RetrogeneDB ID: retro_ptro_406

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:8259560..8260495(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRPF38A
• Ensembl ID: ENSPTRG00000000739
• Aliases: None
• Description: None

Sequence

>retro_ptro_406
ATGGCTAACCGTACACTGAAGGATGCGCACAGCGTCCGCGGCACCAACCCTCAATATCTGGTGGGGAAGATCATTCGAAC
GCGAATCTGTGAGTCCAAGCACTGGAAAGAGGAGTGCTTTGGACTTATGGCTGAACTTGTAGTCGATAAAGCCATGGAGT
TAATGTTTGTGGGTGGCGAATATGGTGGCAACATAAAACCAACACCCTTTCTGTGTTTAATCTTGAAGATGCTTCAAATT
CAATCCGAGAAAGGTATCACTGCAGAGTTTATAGAAAATGAAGATTTCAAGTATGTCCACATGTTGGGGGCACTTTATAT
GAGGCTGATGGGCACTGCAATTGATTGCTACAAGTACTTGGAGCCTTTGTACAATGACTATCGAAAAATCAAGAGCCAGA
ACAGAAATGGGGGTTTGAACTGATGCATGTAGATGAGTTTATTGATGAACTGGTGCACAGTGAGAGAGTCTGTGATATCA
CTCTGCCCCGGCTACAGAAACGCTAGGTATTAGAGGAAGCTGAGCAACTGGAGCCTTGAGTTAGTGCTCTGGAAGAGGAC
ATAGATGATGTGGAGTCCAGTGAAGAGGAAGAAGAGGAGGATGAGAAGTTGGAAAGAGTGCCATCACCTGAGCGCCTCTG
GAGAAGCTACGGAGACTTGGACAAGCCCCGTCCATCTCCCACACTGTGCTACAGAAGGAGTAGGAGTCTGTCTCCCAGAA
GGCGGAATCGATCTCCCAAAAGTAGAAGCCCCTTCTCCCGCCGAGAGAGGCATCCGAGCAAGGGTCCAAGACATCACCGC
AGCAGATCCCGAGACTGGCGGCACAGATCCCGTTCCAAGTCCCCAGATCCTCACCGTAGTCACAAACACAGGAGCTACTC
AAAGTCTCCCAAAAGGTCTAAGAAGAGCCACAAGAAGAGCCGGAGAGGGAATGAG

Alignment

ORF - retro_ptro_406 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.62 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MANRTVKDAHSIHGTNPQYLVEKIIRTRIYESKYWKEECFGLTAELVVDKAMELRFVGGVYGGNIKPTPF
          MANRT.KDAHS..GTNPQYLV.KIIRTRI.ESK.WKEECFGL.AELVVDKAMEL.FVGG.YGGNIKPTPF
Retrocopy MANRTLKDAHSVRGTNPQYLVGKIIRTRICESKHWKEECFGLMAELVVDKAMELMFVGGEYGGNIKPTPF

Parental  LCLTLKMLQIQPEKDIIVEFIKNEDFKYVRMLGALYMRLTGTAIDCYKYLEPLYNDYRKIKSQNRNGE-F
          LCL.LKMLQIQ.EK.I..EFI.NEDFKYV.MLGALYMRL.GTAIDCYKYLEPLYNDYRKIKSQNRNG..F
Retrocopy LCLILKMLQIQSEKGITAEFIENEDFKYVHMLGALYMRLMGTAIDCYKYLEPLYNDYRKIKSQNRNGG<F

Parental  ELMHVDEFIDELLHSERVCDIILPRLQKRYVLEEAEQLEPRVSALEEDMDDVESSEEEEEEDEKLERVPS
          ELMHVDEFIDEL.HSERVCDI.LPRLQKR.VLEEAEQLEP.VSALEED.DDVESSEEEEEEDEKLERVPS
Retrocopy ELMHVDEFIDELVHSERVCDITLPRLQKR*VLEEAEQLEP*VSALEEDIDDVESSEEEEEEDEKLERVPS

Parental  PDHRRRSYRDLDKPRRSPTLRYRRSRSRSPRRRSRSPKRRSPSPRRERHRSKSPRRHRSRSRDRRHRSRS
          P....RSY.DLDKPR.SPTL.YRRSRS.SPRRR.RSPK.RSP..RRERH.SK.PR.HRSRSRD.RHRSRS
Retrocopy PERLWRSYGDLDKPRPSPTLCYRRSRSLSPRRRNRSPKSRSPFSRRERHPSKGPRHHRSRSRDWRHRSRS

Parental  KSPGHHRSHRHRSHSKSPERSKKSHKKSRRGNE
          KSP..HRSH.HRS.SKSP.RSKKSHKKSRRGNE
Retrocopy KSPDPHRSHKHRSYSKSPKRSKKSHKKSRRGNE

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	15.55 RPM
SRP007412_cerebellum	0.00 RPM	34.74 RPM
SRP007412_heart	0.00 RPM	17.84 RPM
SRP007412_kidney	0.00 RPM	23.85 RPM
SRP007412_liver	0.03 RPM	12.90 RPM
SRP007412_testis	0.00 RPM	78.93 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_406 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_406 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_406 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_541
Gorilla gorilla	retro_ggor_494
Pongo abelii	retro_pabe_500

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021594	1 retrocopy	retro_cjac_2862,
Dasypus novemcinctus	ENSDNOG00000013904	1 retrocopy	retro_dnov_443,
Homo sapiens	ENSG00000134748	2 retrocopies	retro_hsap_541, retro_hsap_545,
Gorilla gorilla	ENSGGOG00000003940	4 retrocopies	retro_ggor_493, retro_ggor_494, retro_ggor_496, retro_ggor_563,
Loxodonta africana	ENSLAFG00000025862	1 retrocopy	retro_lafr_794,
Myotis lucifugus	ENSMLUG00000001053	8 retrocopies	retro_mluc_1105, retro_mluc_1208, retro_mluc_1856, retro_mluc_2016, retro_mluc_2150, retro_mluc_2405, retro_mluc_2576, retro_mluc_828,
Monodelphis domestica	ENSMODG00000000644	1 retrocopy	retro_mdom_184,
Mus musculus	ENSMUSG00000063800	2 retrocopies	retro_mmus_1227, retro_mmus_671,
Nomascus leucogenys	ENSNLEG00000017999	2 retrocopies	retro_nleu_715, retro_nleu_719,
Oryctolagus cuniculus	ENSOCUG00000000963	1 retrocopy	retro_ocun_713,
Otolemur garnettii	ENSOGAG00000005423	1 retrocopy	retro_ogar_3216,
Petromyzon marinus	ENSPMAG00000005561	1 retrocopy	retro_pmar_28,
Pongo abelii	ENSPPYG00000001348	2 retrocopies	retro_pabe_500, retro_pabe_503,
Pan troglodytes	ENSPTRG00000000739	2 retrocopies	retro_ptro_406 , retro_ptro_410,
Pteropus vampyrus	ENSPVAG00000009803	1 retrocopy	retro_pvam_967,
Sus scrofa	ENSSSCG00000003858	1 retrocopy	retro_sscr_924,
Ictidomys tridecemlineatus	ENSSTOG00000015610	1 retrocopy	retro_itri_1564,
Taeniopygia guttata	ENSTGUG00000008995	3 retrocopies	retro_tgut_12, retro_tgut_13, retro_tgut_14,