RetrogeneDB ID: retro_ggor_3059

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:126462799..126464083(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TJAP1
• Ensembl ID: ENSGGOG00000015185
• Aliases: None
• Description: None

Sequence

>retro_ggor_3059
CTCAAGAAGGCTGAGATGGATAGGCAGACGCTGGACTGGGAGATCGTGGAGCTGACCAACAAGCTGCTGGATGCCAAGAA
CACCATCAACAAGCTGGAGGAGCTCAACGAGCGGTACCAGGGGGATTGCAATCTGGCTGTGCAGCTCCTCAAGTGCAGCA
AGTCCCACTTCTGAAACTATGAGTTCTCCGACCTGTCCTGTGAGCTACAGGACATGGTTCAGAAACATCTGCATAGTGGT
CAAGAGGCCTCCAGCCCGGGTCCTGCCCCCAGCCTAGCCCCAGCGGCTGTTGTGCCTACTTTGGTCATTGCCCGAGTGTT
AGAGAAGCCAGAGTCTCTACTGCTGAATTCAGCCCGGTCAGGCAGCTCTGGGCACCCCATGGCTGAAGATGTCTTTGTGC
ATGTGGACATCAGTGAGGGTGCCCCAGGCGATCCAGCCAGTCCCCCGGCCCTTGGCAGCCCCACCCCCCAACCCAATGGG
GAGTGTCACTCTCTGGATACTGCTGGGGGCTCCCCAGAGGAAGAGCTGCCCCTGCCAGCCTTTGAGAAGCTGAGCCCCTA
CCCCGCCCCATCTCTACCACTCCCACTGTATCCTGGCTGCAGGGTAATAGAGTTCTCCAAGGATAAAGTTTGGATCCCCT
GCAACAGCCCCCTGCCCAACTGCACTTACACTACCCGCCAGGCCATTTCGCTGAGCCTGGTGGGGGAAGGGAGTGAGCGG
GCCTGCCCCAGCCCAGTGCTCAGCGCCCCTGCCTCAGCCTAGGCCTCACTCAACCACCAGCCCAGCTCAGTGCCCCCAAA
ACTCAGTGCCCCAGCCAGGTCTGTTAGATCTGAAAAGGACCTGCTGGCCAGCTGGCAGTGGGCATTTGTGGACCATACTC
TGCCACCTGCTGCTGTGGCCCAGGTCACAGCCTTTAAGAGTGACACCCTCCCTGAGCTGCAGCACCGTTTTGCCCATAAC
CCCGCTGACAGAGATTAGGTGGTCCAGGCACCTTCTCCCTGAACCAAAGAGAGTAGGCTTTTGCTTCCCACAGAACCTGA
CTCTGGCTTTCCCAGGGAGGAGGAAGAAGAGCTGAACCTGCCCATCAGCCCTGAGGAAGAGCGCCAGAGCCTGCTGCTCA
TTAACAGTGTCACAGAGGAGGGTCCTGGCACTTCCCACACTGAGGGCAGGGCCTGGCCACTCCCCAGCTCCAGCCGCCCC
CAGTGCAGCCCCAAAAGAATGGGGGTTCACCACCTGCACTGCAAGGACAGCCTGACGCAGGCCCAGCAGCAGGGCAACCA
GCTC

Alignment

ORF - retro_ggor_3059 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.18 %
• Parental protein coverage: 76.66 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IKKAEMDRKTLDWEIVELTNKLLDAKNTINKLEELNERYRLDCNLAVQLLKCNKSHFRNHKFADLPCELQ
          .KKAEMDR.TLDWEIVELTNKLLDAKNTINKLEELNERY..DCNLAVQLLKC.KSHF.N..F.DL.CELQ
Retrocopy LKKAEMDRQTLDWEIVELTNKLLDAKNTINKLEELNERYQGDCNLAVQLLKCSKSHF*NYEFSDLSCELQ

Parental  DMVRKHLHSGQEAASPGPAPSLAPGAVVPTSVIARVLEKPESLLLNSAQSGSAGRPLAEDVFVHVDMSEG
          DMV.KHLHSGQEA.SPGPAPSLAP.AVVPT.VIARVLEKPESLLLNSA.SGS.G.P.AEDVFVHVD.SEG
Retrocopy DMVQKHLHSGQEASSPGPAPSLAPAAVVPTLVIARVLEKPESLLLNSARSGSSGHPMAEDVFVHVDISEG

Parental  VPGDPASPPAPGSPTPQPNGECHSLGTARGSPEEELPLPAFEKLNPYPTPSPPHPLYPGRRVIEFSEDKV
          .PGDPASPPA.GSPTPQPNGECHSL.TA.GSPEEELPLPAFEKL.PYP.PS.P.PLYPG.RVIEFS.DKV
Retrocopy APGDPASPPALGSPTPQPNGECHSLDTAGGSPEEELPLPAFEKLSPYPAPSLPLPLYPGCRVIEFSKDKV

Parental  RIPRNSPLPNCTYATRQAISLSLVEEGSERARPSPVPSTPASAQASPHHQPSPAPLTVSAPASSASSEED
          .IP.NSPLPNCTY.TRQAISLSLV.EGSERA.PSPV.S.PASA.AS..HQPS..P...SAPA.S..SE.D
Retrocopy WIPCNSPLPNCTYTTRQAISLSLVGEGSERACPSPVLSAPASA*ASLNHQPSSVPPKLSAPARSVRSEKD

Parental  LLVSWQRAFVDRTPPPAAVAQRTAFGRDALPELQRHFAHSPADRDEVVQAPSARPEESELLLPTEPDSGF
          LL.SWQ.AFVD.T.PPAAVAQ.TAF..D.LPELQ..FAH.PADRD.VVQAPS....ES.LLLPTEPDSGF
Retrocopy LLASWQWAFVDHTLPPAAVAQVTAFKSDTLPELQHRFAHNPADRD*VVQAPSP*TKESRLLLPTEPDSGF

Parental  PR-EEEELNLPISPEEERQSLLPINSGTEEGPGTSHTEGRAWPLPSSSRPQRSPKRMGVHHLHRKDSLTQ
          PR.EEEELNLPISPEEERQSLL.INS.TEEGPGTSHTEGRAWPLPSSSRPQ.SPKRMGVHHLH.KDSLTQ
Retrocopy PREEEEELNLPISPEEERQSLLLINSVTEEGPGTSHTEGRAWPLPSSSRPQCSPKRMGVHHLHCKDSLTQ

Parental  AQEQGNLL
          AQ.QGN.L
Retrocopy AQQQGNQL

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	0.24 RPM	42.34 RPM
SRP007412_cerebellum	0.20 RPM	50.15 RPM
SRP007412_heart	0.09 RPM	13.63 RPM
SRP007412_kidney	0.20 RPM	17.13 RPM
SRP007412_liver	0.13 RPM	13.90 RPM
SRP007412_testis	0.00 RPM	20.51 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_3059 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_3059 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4899
Pan troglodytes	retro_ptro_3267
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,