RetrogeneDB ID: retro_ptro_2758

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:64831317..64832897(-)
• Located in intron of: ENSPTRG00000020316

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRPF3
• Ensembl ID: ENSPTRG00000001254
• Aliases: None
• Description: Pan troglodytes PRP3 pre-mRNA processing factor 3 homolog (S. cerevisiae) (PRPF3), mRNA. [Source:RefSeq mRNA;Acc:NM_001246426]

Sequence

>retro_ptro_2758
AAGACAGTGAAGAGCGTGCTGGGTTTCTCAGAGCCTCCAGTGTTCACAGCAGCATTGAACTGCTGTGGGGAAGAGCATGG
ACAAGAAGAAGGCAGCCGATCATCTGAAACCTTTTCTTGATGATTCTACTCCCCGATTTGTGGACAAACTGAGGCTGTAG
GAGGAAGGCGGAAGCTCTAGGCATTCCAAGTCTAGCAATGACGGAAGCAGAAAACGAAAGCTAAAGAAGGTGTTTGGTGA
TAACTCTTGGCTCTCCAAGGAATCATCAGGAGTAAAGAAGCAGCGAATACCCCATTTTGAGGAGGTGGAAGAAGAGCCAG
AGGTGATCCCTGGGCCTCCATCAGAGTCCTGGCATGCTGACTAAGCTCCACATCAAACAGATGATGGACGCAGCAAAATG
ACAAATCCAGGAGAGGAAAAAACAGCTGCGCTTCATTAGCCCCCCTACACCTCAGCCAAAGACTCCTTCTTCCTCCCAAC
CAGAGCAACTTCCAACTGGCCACACTATTCAGCCCTCCCAGGGTGCCACTTTCATGAATGATGCCATTGAGAAGGCAAGG
AAAACAGCTGAACTACAAGCTCGAATCCAAGCCGGGCTGGCACTGAAGCCAGGACTCATCAGCAATGCCAACATGGTGGG
CCCGGCTAATCTCCATGACATGGGCATTGCTTCCCCAAAGGGGGAGTTAAAAGACCAAATTAAACCTACACCACTGATCC
TAGATGAGCAAGGGTGCATTGTAGATGCAACAGGCAAGGAGATTGAGCTGACACACTGCATGTCTACTCCTGCCAATATT
CGTGCTGTTCCCTCTTCAGAGGGAACCATTCAAGCAACAGCTAAAAGAAAAGCCATCAGAAGACATGGAGTCCAATACCT
TTTTTGACCCCGAGTCTCCACTGTCGCTTCCCAGAGCCAGAAACGCACTTTTAAATTCCATGACAAGGGCAAATTTGAGA
AGACTGCTTAGCGATTAAGGACAAAGGATCAACTGGAGAAGCTTCAGGCAGAGATTTCACAAGCAGCTCAAAAAACAGAC
ATCCATACTTTGACTAGGCTTGCCCTTATTGCTCCTAGGAAGGAGCTAAAGGAAGGAGATATCCCTGAAATTGAGTGGTG
GGACTCTTACATAATCCCCAATGGCTTTAACCTTAGAGAGGAAAATCCCAAGAGAGAAGATTATTTTGGAATCACAAATC
TTGTTGAACATCCAGCCCAGCTCAATGCTCCAGTTGACAATGACACACCAGTTACTTTGGGAGTGTATCTTACCAAGAAG
GAACAGAAAAAACTTCAGAGACAGACAAGGAGGGAAGCACAGAAGGAACTACTAGAAAAAGTCAGGCTGGGCCTGATGCC
TCCTCCAGAACCCAAAGTGAGAATTTCTAATTTGATGCGAGTATTAGGAACAGAAGCTGTTCAAGACCCCACAAAGGTAG
AAGCCCATGTCACAGCTCAGATGGCAAAAAGACAGAAATTGCATGAAGAGGCCAACTCTGCCTGAAAACTCACAGCAAAA
CAGAAAGGTCAAGAAAATTTAAAAGCTTAAGACATTTCACAGGGGGTACACATATCTGTA

Alignment

ORF - retro_ptro_2758 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.36 %
• Parental protein coverage: 77.45 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KTVKRVLGFSEPTVVTAALNC-VGKGMDKKKAADHLKPFLDDSTLRFVDKLFEAVEEGRSSRHSKSSSDR
          KTVK.VLGFSEP.V.TAALNC.VGK.MDKKKAADHLKPFLDDST.RFVDKL....EEG.SSRHSKSS.D.
Retrocopy KTVKSVLGFSEPPVFTAALNC>VGKSMDKKKAADHLKPFLDDSTPRFVDKL-RL*EEGGSSRHSKSSNDG

