RetrogeneDB ID: retro_cjac_2880

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:55445319..55445695(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1R11
• Ensembl ID: ENSCJAG00000020710
• Aliases: None
• Description: protein phosphatase 1, regulatory (inhibitor) subunit 11 [Source:HGNC Symbol;Acc:9285]

Sequence

>retro_cjac_2880
ATGGCCGATACAGGGGCTGGGCTGAGCTAGACGGTCACTGAGACAACGGTTACTGTGACAACTGAGCCTGAGAACTGAAG
CCTTAGCATCAAACTTCGGAAACAGAAGCCAGAGAAAAAGGTGAAATGGATAAGTGACACTGTGGACAATGAGCACATGG
GCGCCACTCATCAGAATGCTGCTGTGTCTGTGAGAACATAAACTCGCCTTTGGTGAGAGCTCCATGGAAAGGATGAGGAG
GAAGAAGAGGGCTGTGTTAACACACTACGTACATGGCCACCGCAAAGGACTGTGTCATGCAACCCTGGGACCGACCCCCA
CCACCCCTCCCCAGCCTCCTGACCCTTCCCAGCCCCCCTCAGGGCCAACGAAGCAC

Alignment

ORF - retro_cjac_2880 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.69 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAEAGAGLSETVTETTVTVTTEPENRSLTIKLRKRKPEKKVEWTSDTVDNEHMG-RRSSKC-C-CIYEKP
          MA..GAGLS............EPEN.SL.IKLRK.KPEKKV.W.SDTVDNEHMG.R.SS.C.C.C..E..
Retrocopy MADTGAGLS*XXXXXXXXXXXEPEN*SLSIKLRKQKPEKKVKWISDTVDNEHMG<RHSSECCC<CL*EHK

Parental  RAFGESSTESDEEEEEGCGHTHCVRGHRKGRRRASLG--PTTPPQPPDPSQPPPGPMQH
          .AFGESS.E...........TH.V.GHRKG...A.LG..PTTPPQPPDPSQPP.GP..H
Retrocopy LAFGESSMERMRRKKRAV-LTHYVHGHRKGLCHATLGPTPTTPPQPPDPSQPPSGPTKH

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	17.46 RPM
SRP051959_heart	0.00 RPM	10.58 RPM
SRP051959_kidney	0.00 RPM	19.30 RPM
SRP051959_liver	0.00 RPM	14.84 RPM
SRP051959_lung	0.00 RPM	20.24 RPM
SRP051959_lymph_node	0.00 RPM	21.03 RPM
SRP051959_skeletal_muscle	0.00 RPM	10.35 RPM
SRP051959_spleen	0.00 RPM	18.30 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2880 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2880 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2880 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020710	1 retrocopy	retro_cjac_2880 ,
Felis catus	ENSFCAG00000013592	1 retrocopy	retro_fcat_1794,
Gorilla gorilla	ENSGGOG00000026830	1 retrocopy	retro_ggor_80,
Macropus eugenii	ENSMEUG00000006493	2 retrocopies	retro_meug_715, retro_meug_933,
Macaca mulatta	ENSMMUG00000012122	1 retrocopy	retro_mmul_359,
Monodelphis domestica	ENSMODG00000016021	1 retrocopy	retro_mdom_98,
Nomascus leucogenys	ENSNLEG00000004933	1 retrocopy	retro_nleu_2257,
Otolemur garnettii	ENSOGAG00000001598	1 retrocopy	retro_ogar_1458,
Pteropus vampyrus	ENSPVAG00000008330	1 retrocopy	retro_pvam_894,
Ictidomys tridecemlineatus	ENSSTOG00000003632	1 retrocopy	retro_itri_159,