RetrogeneDB ID: retro_ptro_2435

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:57592864..57593806(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000038645
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PPP1CC
• Ensembl ID: ENSPTRG00000005448
• Aliases: None
• Description: Serine/threonine-protein phosphatase [Source:UniProtKB/TrEMBL;Acc:H2Q6V8]

Sequence

>retro_ptro_2435
ATGGCGGATTTAGATAAACTCAACATCGACAGCATTATCCAACGGCTGCTGGAAGTGAGAGGGTCCAAGCCTGGTAAGAA
TGTCCAGCTTCAGGAGAATGAAATCAGAGGACTGTGCTTAAAGTCTCGTGAAATCTTTCTCAGTCAGCCTATCCTACTAG
AACTTGAAGCACCACTCAAAATATGTGGTGACATCCATGGACAATACTATGATTTGCTGCGACTTTTTGAGTACGGGGGT
TTCCCACCAGAAAGCAACTACCTGTTTCTTGGGGACTATGTGGACAGGGGAAAGCAGTCATTGGAGACGATCTGCCTCTT
ACTGGCCTACAAAATCAAATATCCTGAGAATTTTTTTCTTCTCAGAGGGAACCATGAATGTGCCAGCATCAACAGAATTT
ATGGATTTTATGATGAATGTAAAAGAAGATACAACATTAAACTATGGAAAACTTTCACAGACTGTTTTAACTGTTTACCG
ATAGCAGCCATCGTGGATGAGAAGATATTCTGCTGTCATGGAGGTTTATCACCAGATCTTCAATCTATGGAGCAGATTCG
GCGAATTATGCGACCAACTGATGTACCAGATCAAGGTCTTCTTTGTGATCTTTTGTGGTCTGACCCCGATAAAGATGTCT
TAGGCTGGGGTGAAAATGACAGAGGAGTGTCCTTCACATTTGGTGCAGAAGTGGTTGCAAAATTTCTCCATAAGCATGAT
TTGGATCTTATATGTAGAGCCCATCAGGTGGTTGAAGATGGATATGAATTTTTTGCAAAGAGGCAGTTGGTCACTCTGTT
TTCTGCGCCCAATTATTGTGGAGAGTTTGACAATGCAGGTGCCATGATGAGTGTGGATGAAACACTAATGTGTTCTTTTC
AGATTTTAAAGCCTGCAGAGAAAAAGAAGCCAAATGCCACGAGACCTGTAACGCCTCCAAGG

Alignment

ORF - retro_ptro_2435 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 93.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADLDKLNIDSIIQRLLEVRGSKPGKNVQLQENEIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYY
          MADLDKLNIDSIIQRLLEVRGSKPGKNVQLQENEIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYY
Retrocopy MADLDKLNIDSIIQRLLEVRGSKPGKNVQLQENEIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYY

Parental  DLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDEC
          DLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDEC
Retrocopy DLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDEC

Parental  KRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPD
          KRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPD
Retrocopy KRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPD

Parental  KDVLGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAG
          KDVLGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAG
Retrocopy KDVLGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAG

Parental  AMMSVDETLMCSFQILKPAEKKKPNATRPVTPPR
          AMMSVDETLMCSFQILKPAEKKKPNATRPVTPPR
Retrocopy AMMSVDETLMCSFQILKPAEKKKPNATRPVTPPR

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	0.41 RPM	9.24 RPM
SRP007412_cerebellum	0.29 RPM	9.64 RPM
SRP007412_heart	0.23 RPM	9.94 RPM
SRP007412_kidney	0.05 RPM	7.27 RPM
SRP007412_liver	0.07 RPM	4.58 RPM
SRP007412_testis	0.95 RPM	50.37 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2435 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2435 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2435 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000004542	1 retrocopy	retro_cint_3,
Callithrix jacchus	ENSCJAG00000009147	7 retrocopies	retro_cjac_1062, retro_cjac_1165, retro_cjac_1408, retro_cjac_2304, retro_cjac_2535, retro_cjac_3288, retro_cjac_822,
Echinops telfairi	ENSETEG00000015721	1 retrocopy	retro_etel_2065,
Oryctolagus cuniculus	ENSOCUG00000009275	2 retrocopies	retro_ocun_1232, retro_ocun_665,
Pan troglodytes	ENSPTRG00000005448	1 retrocopy	retro_ptro_2435 ,
Sorex araneus	ENSSARG00000000571	1 retrocopy	retro_sara_700,
Drosophila melanogaster	FBgn0003134	5 retrocopies	retro_dmel_21, retro_dmel_37, retro_dmel_42, retro_dmel_48, retro_dmel_81,