RetrogeneDB ID: retro_pabe_3811

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:128460254..128461685(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TJAP1
• Ensembl ID: ENSPPYG00000016642
• Aliases: None
• Description: tight junction-associated protein 1 [Source:RefSeq peptide;Acc:NP_001125176]

Sequence

>retro_pabe_3811
GAGCTGGAAATTGGGCAGGACTGCCTGGAGCTGGGCCAGAGCCGTGAGGAGCTGGACAAGTTTAAGGATAAGTTCTGCAG
GCTGCAGAACAGCTACATGGCTTCCCAGCAGACCAACCAGGAGTTGGAGGACAAGCTGCACACACTGCTCAAGAAGGCTG
AGATGGATAGGCAGACGCTGGACTGGGAGATAGTGGAGCTGACCAACAAGCTGCTGGATGCCAAGAACACCATCAACAAG
CTGGAGGAGCTCAACGAGCGGTACCAGGGAGACTGCAACCTGGCTGTGCAGCTCCTCAAGTGCAACAAGTCCCACTTCCG
AAACTATGAGTTCTCTGATCTGTCCTGTGAGCTACAGGACATGGTTCAGAAACATCTGCATAGTGGTCAAGAGGCCGCCA
GCCCGGGTCCTGCTCCCAGCCTAGCCCCAGCGGCTGTTGTGCCTACTTTGGTCATTGCCCAAGTGTTAGAGAAGCCAGAG
TCTCTACTGCCGAATTCAGCCCAGTCAGGCAGCGCTGGGCACCCCATGGCTGAAGATGTCTTTGTGCATGTGGACATCAG
TGAGGGTGCCCCAGGTGATCCAGCCAGTCCCCCGGCCCCTGGCAGTCCCACCCCCCAACCCAATGGGGAGTGTCACTCTC
TGGGTACTGCTGGGCGCTCTCCAGAGGAAGAGCTGCCCCTGCCAGTCTTTGAGAAGCTGAGCCCCTACCTCACTCCATAT
CCACCACACCCACTGTATCCTGGCTGCAGGGTAATAGAGTTCTCCAAGGATAAGGTTTGGATCCCCTGCAACAGCCCCCT
GCCCAACTGCACTTACGCTACCCGCCAGGCCATTTCGCTGAGCCTGGTGGGGGAAGGGAGTGAGCGGGCCTGCCCCAGCC
CAGTGCTCAGCGCCCCTGCCTCAGCCTAGGCCTCACCCAACCACCAGCCCAGCTCAGTGCCCCCAACACTCAGTGCCCCA
GCCAGGTCTGTTAGCTCTGAAGAGGACCTGCTGTCCAGCTGGCAGTGGGCATTTGTGGACCATACTCCACCACCTGCTGC
TGTGGCCCAGGGCACAGCCTTTAAGAGTGACACCCTCCCTGAGCTGCAGCGCCGTTTTGCCCATAACCCAGCTGACAGAG
ATTAGGTGGTCCAGGCACCTTCTCCCCGAACCAAAGAGAGTGGGCTTTTGCTTCCCACAGAACCTGACTCTAGCTTTTCC
AGGGAGGAGGAAGAAGAGCTGAACCTGCCCATCAGCCCTGAGGAAGAGCGCCAGAGCCTGCTGCTCATTAACAGTGTCAC
AGAGGAGGGTCCTGGCACTTCCCACACTGAGAGCAGGGCCTGGCCACTCCCCAGCTCCAGCCGCCCCCAGTGCAGCCCCA
AAAGAATGGGGGTTCACCACCTGCACTGCAAGGACAGCCAGACGCAGGCCCAGCAGCAGGGCAACCAGCTT

