RetrogeneDB ID: retro_cjac_2146

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:68764000..68764854(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000031583
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PPP2R5B
• Ensembl ID: ENSCJAG00000002574
• Aliases: None
• Description: None

Sequence

>retro_cjac_2146
CTCAAGACCATCCTGCACCAGATCTATGGCAAGTTCCTGGGCCTCCGGGCCTACATCCGCAAACAGTGCAACCACATCTT
CCTCCAGTTCATCTATGAGTTCGAGCACTTCAATGGTGTGGCTGAGCTACTGGAGATCCTAGGAAGCATCATCAATGGCT
TTGCGCTGCCCCTGAAGACGGAGCACAAGCAGTTCCTGGTTCGCGTCCTGATCCCCCTGCACTCTGTCAAGTCGCTGTCT
GTCTTTCACGCTCAGATGGCATACTGTGTGGTGCAGTTCCTGGAGAAAGACGCCACTCTAACGGAGCATGTGATCCGGGG
ACTGCTCAAATACTGGCCAAAAACCTGCACCCAGAAGGAGGTGATGTTTCTGGGGGAGATGGAAGAAATTCTTGATGTCA
TCGAGCCATCCCAGTTTGTGAAGATCCAGGAGCCCCTTTTTAAGCAGGTGGCTCGCTGTGTTTCCAGCCCCCATTTCCAG
GTTGCAGAGCGGGCTCTGTATTTCTGGAACAATGAGTATATCCTAAGCCTCACTGAGGACAGCTGCCACACTGTGCTGCC
CGCTGTGTTTGGGACCCTCTACCAAGTCTCCAAGGAGCACTGGAACCAAACCATCATATCGCTGACTACAATGTGCTCAA
GACCTTCATGGAGATGAATGGGAAGCTGTTTGATGAGCTCACAGCCTCCTACAAGCTGGAAAAGCAGCAGGAGCAGCAGA
AGGCCCAGGAGCGTCAGGAGTTATGGCAAAGTTTGGAGGAGCTGCAGCTATGCCGGCTACAGGGGACCCAGGGGGCCAAG
GAGGCTCCCTTCCAGCGGCTTACACCCCAGGTGGCCACCAGTGGGGGTCAGAGC

Alignment

ORF - retro_cjac_2146 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.8 %
• Parental protein coverage: 57.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LKTILHRVYGKFLGLRAYIRKQCNHIFLRFIYEFEHFNGVAELLEILGSIINGFALPLKTEHKQFLVRVL
          LKTILH..YGKFLGLRAYIRKQCNHIFL.FIYEFEHFNGVAELLEILGSIINGFALPLKTEHKQFLVRVL
Retrocopy LKTILHQIYGKFLGLRAYIRKQCNHIFLQFIYEFEHFNGVAELLEILGSIINGFALPLKTEHKQFLVRVL

Parental  IPLHSVKSLSVFHAQLAYCVVQFLEKDATLTEHVIRGLLKYWPKTCTQKEVMFLGEMEEILDVIEPSQFV
          IPLHSVKSLSVFHAQ.AYCVVQFLEKDATLTEHVIRGLLKYWPKTCTQKEVMFLGEMEEILDVIEPSQFV
Retrocopy IPLHSVKSLSVFHAQMAYCVVQFLEKDATLTEHVIRGLLKYWPKTCTQKEVMFLGEMEEILDVIEPSQFV

Parental  KIQEPLFKQVARCVSSPHFQVAERALYFWNNEYILSLIEDNCHTVLPAVFGTLYQVSKEHWNQTIVSLI-
          KIQEPLFKQVARCVSSPHFQVAERALYFWNNEYILSL.ED.CHTVLPAVFGTLYQVSKEHWNQTI.SL..
Retrocopy KIQEPLFKQVARCVSSPHFQVAERALYFWNNEYILSLTEDSCHTVLPAVFGTLYQVSKEHWNQTIISLT<

Parental  YNVLKTFMEMNGKLFDELTASYKLEKQQEQQKAQERQELWQGLEELRLRRLQGTQGAKEAPFQRLTPQVA
          YNVLKTFMEMNGKLFDELTASYKLEKQQEQQKAQERQELWQ.LEEL.L.RLQGTQGAKEAPFQRLTPQVA
Retrocopy YNVLKTFMEMNGKLFDELTASYKLEKQQEQQKAQERQELWQSLEELQLCRLQGTQGAKEAPFQRLTPQVA

Parental  TSGGQS
          TSGGQS
Retrocopy TSGGQS

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	0.20 RPM	3.00 RPM
SRP051959_heart	0.54 RPM	9.42 RPM
SRP051959_kidney	0.51 RPM	8.63 RPM
SRP051959_liver	0.13 RPM	5.09 RPM
SRP051959_lung	0.62 RPM	12.30 RPM
SRP051959_lymph_node	0.23 RPM	7.90 RPM
SRP051959_skeletal_muscle	0.26 RPM	5.66 RPM
SRP051959_spleen	0.65 RPM	12.71 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2146 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2146 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2146 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	ENSCJAG00000002574	1 retrocopy	retro_cjac_2146 ,
Callithrix jacchus	ENSCJAG00000019290	1 retrocopy	retro_cjac_3825,