RetrogeneDB ID: retro_ptro_2551

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:94313333..94313758(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSN
• Ensembl ID: ENSPTRG00000012420
• Aliases: None
• Description: None

Sequence

>retro_ptro_2551
CACGAGGTTCATGAGCACTGGAGGTTTGTGTTGCAGCATACGGTTGTCTTCCCAGAACTTGTTGCGTGTTTGGAAACAGA
AACTCCAGAAGCCATTACAGAAATTCGTGTCATTGAGCCAGATAAGGAGAAACGATTTCATGTGGATGTGGAAGATCCTC
TCTCAGGAGTTCAATTCTTGCTAGTGAGCTGCTGAGGTTGTCCCTCAGTGGCATGAGTGCTGGAGACAACTCCCAGCCCC
TCCATGTCGCCACCTTTAACAATGAGTGGCATCCCAATTTCCACCTTCTCAGCCTAAAACACTATTCTTCTCTAAGGAAG
CCTTATGATGGTTTGTGGTAGGACGTGAAGAAAACAGAAGAGGTATTCTATATTCTTTCCATCCAAGGCTTCAATAAAGA
GATAGAAGCCGCTTGTACTGAAAAA

Alignment

ORF - retro_ptro_2551 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.33 %
• Parental protein coverage: 63.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YRFHEHWRFVLQRLVFLAAFVVYLETETLVTREAVTEILGIEPDREKGFHLDVEDYLSGVL-ILASELSR
          ...HEHWRFVLQ..V.....V..LETE...T.EA.TEI..IEPD.EK.FH.DVED.LSGV..ILASEL.R
Retrocopy HEVHEHWRFVLQHTVVFPELVACLETE---TPEAITEIRVIEPDKEKRFHVDVEDPLSGVQ<ILASELLR

Parental  LSVNSVTAGDYSRPLHISTFINELDSGFRLLNLKN-DSLRKRYDGLKYDVKKVEEVVYDLSIRGFNKETA
          LS.....AGD.S.PLH..TF.NE....F.LL.LK...SLRK.YDGL..DVKK.EEV.Y.LSI.GFNKE..
Retrocopy LSLSGMSAGDNSQPLHVATFNNEWHPNFHLLSLKHYSSLRKPYDGLW*DVKKTEEVFYILSIQGFNKEIE

Parental  AACVEK
          AAC.EK
Retrocopy AACTEK

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	35.18 RPM
SRP007412_cerebellum	0.00 RPM	44.88 RPM
SRP007412_heart	0.03 RPM	26.87 RPM
SRP007412_kidney	0.00 RPM	46.84 RPM
SRP007412_liver	0.00 RPM	32.01 RPM
SRP007412_testis	0.00 RPM	97.16 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2551 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2551 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2551 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3760
Gorilla gorilla	retro_ggor_2528

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006059	1 retrocopy	retro_btau_1598,
Dasypus novemcinctus	ENSDNOG00000025740	2 retrocopies	retro_dnov_1581, retro_dnov_907,
Felis catus	ENSFCAG00000027149	1 retrocopy	retro_fcat_1577,
Homo sapiens	ENSG00000211460	1 retrocopy	retro_hsap_3760,
Gorilla gorilla	ENSGGOG00000002216	2 retrocopies	retro_ggor_2528, retro_ggor_2610,
Myotis lucifugus	ENSMLUG00000012656	1 retrocopy	retro_mluc_1420,
Macaca mulatta	ENSMMUG00000021119	1 retrocopy	retro_mmul_1718,
Monodelphis domestica	ENSMODG00000000147	1 retrocopy	retro_mdom_1896,
Nomascus leucogenys	ENSNLEG00000001202	1 retrocopy	retro_nleu_170,
Ornithorhynchus anatinus	ENSOANG00000003457	1 retrocopy	retro_oana_120,
Oryctolagus cuniculus	ENSOCUG00000023529	1 retrocopy	retro_ocun_271,
Otolemur garnettii	ENSOGAG00000030436	3 retrocopies	retro_ogar_1221, retro_ogar_2875, retro_ogar_3426,
Pan troglodytes	ENSPTRG00000012420	1 retrocopy	retro_ptro_2551 ,
Tarsius syrichta	ENSTSYG00000004395	1 retrocopy	retro_tsyr_1593,