RetrogeneDB ID: retro_ptro_375

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:183371326..183372171(-)
• Located in intron of: ENSPTRG00000001889

Retrocopy information

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

Parental gene information

• Parental gene symbol: PEF1
• Ensembl ID: ENSPTRG00000000463
• Aliases: None
• Description: None

Sequence

>retro_ptro_375
GCCAGCTATCTGTATGGGCAGGGCTGCCCTGGAGATGTAGGGCAAGCGCCAGGAACCCCTCCAGGTAGCTACTACCTTGG
ACCCCCCCCAATAGTGGAGGGCAGTATGGCAGCGTGCTACCCCCTGGTGGCGGCTATGGGGGTCCTGCCCCTGGAGGGCC
TTATGGACCACCAGCTGGTAGAGGGCCCTATGGACACCTCAATCCTGGGATGTTCCCCTCTGGAACTCCAGGAGGACCAA
ATGATGGTACAGCTCCAGGGGGCCCCTAGGGTCAGCCACCTCCAAATTCCTACGGTGCCCAGCAGCCCAGGCCTCATGGA
CAGGGTGGCTCCCCTCCCAATATGGATGAGGCCTACTCCTGGTTCCAGTCGGTGACTCTGATCACAGTGGCTTTATCTCC
ATGCAGGAGGTGAAGCAGGCTCTGGTCAACTGCAACTGGTCCTTGTTCAATGATAAGACCTGCCTCATGATGATAAACAT
GTTTGACAAGACCTAATCAGGCCACATCAATGTCTACGGCTTCTCAGCCCTGTGGAAATTCATCCAGCAGTGGAAGCAGC
TCTTCCAGCAGTTATGACTGGGACAACTGAGGCTCCATTAGCTACACAGAGCTGCAGCAAGCTCTGTCCCAAAAGGGCTA
CAACCTGAGCCCCCAGTTCACCCAGCTACTGGTCTCCAGCTACTGCCCACGCTCTGTCAATCCTGCCAGACAGCTTGATT
GCTTCATCCAGGTGTGCACCCAGCTGCAGATGCCGACAGAGGCCTTCCGGGAGAAGGACACAGCTGTACAAGGCAACATT
CGGCTCAGCTTCAAGGACGTCGTCACCATGACAGCTCGGATGCTA

Alignment

ORF - retro_ptro_375 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.79 %
• Parental protein coverage: 99.65 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ASYPYRQGCPGAAGQAPGAPPGSYY-PGPPNSGGQYGSGLPPGG-GYGGPAPGGPYGPPAGGGPYGHPNP
          ASY.Y.QGCPG..GQAPG.PPGSYY.P......G.......P.G.GYGGPAPGGPYGPPAG.GPYGH.NP
Retrocopy ASYLYGQGCPGDVGQAPGTPPGSYY<PWXXXNSGGQYGSVLPPGGGYGGPAPGGPYGPPAGRGPYGHLNP

Parental  GMFPSGTPGGPYGGAAPGGPYGQPPPSSYGAQQPGLYGQGGAPPNVDPEAYSWFQSV-DSDHSGYISMKE
          GMFPSGTPGGP..G.APGGP.GQPPP.SYGAQQP...GQGG.PPN.D.EAYSWFQSV.DSDHSG.ISM.E
Retrocopy GMFPSGTPGGPNDGTAPGGP*GQPPPNSYGAQQPRPHGQGGSPPNMD-EAYSWFQSV<DSDHSGFISMQE

Parental  LKQALVNCNWSSFNDETCLMMINMFDKTKSGRIDVYGFSALWKFIQQWKNLFQQ-YDRDRSGSISYTELQ
          .KQALVNCNWS.FND.TCLMMINMFDKT.SG.I.VYGFSALWKFIQQWK.LFQQ.YD.D..GSISYTELQ
Retrocopy VKQALVNCNWSLFNDKTCLMMINMFDKT*SGHINVYGFSALWKFIQQWKQLFQQ>YDWDN*GSISYTELQ

Parental  QALSQMGYNLSPQFTQLLVSRYCPRSANPAMQLDRFIQVCTQLQVLTEAFREKDTAVQGNIRLSFEDFVT
          QALSQ.GYNLSPQFTQLLVS.YCPRS.NPA.QLD.FIQVCTQLQ..TEAFREKDTAVQGNIRLSF.D.VT
Retrocopy QALSQKGYNLSPQFTQLLVSSYCPRSVNPARQLDCFIQVCTQLQMPTEAFREKDTAVQGNIRLSFKDVVT

Parental  MTASRML
          MTA.RML
Retrocopy MTA-RML

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	0.14 RPM	53.48 RPM
SRP007412_cerebellum	0.29 RPM	32.08 RPM
SRP007412_heart	0.00 RPM	21.04 RPM
SRP007412_kidney	0.03 RPM	61.93 RPM
SRP007412_liver	0.00 RPM	45.70 RPM
SRP007412_testis	0.00 RPM	36.15 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_375 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_375 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_375 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_497
Gorilla gorilla	retro_ggor_464
Pongo abelii	retro_pabe_238

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006355	1 retrocopy	retro_cjac_1745,
Homo sapiens	ENSG00000162517	1 retrocopy	retro_hsap_497,
Gorilla gorilla	ENSGGOG00000015897	1 retrocopy	retro_ggor_464,
Macropus eugenii	ENSMEUG00000014458	1 retrocopy	retro_meug_375,
Microcebus murinus	ENSMICG00000001374	1 retrocopy	retro_mmur_937,
Macaca mulatta	ENSMMUG00000023397	1 retrocopy	retro_mmul_146,
Monodelphis domestica	ENSMODG00000017573	1 retrocopy	retro_mdom_1930,
Nomascus leucogenys	ENSNLEG00000001979	1 retrocopy	retro_nleu_2422,
Oryctolagus cuniculus	ENSOCUG00000005744	1 retrocopy	retro_ocun_461,
Pongo abelii	ENSPPYG00000001611	1 retrocopy	retro_pabe_238,
Pan troglodytes	ENSPTRG00000000463	1 retrocopy	retro_ptro_375 ,
Rattus norvegicus	ENSRNOG00000013972	2 retrocopies	retro_rnor_1563, retro_rnor_2505,