Parental  SRKRELKEVFGDDSEISKESSGVKKRRIPRFEEVEEEPEVIPGPPS-ESPGMLTKLQIKQMMEAATRQIE
          SRKR.LK.VFGD.S..SKESSGVKK.RIP.FEEV.EE.......P...SPGMLTKL.IKQMM.AA..QI.
Retrocopy SRKRKLKKVFGDNSWLSKESSGVKKQRIPHFEEV-EEEPEVIPGPP>QSPGMLTKLHIKQMMDAAK*QIQ

Parental  ERKKQLSFISPPTPQPKTPSSSQPERLPIGNTIQPSQAATFMNDAIEKARKAAELQARIQAQLALKPGLI
          ERKKQL.FISPPTPQPKTPSSSQPE.LP.G.TIQPSQ.ATFMNDAIEKARK.AELQARIQA.LALKPGLI
Retrocopy ERKKQLRFISPPTPQPKTPSSSQPEQLPTGHTIQPSQGATFMNDAIEKARKTAELQARIQAGLALKPGLI

Parental  GNANMVGLANLHAMGIAPPKVELKDQTKPTPLILDEQGRTVDATGKEIELTHRMPTLKANIRAVKREQ--
          .NANMVG.ANLH.MGIA.PK.ELKDQ.KPTPLILDEQG..VDATGKEIELTH.M.T..ANIRAV......
Retrocopy SNANMVGPANLHDMGIASPKGELKDQIKPTPLILDEQGCIVDATGKEIELTHCMST-PANIRAVPSSEGT

Parental  FKQQLKEKPSEDMESNTFFDPRVSIAPSQRQRRTFKFHDKGKFEKIAQRLRTKAQLEKLQAEISQAARKT
          .....K.K..........F.PRVS...SQ.Q.RTFKFHDKGKFEK.A.RLRTK.QLEKLQAEISQAA.KT
Retrocopy IQATAKRKAIRRHGVQYLF*PRVSTVASQSQKRTFKFHDKGKFEKTA*RLRTKDQLEKLQAEISQAAQKT

Parental  GIHTSTRLALIAPKKELKEGDIPEIEWWDSYIIPNGFDLTEENPKREDYFGITNLVEHPAQLNPPVDNDT
          .IHT.TRLALIAP.KELKEGDIPEIEWWDSYIIPNGF.L.EENPKREDYFGITNLVEHPAQLN.PVDNDT
Retrocopy DIHTLTRLALIAPRKELKEGDIPEIEWWDSYIIPNGFNLREENPKREDYFGITNLVEHPAQLNAPVDNDT

Parental  PVTLGVYLTKKEQKKLRRQTRREAQKELQEKVRLGLMPPPEPKVRISNLMRVLGTEAVQDPTKVEAHVRA
          PVTLGVYLTKKEQKKL.RQTRREAQKEL.EKVRLGLMPPPEPKVRISNLMRVLGTEAVQDPTKVEAHV.A
Retrocopy PVTLGVYLTKKEQKKLQRQTRREAQKELLEKVRLGLMPPPEPKVRISNLMRVLGTEAVQDPTKVEAHVTA

Parental  QMAKRQKAHEEANAARKLTAEQRKVKKIKKLKEDISQGVHISV
          QMAKRQK.HEEAN.A.KLTA.Q......K....DISQGVHISV
Retrocopy QMAKRQKLHEEANSA*KLTAKQKGQENLK--A*DISQGVHISV

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	0.02 RPM	24.15 RPM
SRP007412_cerebellum	0.00 RPM	62.27 RPM
SRP007412_heart	0.03 RPM	21.36 RPM
SRP007412_kidney	0.13 RPM	36.64 RPM
SRP007412_liver	0.00 RPM	45.11 RPM
SRP007412_testis	0.95 RPM	64.28 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2758 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2758 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2758 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4069
Macaca mulatta	retro_mmul_2348
Callithrix jacchus	retro_cjac_1499

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009926	1 retrocopy	retro_cjac_1499,
Macaca mulatta	ENSMMUG00000016301	1 retrocopy	retro_mmul_2348,
Nomascus leucogenys	ENSNLEG00000009841	1 retrocopy	retro_nleu_2529,
Otolemur garnettii	ENSOGAG00000005352	4 retrocopies	retro_ogar_2360, retro_ogar_3052, retro_ogar_374, retro_ogar_409,
Pan troglodytes	ENSPTRG00000001254	1 retrocopy	retro_ptro_2758 ,