RetrogeneDB ID: retro_ptro_2969

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL389150.1:48504..48876(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1R11
• Ensembl ID: ENSPTRG00000017915
• Aliases: None
• Description: Pan troglodytes protein phosphatase 1, regulatory (inhibitor) subunit 11 (PPP1R11), mRNA. [Source:RefSeq mRNA;Acc:NM_001071817]

Sequence

>retro_ptro_2969
GAGGCAGGGGCTGGGCTGAGCGAGACCGTCACTGAGACAACAGTTACCGTGACAACCGAGCCCGAGAACCGGAGCCTTAC
CATCAAACTTCCGAAATGGAAGCCAGAGAAAAAGGTGGAATGGACAAGTGACACTGTGGACAATGAACGCATGAGCCGCC
GCTCATCAAAATGCTGCTCTATTTATGAAAAATCCCGGGCCTTTGGCGAGAGCTCCACGGAAAGTGATGAGGAGGAAGAA
GAGGGCTGTGGTCATACACACTGTGTACGTGGCCACCGCAAAGGATGGCGTCCTGCAACCCTGGGACCGGCCCCCACCAC
CCCTCCCCGGCCTCCTGACCCTTCCCAGACCCACGCAGGGCCAATGCAGCAC

Alignment

ORF - retro_ptro_2969 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.52 %
• Parental protein coverage: 98.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EAGAGLSETVTETTVTVTTEPENRSLTIKLRKRKPEKKVEWTSDTVDNEHMGRRSSKCCCIYEKPRAFGE
          EAGAGLSETVTETTVTVTTEPENRSLTIKL.K.KPEKKVEWTSDTVDNE.M.RRSSKCC.IYEK.RAFGE
Retrocopy EAGAGLSETVTETTVTVTTEPENRSLTIKLPKWKPEKKVEWTSDTVDNERMSRRSSKCCSIYEKSRAFGE

Parental  SSTESDEEEEEGCGHTHCVRGHRKGRRRATLGPTPTTPPQPPDPSQPPPGPMQH
          SSTESDEEEEEGCGHTHCVRGHRKG.R.ATLGP.PTTPP.PPDPSQ...GPMQH
Retrocopy SSTESDEEEEEGCGHTHCVRGHRKGWRPATLGPAPTTPPRPPDPSQTHAGPMQH

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	53.32 RPM
SRP007412_cerebellum	0.00 RPM	26.49 RPM
SRP007412_heart	0.00 RPM	18.01 RPM
SRP007412_kidney	0.00 RPM	41.16 RPM
SRP007412_liver	0.00 RPM	30.87 RPM
SRP007412_testis	0.11 RPM	49.95 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2969 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2969 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2969 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_121

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
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,
Monodelphis domestica	ENSMODG00000016021	1 retrocopy	retro_mdom_98,
Otolemur garnettii	ENSOGAG00000001598	1 retrocopy	retro_ogar_1458,
Pongo abelii	ENSPPYG00000029642	1 retrocopy	retro_pabe_492,
Pan troglodytes	ENSPTRG00000017915	1 retrocopy	retro_ptro_2969 ,
Pteropus vampyrus	ENSPVAG00000008330	1 retrocopy	retro_pvam_894,
Ictidomys tridecemlineatus	ENSSTOG00000003632	1 retrocopy	retro_itri_159,