RetrogeneDB ID: retro_ptro_3267

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:129644114..129645344(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TJAP1
• Ensembl ID: ENSPTRG00000018199
• Aliases: None
• Description: None

Sequence

>retro_ptro_3267
ATGACCAGTGCAGCCCATGCTAAGAAACCCTACCGTAAGGCACCACCAGAGCATTGGGAGCTGCGACTGGAAATTCCTGG
ATCCAGGTTTGAGCAGGAGGAATCCCTGACTGACTTGGAAAGGATGAAGCTCTCGCAGCAGGATAATGAAGAGCTTCATC
GGCGCCTGGCCTCGGCCACGAGATGCACTGAGGTCCTGGAATGTGAGCTGGAAATTGGGCAGGACTGCCTGGAGCTGGAG
CTGGGCCAGAGCCACGAGGAGCTGGACAAGTTTTAAGGATAAGTTCTGCAGGCTGCAGAACAGCTACATGGCTTCTCAGC
AGACCAACCAGGAGTTGGAGGACAAGCTGCACACACTGCTCAAGAAGGCTGAGATGGATAGGCAGACGCTGGACTGGGAG
ATCGTGGAGCTGACCAACAAGCTGCTGGATGCCAAGAACACCATCAACAAGCTGGAGGAGCTCAACGAGTGGTACCAGGG
GGATTGCAACCTGACTGTGCAGCTCCTCAAGTGCAGCAAGTCCCACTTCCGAAACTATGAGTTCTCCGATCTGTCCTGTG
AGCTACAGGACATGGTTCAGAAACATCTGCATAGTGGTCAAGAGGCCGCCAGCCCTGGTCCTGCTCCCAGCCTAGCCCCA
GCGGCTGTTGTGCCTACTTTGGTCATTGCCCGAGTGTTAGAGAAGCCAGAGTCTCTACTGCTGAATTCAGCCCGGTCAGG
CAGCGCTGGGCACCCCATGGCTGAAGATGTCTTTGTGCATGTGGACATCAGTGAGGGTGCCCCAGGCGATCCAGCCAGTC
CCCCAGCCCCTGGCAGCCCCACCCCCCAACCCAATGGGGAGTGTCACTCTCTGGATACTGTTGGGGGCTCCCCAGAGGAA
GAGCTGCCCCTGCCAGCCTTTGAGAAGCTGAGCCCCTACCCCACCCCATCTCCACCACTCCCACTGTATCCTGGCTGCAG
GGTAATAGAGTTCTCCAAGGATAAAGTTTGGATCCCCTGCAACAGCCCCCTGCCCAACTGCACTTACACTACCCGCCAGG
CCATTTCGCTGAGCCTGGTGGGGGAAGGGAGTGAGCGGGCCTGCCCCAGCCCAGTGCTCAGCGCCCCTGCCTCAGCCTAG
GCCTCACTCAACCACCAGCTCAGCTCAGTGCCCCCACACTCAGTGCCCCAGCCCAGTCTGTTAGCTCTGAAAAGGACCTG
CTGGGCAGCTGGCAGTGGGCATTTGTGGAC

Alignment

ORF - retro_ptro_3267 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.04 %
• Parental protein coverage: 74.95 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTSAAPAKKPYRKAPPEHRELRLEIPGSRLEQEEPLTDAERMKLLQQENEELRRRLASATRRTEALEREL
          MTSAA.AKKPYRKAPPEH.ELRLEIPGSR.EQEE.LTD.ERMKL.QQ.NEEL.RRLASATR.TE.LE.EL
Retrocopy MTSAAHAKKPYRKAPPEHWELRLEIPGSRFEQEESLTDLERMKLSQQDNEELHRRLASATRCTEVLECEL

Parental  EIGQDCLELELGQSREELDKF-KDKFRRLQNSYTASQRTNQELEDKLHTLIKKAEMDRKTLDWEIVELTN
          EIGQDCLELELGQS.EELDKF.KDKF.RLQNSY.ASQ.TNQELEDKLHTL.KKAEMDR.TLDWEIVELTN
Retrocopy EIGQDCLELELGQSHEELDKF>KDKFCRLQNSYMASQQTNQELEDKLHTLLKKAEMDRQTLDWEIVELTN

Parental  KLLDAKNTINKLEELNERYRLDCNLAVQLLKCNKSHFRNHKFADLPCELQDMVRKHLHSGQEAASPGPAP
          KLLDAKNTINKLEELNE.Y..DCNL.VQLLKC.KSHFRN..F.DL.CELQDMV.KHLHSGQEAASPGPAP
Retrocopy KLLDAKNTINKLEELNEWYQGDCNLTVQLLKCSKSHFRNYEFSDLSCELQDMVQKHLHSGQEAASPGPAP

Parental  SLAPGAVVPTSVIARVLEKPESLLLNSAQSGSAGRPLAEDVFVHVDMSEGVPGDPASPPAPGSPTPQPNG
          SLAP.AVVPT.VIARVLEKPESLLLNSA.SGSAG.P.AEDVFVHVD.SEG.PGDPAS............G
Retrocopy SLAPAAVVPTLVIARVLEKPESLLLNSARSGSAGHPMAEDVFVHVDISEGAPGDPASXXXXXXXXXXXXG

Parental  ECHSLGTARGSPEEELPLPAFEKLNPYPTPSPPHPLYPGRRVIEFSEDKVQIPRNSPLPNCTYATRQAIS
          ECHSL.T..GSPEEELPLPAFEKL.PYPTPSPP.PLYPG.RVIEFS.DKV.IP.NSPLPNCTY.TRQAIS
Retrocopy ECHSLDTVGGSPEEELPLPAFEKLSPYPTPSPPLPLYPGCRVIEFSKDKVWIPCNSPLPNCTYTTRQAIS

Parental  LSLVEEGSERARPSPVPSTPASAQASPHHQPSPAP-LTLSAPASSASSEEDLLVSWQRAFVD
          LSLV.EGSERA.PSPV.S.PASA.AS..HQ.S..P..TLSAPA.S.SSE.DLL.SWQ.AFVD
Retrocopy LSLVGEGSERACPSPVLSAPASA*ASLNHQLSSVP<PTLSAPAQSVSSEKDLLGSWQWAFVD

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	0.07 RPM	63.53 RPM
SRP007412_cerebellum	0.00 RPM	35.49 RPM
SRP007412_heart	0.00 RPM	10.73 RPM
SRP007412_kidney	0.00 RPM	31.51 RPM
SRP007412_liver	0.00 RPM	21.77 RPM
SRP007412_testis	0.00 RPM	16.76 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3267 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3267 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3267 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4899
Gorilla gorilla	retro_ggor_3059
Pongo abelii	retro_pabe_3811

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000137221	1 retrocopy	retro_hsap_4899,
Gorilla gorilla	ENSGGOG00000015185	1 retrocopy	retro_ggor_3059,
Pongo abelii	ENSPPYG00000016642	1 retrocopy	retro_pabe_3811,
Pan troglodytes	ENSPTRG00000018199	1 retrocopy	retro_ptro_3267 ,