Alignment

ORF - retro_pabe_3811 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.12 %
• Parental protein coverage: 86.02 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELELGQSREELDKFKDKFRRLQNSYTASQRTNQELEDKLHTLASLSHSWIFAIKKAEMDRKTLDWEIVEL
          ELE.GQ...EL.................Q............L....H......KKAEMDR.TLDWEIVEL
Retrocopy ELEIGQDCLELGQSREELDKFKDKFCRLQNSYMASQQTNQELEDKLHT---LLKKAEMDRQTLDWEIVEL

Parental  TNKLLDAKNTINKLEELNERYRLDCNLAVQLLKCNKSHFRNHKFADLPCELQDMVQKHLHSGQEAASPGP
          TNKLLDAKNTINKLEELNERY..DCNLAVQLLKCNKSHFRN..F.DL.CELQDMVQKHLHSGQEAASPGP
Retrocopy TNKLLDAKNTINKLEELNERYQGDCNLAVQLLKCNKSHFRNYEFSDLSCELQDMVQKHLHSGQEAASPGP

Parental  APSLAPGAVVPTSVIARVLEKPESLLLNSAQSGSAGRPLAEDVFVHVDMSEGVPGDPASPPVPGSPTPQP
          APSLAP.AVVPT.VIA.VLEKPESLL.NSAQSGSAG.P.AEDVFVHVD.SEG.PGDPASPP.PGSPTPQP
Retrocopy APSLAPAAVVPTLVIAQVLEKPESLLPNSAQSGSAGHPMAEDVFVHVDISEGAPGDPASPPAPGSPTPQP

Parental  NGECHSLSTARGSPEEELPLPAFEKLSPYPTPSPPHPLYPGRRVIEFSEDKVRIPHNSPLPNCTYATRQA
          NGECHSL.TA..SPEEELPLP.FEKLSPY.TP.PPHPLYPG.RVIEFS.DKV.IP.NSPLPNCTYATRQA
Retrocopy NGECHSLGTAGRSPEEELPLPVFEKLSPYLTPYPPHPLYPGCRVIEFSKDKVWIPCNSPLPNCTYATRQA

Parental  ISLSLVEEGSERARPSPVPSTPASAQASPHHQPSPAPLTLSAPASSASSEEDLLVSWQRAFVDRTPPPAA
          ISLSLV.EGSERA.PSPV.S.PASA.ASP.HQPS..P.TLSAPA.S.SSEEDLL.SWQ.AFVD.TPPPAA
Retrocopy ISLSLVGEGSERACPSPVLSAPASA*ASPNHQPSSVPPTLSAPARSVSSEEDLLSSWQWAFVDHTPPPAA

Parental  VAQRTAFGRDALPELQRHFAHSPADRDEVVQAPSPRPEESELLLPTEPDSGFPREEEEELNLPIGPEEER
          VAQ.TAF..D.LPELQR.FAH.PADRD.VVQAPSPR..ES.LLLPTEPDS.F.REEEEELNLPI.PEEER
Retrocopy VAQGTAFKSDTLPELQRRFAHNPADRD*VVQAPSPRTKESGLLLPTEPDSSFSREEEEELNLPISPEEER

Parental  QSLLPINSGTQEGPGTSHTEGRAWPLPSSSRPQRSPKRMGVHHLHRKDSLTQAQEQGNLL
          QSLL.INS.T.EGPGTSHTE.RAWPLPSSSRPQ.SPKRMGVHHLH.KDS.TQAQ.QGN.L
Retrocopy QSLLLINSVTEEGPGTSHTESRAWPLPSSSRPQCSPKRMGVHHLHCKDSQTQAQQQGNQL

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	14.76 RPM
SRP007412_cerebellum	0.00 RPM	25.66 RPM
SRP007412_heart	0.00 RPM	4.52 RPM
SRP007412_kidney	0.10 RPM	14.98 RPM
SRP007412_liver	0.03 RPM	7.62 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3811 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3811 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3811 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4899
Pan troglodytes	retro_ptro_3267
Gorilla gorilla	retro_ggor_3059

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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,