RetrogeneDB ID: retro_ptro_2480

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:127517781..127518197(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1R14B
• Ensembl ID: ENSPTRG00000041138
• Aliases: None
• Description: protein phosphatase 1, regulatory (inhibitor) subunit 14B [Source:HGNC Symbol;Acc:9057]

Sequence

>retro_ptro_2480
GCCCTGGCAGCCGCCATGGCCCCAGGGCGGGGCAGTGGTGGCTCAGGACCACGTGTTTACTTTCAGAGCCCACCCCCCAG
GGCCGCAGGAAGAGGCCTGGGCGGCACAGACGATAAGGGCCCAGTGAGGCGCCAAGGGAAGGTCACCATCAAGTATTACC
ACAAGGAGCTACAAAGTGCCTCAACCTGGAGGAGTGGATCATGGAGCAGCTGACACAACTCCCCGACTGCCAGGAAAAGG
AGATCCCAGAACTGGAGATTGACGTGGATGAACTCCTGGACATGGAGAGTGAGGATGCCCAGGCTGCCAGGGTCGAGGAG
CTGCTGGTTGACTGTTACAAACCCACCGAGGCCTTCATCTCTGACCTGCTGGACAAGATCCAGGGCATGCAGAAGCTGAG
CACACCCCAGAAGAAA

Alignment

ORF - retro_ptro_2480 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.43 %
• Parental protein coverage: 93.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AALAAPAPGPGSGGPGPRVYFQSPPG-AAGEGPGGADDEGPVRRQGKVTVKYDRKELR-KRLNLEEWILE
          A..AA.APG.GSGG.GPRVYFQSPP..AAG.G.GG.DD.GPVRRQGKVT.KY..KEL..K.LNLEEWI.E
Retrocopy ALAAAMAPGRGSGGSGPRVYFQSPPPRAAGRGLGGTDDKGPVRRQGKVTIKYYHKELQ<KCLNLEEWIME

Parental  QLTRLYDCQEEEIPELEIDVDELLDMESDDARAARVKELLVDCYKPTEAFISGLLDKIRGMQKLSTPQKK
          QLT.L.DCQE.EIPELEIDVDELLDMES.DA.AARV.ELLVDCYKPTEAFIS.LLDKI.GMQKLSTPQKK
Retrocopy QLTQLPDCQEKEIPELEIDVDELLDMESEDAQAARVEELLVDCYKPTEAFISDLLDKIQGMQKLSTPQKK

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	8.51 RPM
SRP007412_cerebellum	0.04 RPM	2.80 RPM
SRP007412_heart	0.00 RPM	8.10 RPM
SRP007412_kidney	0.00 RPM	10.96 RPM
SRP007412_liver	0.00 RPM	14.14 RPM
SRP007412_testis	0.00 RPM	3.16 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2480 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2480 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2480 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3655

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018111	3 retrocopies	retro_cjac_3591, retro_cjac_428, retro_cjac_532,
Homo sapiens	ENSG00000173457	4 retrocopies	retro_hsap_2205, retro_hsap_3101, retro_hsap_3655, retro_hsap_3838,
Mustela putorius furo	ENSMPUG00000013208	2 retrocopies	retro_mputfur_235, retro_mputfur_798,
Nomascus leucogenys	ENSNLEG00000004890	2 retrocopies	retro_nleu_324, retro_nleu_335,
Pan troglodytes	ENSPTRG00000041138	6 retrocopies	retro_ptro_1674, retro_ptro_2097, retro_ptro_2480 , retro_ptro_2614, retro_ptro_3089, retro_ptro_935,
Sus scrofa	ENSSSCG00000013035	2 retrocopies	retro_sscr_1087, retro_sscr_892,
Ictidomys tridecemlineatus	ENSSTOG00000021959	1 retrocopy	retro_itri_1110,