RetrogeneDB ID: retro_cjac_2944

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:127589258..127590251(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000034623
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PHF11
• Ensembl ID: ENSCJAG00000008839
• Aliases: None
• Description: PHD finger protein 11 [Source:HGNC Symbol;Acc:17024]

Sequence

>retro_cjac_2944
ATGGCCCAGGCGTCACCACCTCTGCCGGAGTCAATGCACAGCACTGGCAGCTGGGAGGCCCAGCCGGAGCAGGAGGCGCT
CCTCCTTCCCACCGGTGTCTTTCAGGTTGCAGAAAAGATGGAAAAAAGGACATGTGCACTTTGCCCCAAAGATGTCGAGT
ATAATATCCTGTACTTTGCACAATCAGAGAATATAGCTGCCCATGAAAATTGTTTGCTGTATTCTTCAGGACTTGTGGAA
TGTGAGGATCATGATCCACTTAATCTTGATAGAAATTTTGATGTGGAATCGGTAAAGAAAGAAATCCAGAGAGGAAGGAA
GTTGAAATGCACATTTTGTCGTAAAAGAGGAGCCACCGTGGGATGTGATTTAAAAGCCTATAACAAGAATTACCACTTTT
TCTGTGCCAAGAAGGACCATGCAGTTCCAAAGTCTGATGGAGCTCGAGGAATTTATAAATTGTTTTGCCAACAACATGCT
CAATTCCCGATCATCACTCAAAGTGCTAAATTTTCAGGAGTTAAAGGAAAAAGAGGAAGGAAGAAACACTTCACAGTCAA
TCACATACAGCCACCCGAAACAATGACACATAATAGATTCGTAAGACACGTGAAAGAAGAGCATGGCAAACGCACAGATG
CAACTGTGAAAGTTCCTTTTCTTAAGAAGTGCAAGGAAGCAGGACTTCTTACATACGTACTTGAAGAAATATTAGACAAA
GTTCATTCAATTCCAGAAAAACTCATGGATGAGACTACTTCAGAAGCAGACTATGAAGAAATCGGGAGTGCACTTTTTGA
ATGCAGATTGTTCGAAGACACATTTGAAAATTTTCAAGCAGCAATAGAGAAAAAAATTGACACATCTCAACAAAGGCGGC
AGCAGTTGAAGGAAGAGATTGAGCTACTTCATGACTTAAAACAAACCTTGTGCTCTCTTCAAGAAAGTAGAGAGCCTATG
TCAAGTTCTACATCAATATCGTCCCTGTCATCT

Alignment

ORF - retro_cjac_2944 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.2 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAQASPPLPESMHSTGSWEAQPEQEALLLPTGVFQVAEKMEKRTCALCPKDVEYNILYFAQSENIAAHEN
          MAQASPPLPESMHSTGSWEAQPEQEALLLPTGVFQVAEKMEKRTCALCPKDVEYNILYFAQSENIAAHEN
Retrocopy MAQASPPLPESMHSTGSWEAQPEQEALLLPTGVFQVAEKMEKRTCALCPKDVEYNILYFAQSENIAAHEN

Parental  CLLYSSGLVECEDHDPLNLDRNFDVESVKKEIQRGRKLKCTFCRKRGATVGCDLKACNKNYHFFCAKKDH
          CLLYSSGLVECEDHDPLNLDRNFDVESVKKEIQRGRKLKCTFCRKRGATVGCDLKA.NKNYHFFCAKKDH
Retrocopy CLLYSSGLVECEDHDPLNLDRNFDVESVKKEIQRGRKLKCTFCRKRGATVGCDLKAYNKNYHFFCAKKDH

Parental  AVPKSDGARGIYKLFCQQHAQFPIITQSAKFSGVKGKRGRKKHFTVNHIQPPETMTHNRFVRHVKEEHGK
          AVPKSDGARGIYKLFCQQHAQFPIITQSAKFSGVKGKRGRKKHFTVNHIQPPETMTHNRFVRHVKEEHGK
Retrocopy AVPKSDGARGIYKLFCQQHAQFPIITQSAKFSGVKGKRGRKKHFTVNHIQPPETMTHNRFVRHVKEEHGK

Parental  RTGNFLKI-LFVANARKQDF-LTIITEEILAKVHSIPRKLMDETTSEADYEEIGSALFECRLFEDTFENF
          RT....K..LF...ARKQDF.LT...EEIL.KVHSIP.KLMDETTSEADYEEIGSALFECRLFEDTFENF
Retrocopy RTDATVKV>LFLRSARKQDF<LTYVLEEILDKVHSIPEKLMDETTSEADYEEIGSALFECRLFEDTFENF

Parental  QAAIEKKIDTSQQRRQQLKEEIELLHDLKQTLCSLQESREPMSSSTSISSLSS
          QAAIEKKIDTSQQRRQQLKEEIELLHDLKQTLCSLQESREPMSSSTSISSLSS
Retrocopy QAAIEKKIDTSQQRRQQLKEEIELLHDLKQTLCSLQESREPMSSSTSISSLSS

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	2.71 RPM	6.37 RPM
SRP051959_heart	2.60 RPM	7.10 RPM
SRP051959_kidney	4.75 RPM	11.58 RPM
SRP051959_liver	3.44 RPM	6.71 RPM
SRP051959_lung	6.26 RPM	14.71 RPM
SRP051959_lymph_node	6.53 RPM	15.25 RPM
SRP051959_skeletal_muscle	1.75 RPM	4.91 RPM
SRP051959_spleen	8.07 RPM	17.69 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2944 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2944 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2944 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	ENSCJAG00000004238	1 retrocopy	retro_cjac_3034,
Callithrix jacchus	ENSCJAG00000008839	1 retrocopy	retro_cjac_2944 ,