RetrogeneDB ID: retro_ptro_1168

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 17:21552083..21552959(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DTWD2
• Ensembl ID: ENSPTRG00000017164
• Aliases: None
• Description: DTW domain containing 2 [Source:HGNC Symbol;Acc:19334]

Sequence

>retro_ptro_1168
AGAAAGAGGCGCGACCCCGTCACGCGACCGCCTGGGGCCTCAAGGTCTCAGACGCCAAACTACAAGGAGCAGCGGGAGGG
CGGCGCAGTGCTGGCGACGGCTGCCCTGGGAACAGAGGCGGACGACGCTAGTGCGGGCGGGCTGTGGGAGCTGCAGGTGG
AGCCGGCCGAGCTGAGGCCTGAGTGCAGCCGCTGCAAGCCGGCCTCAGAAAGTGTGTTTTTGTCCATTTCTCCCAGCGCA
CCCTTTGCATATCTCTACCTACTTGTGCATAATTCAGCATCCAGCAGAGGAAGACAAAATGCTGCGGACAGTTCCTCTAC
CAGCAGCATGCCTCCCCCAGGACAAGCGCAAAGTGAAGACTGGTCGTCGCTTCAGTGAAGAAAGAGATCCTGAACTTTCA
ACTGTTTGCCGGTAGTTTGGTACATTAATATTATATCCAGGGGCTGAAGCTGCTAATCTGGAAGAATTTATATTAGATTC
TCCTGTTTATCCTTCTACAATCATCGTCATTGATGGTACACGGAGCCAGGCTAAGGACATTTTCTGTAAGAATTCCTTGT
TCTGACACCCCCAAACAGGTGCAGTTAAAAACGAGCATTTCTAGTCAGTATGTAATTCGGATGCAGCCAATTAATAGATG
TCTTTCTACACTGGAGTGTGCACCTGTTGCTCTTTCCATCTTGGAGAAAAATAATTACATACAAGAGACTTTGCTTCACC
CTCTTGAAGCTTTATGCTCTTTCCAGATTTAGCATGGTGCCCAAAATTGACCTCAGCAAGCAACACCTTCTGAAAAATGG
ATTATATCCTAAACCAATGCCAAAGAACAAACACAAACTCAGGAAAATGAAACTATTAAAGAATAGTGTTAAAATT

Alignment

ORF - retro_ptro_1168 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.35 %
• Parental protein coverage: 97.65 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RTLQEPVARPSGASSSQTPNDKERREGGAVPAAAALGAEADDDSADGLWELPVEPAERRPECTRC-SRPQ
          R....PV.RP.GAS.SQTPN.KE.REGGAV.A.AALG.EADD.SA.GLWEL.VEPAE.RPEC.RC.SRPQ
Retrocopy RKRRDPVTRPPGASRSQTPNYKEQREGGAVLATAALGTEADDASAGGLWELQVEPAELRPECSRC>SRPQ

Parental  KVCLCPFLPAHPLHISTHLYIIQHPAEENKVLRTVPLLAACLPQDKCKVKIGRRFSEERDPELSTVCRKS
          KVC.CPFLPAHPLHIST.L.IIQHPAEE.K.LRTVPL.AACLPQDK.KVK.GRRFSEERDPELSTVCR..
Retrocopy KVCFCPFLPAHPLHISTYLCIIQHPAEEDKMLRTVPLPAACLPQDKRKVKTGRRFSEERDPELSTVCR*F

Parental  GTLILYPGSEAANLEEFILDSPVYPSTIIIIDGTWSQAKDIFYKNSLFRH-PKQVQLKTSISSQYVIRMQ
          GTLILYPG.EAANLEEFILDSPVYPSTII.IDGT.SQAKDIF.KNSLF.H.PKQVQLKTSISSQYVIRMQ
Retrocopy GTLILYPGAEAANLEEFILDSPVYPSTIIVIDGTRSQAKDIFCKNSLF*H>PKQVQLKTSISSQYVIRMQ

Parental  PTNRCLSTLECAAVALSILEKNNYIQETLLRPLQALCSFQLQHGAQ-IRLSKEHLLKNGLYPKPMPKNKR
          P.NRCLSTLECA.VALSILEKNNYIQETLL.PL.ALCSFQ..HGAQ.I.LSK.HLLKNGLYPKPMPKNK.
Retrocopy PINRCLSTLECAPVALSILEKNNYIQETLLHPLEALCSFQI*HGAQ>IDLSKQHLLKNGLYPKPMPKNKH

Parental  KLRKMELLMNSVKI
          KLRKM.LL.NSVKI
Retrocopy KLRKMKLLKNSVKI

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	0.39 RPM	3.70 RPM
SRP007412_cerebellum	0.32 RPM	8.85 RPM
SRP007412_heart	1.08 RPM	9.39 RPM
SRP007412_kidney	4.84 RPM	9.41 RPM
SRP007412_liver	0.88 RPM	2.36 RPM
SRP007412_testis	0.84 RPM	9.70 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1168 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1168 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1168 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2167

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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	ENSDNOG00000014789	1 retrocopy	retro_dnov_2188,
Gorilla gorilla	ENSGGOG00000009599	1 retrocopy	retro_ggor_2167,
Pongo abelii	ENSPPYG00000015707	2 retrocopies	retro_pabe_1493, retro_pabe_1494,
Pan troglodytes	ENSPTRG00000017164	1 retrocopy	retro_ptro_1168 ,