPQDQHTDAICSVNYNSSANMYVTG
          FKYIQEAEMLRSISFHPSGDFILVGTQHPTLRLYDINTFQCFVSCNPQDQHTDAICSVNYNSSANMYVTG
Retrocopy FKYIQEAEMLRSISFHPSGDFILVGTQHPTLRLYDINTFQCFVSCNPQDQHTDAICSVNYNSSANMYVTG

Parental  SKDGCIKLWDGVSNRCITTFEKAHDGAEVCSAIFSKNSKYILSSGKDSVAKLWEISTGRTLVRYTGAGLS
          SKDGCIKLWDGVSNRCITTFEKAHDGAEVCSAIFSKNSKYILSSGKDSVAKLWEISTGRTLVRYTGAGLS
Retrocopy SKDGCIKLWDGVSNRCITTFEKAHDGAEVCSAIFSKNSKYILSSGKDSVAKLWEISTGRTLVRYTGAGLS

Parental  GRQVHRTQAVFNHTEDYVLLPDERTISLCCWDSRTAERRNLLSLGHNNIVRCIVHSPTNPGFMTCSDDFR
          GRQVHRTQA.FNHTEDYVLLPDERTISLCCWDS.TAERRNLLSLGHNNIVRCIVHSPTNPGFMTCSDDFR
Retrocopy GRQVHRTQAMFNHTEDYVLLPDERTISLCCWDSTTAERRNLLSLGHNNIVRCIVHSPTNPGFMTCSDDFR

Parental  ARFWYRRSTTD
          ARFWYRRSTTD
Retrocopy ARFWYRRSTTD

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	5.84 RPM
SRP051959_heart	0.00 RPM	4.68 RPM
SRP051959_kidney	0.00 RPM	7.41 RPM
SRP051959_liver	0.00 RPM	5.29 RPM
SRP051959_lung	0.02 RPM	9.27 RPM
SRP051959_lymph_node	0.00 RPM	12.03 RPM
SRP051959_skeletal_muscle	0.02 RPM	5.15 RPM
SRP051959_spleen	0.00 RPM	11.60 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4012 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4012 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4012 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011281	2 retrocopies	retro_cjac_3572, retro_cjac_4012 ,
Tarsius syrichta	ENSTSYG00000003181	2 retrocopies	retro_tsyr_1543, retro_tsyr_32,