RetrogeneDB ID: retro_ptro_2469

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:113446144..113447138(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PINX1
• Ensembl ID: ENSPTRG00000019980
• Aliases: None
• Description: None

Sequence

>retro_ptro_2469
ATGTTGATGCTGGCTGAGCAGCAGCAGAAGCAGAAGTGGGCTGTGAATACTCAAAACACTGCCTGGAGTAATGCTGATTC
TAAATTTGGCCAGAGGATACTAGAGAAGATGGAATGGTCTAAAGGAAGGGGTTTAGGGGTTCAGGAGCAAGGAGGCCCAG
ATGATATTAAAGTTCAAGTTAAAAATAATGACCTGGGACTTCAAGCTACAATCAATAATGAAGCCAACTGGATTGCCCAT
CAAGATGATTTTAACTGGCTTCTGGCGGAACTGAACACTTGTCAGAGGCAGGAAACAGCAGACTCCTTAGACAACAAGAA
AAAGAAATATTTTAGTCTTGAAGAAATTCCAAAATCTTCAAAAACCGTGTTCATCATAGGAAATTTACAAAAGAAAAGGA
TCTATCATCTCGGAGCAAAACAGATCTTCACTGCATTTTTGGGAAAAAACAGAGTAAGAAGACTCCCGAGGGTAATTCCA
GTCCCTCCACTCCAGACAGAACAAAACCACGATGACAACCCATGCCTTCACCATCCAGGAGCGTTTTGCCAAGCAAATGG
CAGCACTGAAGAACAAGCCCCAGGTTGCAGCTCCAGGGCCTGACATTTCCAAGACCCAAGTGGAATGCAAAAGGGGGAAG
AAAAGAAACAAAGAGGCAACAGGTAAAAATGGGGAGAGTTACCCCCCAACACAGCCTAAGGCCAAGCGGCCTAAAGAGGG
AAAGCCTAAGAGAGACAAGGTCCAGAAGTCGGCATCCAAGGAGAAAAGAGCATGGACAGACGGACAGTGCAGAGGCCTCT
GCTGGGAAGAGAGTTCTGAGGCCTCTGCTCAGGGTGCAGGGAATTGTGTGCAGCCACCTGATGGCCAGGATTTCACCCTG
AAGCCCAAAAAGACAAAAGGAAAAAAAAAAGCTGCAAAGCCAGTAGAGGTAGCAATGGACACTACACTGAAAGAAACACC
AATGAAAAATAAGAAAAAGAAGAAAGGTTCCAAA

Alignment

ORF - retro_ptro_2469 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.96 %
• Parental protein coverage: 98.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSMLAERRRKQKWAVDPQNTAWSNDDSKFGQRMLEKMGWSKGKGLGAQEQGATDHIKVQVKNNHLGLGAT
          M.MLAE...KQKWAV..QNTAWSN.DSKFGQR.LEKM.WSKG.GLG.QEQG..D.IKVQVKNN.LGL.AT
Retrocopy MLMLAEQQQKQKWAVNTQNTAWSNADSKFGQRILEKMEWSKGRGLGVQEQGGPDDIKVQVKNNDLGLQAT

Parental  INNEDNWIAHQDDFNQLLAELNTCHGQETADSSDKKEKKSFSLEE-KSKISKNRVHYMKFTKGKDLSSRS
          INNE.NWIAHQDDFN.LLAELNTC..QETADS.D.K.KK.FSLEE..SKI.KNRVH..KFTK.KDLSSRS
Retrocopy INNEANWIAHQDDFNWLLAELNTCQRQETADSLDNKKKKYFSLEE<NSKIFKNRVHHRKFTKEKDLSSRS

Parental  KTDLDCIFGKRQSKKTPEGDASPSTSD-ENETT-TTSAFTIQEYFAKRMAALKNKPQVPVPGSDISETQV
          KTDL.CIFGK.QSKKTPEG..SPST.D..N.TT.TT.AFTIQE.FAK.MAALKNKPQV..PG.DIS.TQV
Retrocopy KTDLHCIFGKKQSKKTPEGNSSPSTPD<QNKTTMTTHAFTIQERFAKQMAALKNKPQVAAPGPDISKTQV

Parental  ERKRGKKRNKESTGKDVESY--LQPKAKRHTEGKPERAEAQERVAKKKSVPAEEQLRGPCWDQSSKASAQ
          E.KRGKKRNKE.TGK..ESY...QPKAKR..EGKP.R...Q....K.K......Q.RG.CW..SS.ASAQ
Retrocopy ECKRGKKRNKEATGKNGESYPPTQPKAKRPKEGKPKRDKVQKSASKEKRAWTDGQCRGLCWEESSEASAQ

Parental  DAGDHVQPPEGQDFTLKPKKRRGKKKLQKPVEIAEDATLEETLVKNKKKKKKKK
          .AG..VQPP.GQDFTLKP..........KPVE.A.D.TL.ET..KNKKKKK..K
Retrocopy GAGNCVQPPDGQDFTLKPXXXXXXXXAAKPVEVAMDTTLKETPMKNKKKKKGSK

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	2.22 RPM
SRP007412_cerebellum	0.00 RPM	3.41 RPM
SRP007412_heart	0.00 RPM	1.52 RPM
SRP007412_kidney	0.00 RPM	4.42 RPM
SRP007412_liver	0.00 RPM	4.26 RPM
SRP007412_testis	0.00 RPM	14.12 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2469 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2469 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2469 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3644
Gorilla gorilla	retro_ggor_2460

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008087	1 retrocopy	retro_cfam_736,
Homo sapiens	ENSG00000254093	1 retrocopy	retro_hsap_3644,
Pan troglodytes	ENSPTRG00000019980	1 retrocopy	retro_ptro_2469 ,