RetrogeneDB ID: retro_cjac_816

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:118801799..118802492(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PPP1R7
• Ensembl ID: ENSCJAG00000006275
• Aliases: None
• Description: protein phosphatase 1, regulatory subunit 7 [Source:HGNC Symbol;Acc:9295]

Sequence

>retro_cjac_816
ATGAAAACCATCAACCTGAACAGAGATGCAGAGGATGTTGATTTGAATCACTATCACATTGGGAAGACTGAAGGATTTGA
GATACTGAAGAAAGTGAAGACTCTCTGCCTCTGCCAAAATTTAATTAAATGCATTGAGAATCTGGAGGAGCTACAGAGTC
TTCGAGAGCTGGATCTTTACAACGACCAGATCAAGGAGACTGAGAATCTAGAGGCGCTAACAGAGCTGGAGATTCTAGCT
ATTTATTTTAATCTGCTGAGAAACATCGAAGGGGTTGATAAGTTGACACAACTGAAAAAACTCTTCTTGGTCAACAATAA
AATCAGTAAAATTGAGAACTTAAGCAACTTACATCAACTACAGATGCTAGAGCTGGGATCTAACTGCATCCGGGCAATCG
AAAATATTAACACGTTAACCAATCTGGAGAGTTTGTTTTTGGGGAAAAGCAAAATTACTAAACTTCAGAACCTGGATGCG
CTCACTAACCTGACGGTCCTCAGCATGCACAGCAACCAGCTGACCAAGATCGAGGGTCTGCAGAACCTGGTGAACCTGTA
GGAGCTGTACCTCAGCCACAACGGCATTGAGGTCATCGAGGGCCTGGAGAACAATAACAAACTCATCATGTTGGACATTG
CATCAAATAGAATCAAAAAGATTGAAAACGTCAGCCATCTAACAGAGCTGAAG

Alignment

ORF - retro_cjac_816 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.22 %
• Parental protein coverage: 64.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  METINLDRDAEDVDLNHYRIGKIEGFEVLKKVKTLCLRQNLIKCIERVVEELQSLRELDLXDNQIKKIEN
          M.TINL.RDAEDVDLNHY.IGK.EGFE.LKKVKTLCL.QNLIKCIE...EELQSLRELDL...QIK..EN
Retrocopy MKTINLNRDAEDVDLNHYHIGKTEGFEILKKVKTLCLCQNLIKCIENL-EELQSLRELDLYNDQIKETEN

Parental  LEALTELEILDISFNLLRNIEGVDKLTQLKKLFLVNNKISKIENLSNLHQLQMLELGSNRIRAIENIDTL
          LEALTELEIL.I.FNLLRNIEGVDKLTQLKKLFLVNNKISKIENLSNLHQLQMLELGSN.IRAIENI.TL
Retrocopy LEALTELEILAIYFNLLRNIEGVDKLTQLKKLFLVNNKISKIENLSNLHQLQMLELGSNCIRAIENINTL

Parental  TNLESLFLGKNKITKLQNLDALTNLTVLSMQSNRLTKIEGLQNLVNLRELYLSHNGIEVIEGLENNNKLT
          TNLESLFLGK.KITKLQNLDALTNLTVLSM.SN.LTKIEGLQNLVNL.ELYLSHNGIEVIEGLENNNKL.
Retrocopy TNLESLFLGKSKITKLQNLDALTNLTVLSMHSNQLTKIEGLQNLVNL*ELYLSHNGIEVIEGLENNNKLI

Parental  MLDIASNRIKKIENISHLTELQ
          MLDIASNRIKKIEN.SHLTEL.
Retrocopy MLDIASNRIKKIENVSHLTELK

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	4.77 RPM	3.57 RPM
SRP051959_heart	6.31 RPM	3.54 RPM
SRP051959_kidney	7.37 RPM	5.01 RPM
SRP051959_liver	8.32 RPM	4.87 RPM
SRP051959_lung	6.46 RPM	4.44 RPM
SRP051959_lymph_node	5.64 RPM	4.84 RPM
SRP051959_skeletal_muscle	6.44 RPM	3.65 RPM
SRP051959_spleen	6.74 RPM	4.05 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_816 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_816 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_816 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	ENSCJAG00000006275	1 retrocopy	retro_cjac_816 ,