RetrogeneDB ID: retro_ptro_3013

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL391667.1:86190..87125(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000041406
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TNFAIP1
• Ensembl ID: ENSPTRG00000008912
• Aliases: None
• Description: None

Sequence

>retro_ptro_3013
ATGTCAGGAGAAAATGTGGTGAGCTCAGCGGTGCCAGCGGCTGCTACCCGCACCACTTCCTTCAAGGGCACGAGCCCCAG
CTCCAAATACGTGAAGCTGAATGTGGGTGGAGCCCTCTACTATTCCACCATGCAGACGCTGACCAAGCAGGACACATGCT
GAAGGCCATGTTCAGCGGGCGCATGGAAGTGCTCACCGACAGTGAAGGCTGGATCCTCATTGACCGCTGTGGGAAGCACT
TTGGTACGATACTCAACTACCTTCGAGACGGGGCGGTGCCTTTACCCGAGAGCCGCCGGGAGATCGAGGAGCTGCTAGCA
GAAGCCAAGTACTACCTAGTCCAAGGCCTGGTGGAAGAGTGCCAGGCGGCCCTACAAAACAAAGATACTTATGAGCCTTT
CTGCAAGGTCCCTGTGATCACCTCATCCAAGGAAGAACAAAAACTTATAGCGACTTCAAATAAGCCAGCCGTGAAGTTGC
TCTACAACAGAAGTAACAACAAATACTCATATACCAGCAATTCTGACGACAATATGTTGAAAAACATTGAATTGTTTGAT
AAGCTGTCTCTGCGCTTTAACGGAAGGGTCCTGTTCATAAAGAATTTCATTGGGGATGAAATCTACTGCTGGTCCTTTTA
TGGTCAGGGCCGGAAGATTGCTGAAGTCTGTTGTACCTCCGTCATCTATGCCACTGAGAAGAAACAGACCAAGGTGGAGT
TTCCCAAAGCCCGGATTTATGAGGAGACCCTGAACATTTTGCTGTATGAGGCCCAGGATGGCCGGGGACCTGACAATGCG
CTCCTGGAGGCCACAGGCCGGGCGGCAGGGCGCTCCCACCACCTGGACAAGGACGAGGAGCGGGAGCGGGAGCGGATCGA
GCGCGTGCGGAGGATCCACATCAAGCGCCCCGATGACCGGGCCCACCTCCACCAG

Alignment

ORF - retro_ptro_3013 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.45 %
• Parental protein coverage: 98.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSGDTCLCPA-SGAKPKLSGLKGGGLGNKYVQLNVGGSLYYTTVRALTRHDT-MLKAMFSGRMEVLTDKE
          MSG......A...A.......KG.....KYV.LNVGG.LYY.T...LT..DT.MLKAMFSGRMEVLTD.E
Retrocopy MSGENVVSSAVPAAATRTTSFKGTSPSSKYVKLNVGGALYYSTMQTLTKQDT<MLKAMFSGRMEVLTDSE

Parental  GWILIDRCGKHFGTILNYLRDDTITLPQNRQEIKELMAEAKYYLIQGLVNMCQSALQDKKDSYQPVCNIP
          GWILIDRCGKHFGTILNYLRD....LP..R.EI.EL.AEAKYYL.QGLV..CQ.ALQ.K.D.Y.P.C..P
Retrocopy GWILIDRCGKHFGTILNYLRDGAVPLPESRREIEELLAEAKYYLVQGLVEECQAALQNK-DTYEPFCKVP

Parental  IITSLKEEERLIESSTKPVVKLLYNRSNNKYSYTSNSDDHLLKNIELFDKLSLRFNGRVLFIKDVIGDEI
          .ITS.KEE..LI..S.KP.VKLLYNRSNNKYSYTSNSDD..LKNIELFDKLSLRFNGRVLFIK..IGDEI
Retrocopy VITSSKEEQKLIATSNKPAVKLLYNRSNNKYSYTSNSDDNMLKNIELFDKLSLRFNGRVLFIKNFIGDEI

Parental  CCWSFYGQGRKLAEVCCTSIVYATEKKQTKVEFPEARIYEETLNVLLYETP--RVPDNSLLEATSRS--R
          .CWSFYGQGRK.AEVCCTS..YATEKKQTKVEFP.ARIYEETLN.LLYE....R.PDN.LLEAT.R...R
Retrocopy YCWSFYGQGRKIAEVCCTSVIYATEKKQTKVEFPKARIYEETLNILLYEAQDGRGPDNALLEATGRAAGR

Parental  SQASPSEDEETFELRDRVRRIHVKRYSTYDDRQLGHQ
          S.......E...E...RVRRIH.KR....DDR...HQ
Retrocopy SHHLDKDEERERERIERVRRIHIKR---PDDRAHLHQ

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	1.20 RPM	51.44 RPM
SRP007412_cerebellum	1.97 RPM	41.08 RPM
SRP007412_heart	2.59 RPM	29.53 RPM
SRP007412_kidney	3.16 RPM	48.59 RPM
SRP007412_liver	0.82 RPM	65.86 RPM
SRP007412_testis	1.69 RPM	31.30 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3013 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3013 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3013 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000010870	1 retrocopy	retro_dnov_1699,
Monodelphis domestica	ENSMODG00000019235	1 retrocopy	retro_mdom_1565,
Mus musculus	ENSMUSG00000017615	2 retrocopies	retro_mmus_3457, retro_mmus_3615,
Pan troglodytes	ENSPTRG00000008912	1 retrocopy	retro_ptro_3013 ,