RetrogeneDB ID: retro_cjac_2116

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 22:38228558..38229848(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022850
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: INPP5K
• Ensembl ID: ENSCJAG00000002060
• Aliases: None
• Description: inositol polyphosphate-5-phosphatase K [Source:HGNC Symbol;Acc:33882]

Sequence

>retro_cjac_2116
ATGAGCTCTCGGAAGCCGAGCGGGCCGAAAGGCAGGAGGCTGGGCATCCACGTTGTGACTTGGAATGTGGCCTCAGCAGC
ACCCCCTCTAGATCTCAGTGACCTGCTTCAGCTGAACAACCAGAATGCAAATCTTGACATATATATCATTGGTTTGCAGG
AATTGAACTCTGGAATCATAAGCCTCCTTTCCGATGCTGCCTTTAATGACTCATGGAGCAGTTTCCTCATGGATACGCTT
TCCCCTCTGAGCTTCATCAAGGTCTCCCACGTGCGTATACAAGGGATCCTCTTACTGGTCTTTGCCAAGTATCAGCATTT
GCCCTATCTCCAGATTCTCTCTACTAAATCCACCCCCACCGGCCTGTTTGGGTACTGGGGGAACAAAGGAGGAGTCAACA
TCTGCCTGAAGCTGTATGGCTACTACATCAGCATCATCAACTGCCACCTGCCTCCCCACATTTCCAACAATTACCAGCGG
CTGGAGCACTTTGACCAGATCCTGGAGATGCAGAATTTTGGGGGACAAGATATTCCCAACATCCTGGATCATGACCTCAT
TATCTGGTTTGGAGACATGAACTTTCGCATCGAGGACTTTGGGTTGCACTTTGTCCGGGAATCCATTAAAAATCGGTGCT
ACAGTGACCTGTGGGAGAAGGATCAGCTCAGCATTGCCAAGAAACATGACCCGCTGCTCCGGGAGTTCCAGGAGGGCCGC
CTGCTCTTCCCACCCACCTACAAGTTTGATAGGAACTCCAGCAACTACGACACCAGTGAGAAGAAACGAAAGCCCGCATG
GACAGACCGCATCCTGTGGAGGTTGAAGCGGCAGCCCCAGGCCGGCCCCCACACCACTGGACTGCCAGCCCCAGACTTCT
CCCTGTCTCAGAGGAGCTATGGCAGCTACATGACGTACACCATCAGTGACCATAAGCCTGTTGCAGGCACTTTCGACTTG
GAGCTGAAGCCGTTGCTGTCTGCTCCACTGATCGTTCTGATGCCAGAGGACCTGTGGACCCTGGAGAACAACCTGATGGT
CAGCTACTCCTCAACCTCAGACTTCCCCAGGAGCCCGTGGGACTGGATCGGACTGTACAAGGTGGGGCTGCGTGACATTC
ATGACTACGTGTCCTACATCTGGGTTGGGGACAACCAGGTCTCCTTCAGCAACAACCTGAACCAGGTTTACATTGACATC
AGCAACATCCCTGCAACAGAAGAAAAGTTTCTCGTCTGTTACTACAGCAACAACCTGCGTTCTGTAGCGGGGATAAGCAG
ACCCTTCCAG

Alignment

ORF - retro_cjac_2116 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.84 %
• Parental protein coverage: 95.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSRKPSGPKGRRLSIHVVTWNVASAAPPLDLSDLLQLNNQNANLDIYIIGLQELNSGIISLLSDAAFND
          MSSRKPSGPKGRRL.IHVVTWNVASAAPPLDLSDLLQLNNQNANLDIYIIGLQELNSGIISLLSDAAFND
Retrocopy MSSRKPSGPKGRRLGIHVVTWNVASAAPPLDLSDLLQLNNQNANLDIYIIGLQELNSGIISLLSDAAFND

Parental  SWSSFLMDTLSPLSFIKVSHVRMQGILLLVFAKYQHLPYLQILSTKSTPTGLFGYWGNKGGVNICLKLYG
          SWSSFLMDTLSPLSFIKVSHVR.QGILLLVFAKYQHLPYLQILSTKSTPTGLFGYWGNKGGVNICLKLYG
Retrocopy SWSSFLMDTLSPLSFIKVSHVRIQGILLLVFAKYQHLPYLQILSTKSTPTGLFGYWGNKGGVNICLKLYG

Parental  YYISIINCHLPPHISNNYQRLEHFDRILEMQNFGGQDIPNILDHDLIIWFGDMNFRIEDFGLHFVRESIK
          YYISIINCHLPPHISNNYQRLEHFD.ILEMQNFGGQDIPNILDHDLIIWFGDMNFRIEDFGLHFVRESIK
Retrocopy YYISIINCHLPPHISNNYQRLEHFDQILEMQNFGGQDIPNILDHDLIIWFGDMNFRIEDFGLHFVRESIK

Parental  NRCYSDLWEKDQLSIAKKHDPLLREFQEGRLLFPPTYKFDRNSSNYDTSEKKRKPAWTDRILWRLKRQPQ
          NRCYSDLWEKDQLSIAKKHDPLLREFQEGRLLFPPTYKFDRNSSNYDTSEKKRKPAWTDRILWRLKRQPQ
Retrocopy NRCYSDLWEKDQLSIAKKHDPLLREFQEGRLLFPPTYKFDRNSSNYDTSEKKRKPAWTDRILWRLKRQPQ

Parental  AGPHTTGLPAPDFSLSQRSYGSYMTYTISDHKPVAGTFDLELKPLLSAPLIVLMPEDLWTLENNLMVSYS
          AGPHTTGLPAPDFSLSQRSYGSYMTYTISDHKPVAGTFDLELKPLLSAPLIVLMPEDLWTLENNLMVSYS
Retrocopy AGPHTTGLPAPDFSLSQRSYGSYMTYTISDHKPVAGTFDLELKPLLSAPLIVLMPEDLWTLENNLMVSYS

Parental  STSDFPRSPWDWIGLYKVGLRDIHDYVSYIWVGDNQVSFSNNLNQVYIDISNIPATEEEFLLCYYSNNLR
          STSDFPRSPWDWIGLYKVGLRDIHDYVSYIWVGDNQVSFSNNLNQVYIDISNIPATEE.FL.CYYSNNLR
Retrocopy STSDFPRSPWDWIGLYKVGLRDIHDYVSYIWVGDNQVSFSNNLNQVYIDISNIPATEEKFLVCYYSNNLR

Parental  SVAGISRPFQ
          SVAGISRPFQ
Retrocopy SVAGISRPFQ

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	0.38 RPM	10.25 RPM
SRP051959_heart	0.49 RPM	19.38 RPM
SRP051959_kidney	0.55 RPM	17.31 RPM
SRP051959_liver	0.30 RPM	8.56 RPM
SRP051959_lung	0.47 RPM	15.63 RPM
SRP051959_lymph_node	0.37 RPM	16.73 RPM
SRP051959_skeletal_muscle	0.98 RPM	19.44 RPM
SRP051959_spleen	0.32 RPM	14.60 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2116 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2116 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2116 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002060	1 retrocopy	retro_cjac_2116 ,