RetrogeneDB ID: retro_ptro_2846

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:88221322..88221829(+)
• Located in intron of: ENSPTRG00000022584

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPTRG00000005076
• Aliases: None
• Description: None

Sequence

>retro_ptro_2846
GAGGACCTGGTCGTGACCAACTATAAGATGGGGGGCGACATTGCCAATGGGGTACTTTGGTCCTTGGTGGACGCATCTAG
CTCAGGTGTGTCAGTACTGAGCCTGTGTGAGAAAGGTGATGCCGTGATTATGCAAGAAACAGGGAAAATCTTCAAGAAAG
AAAAAGAGATGAAGAAACGTATTGCTTTTCCCACCAGCATTTTGGTAAATAACTGTGTATGTCACTTCTCCCCTTTGAAG
AGAGACCAGGATTATATTCTCAAGGAAGGTGACTTGGTAAAAATTGACCTTGGGGTCCATGTGAATGGCTTCATCACTAA
TGTAGCTCGTACTTTTGTGACTGATGTAGCTCAGGGGACCCAAGTAACAGGGAGGAAAGCAGATGTTATTAAGGCAGCTC
ACCGTTGTGCTGAAGCTGCCCTATGCCTGGTCACACTTGGAAATCAGAACACACGAGTGACAGAAGCCTGGAACAAAGTT
GCCCACTTATTTAACTGCATGCCAATA

Alignment

ORF - retro_ptro_2846 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.25 %
• Parental protein coverage: 81.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEEDVNGYVMPDTHLKGVLRSLVEASSSGVSVLSLCEKGDAMIMEETGKIFKKEKEMKKGIAFPTSISVN
          E...V..Y.M......GVL.SLV.ASSSGVSVLSLCEKGDA.IM.ETGKIFKKEKEMKK.IAFPTSI.VN
Retrocopy EDLVVTNYKMGGDIANGVLWSLVDASSSGVSVLSLCEKGDAVIMQETGKIFKKEKEMKKRIAFPTSILVN

Parental  NCVCHFSPLKSDQDYILKEGDLVKIDLGVHVDGFIANVAHTFVVDVAQGTQVTGRKADVIKAAHLCAEAA
          NCVCHFSPLK.DQDYILKEGDLVKIDLGVHV.GFI.NVA.TFV.DVAQGTQVTGRKADVIKAAH.CAEAA
Retrocopy NCVCHFSPLKRDQDYILKEGDLVKIDLGVHVNGFITNVARTFVTDVAQGTQVTGRKADVIKAAHRCAEAA

Parental  LRLVKPGNQNTQVTEAWNKVAHSFNCTPI
          L.LV..GNQNT.VTEAWNKVAH.FNC.PI
Retrocopy LCLVTLGNQNTRVTEAWNKVAHLFNCMPI

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	0.23 RPM	39.27 RPM
SRP007412_cerebellum	0.04 RPM	26.49 RPM
SRP007412_heart	0.09 RPM	18.10 RPM
SRP007412_kidney	0.10 RPM	109.58 RPM
SRP007412_liver	0.00 RPM	75.35 RPM
SRP007412_testis	0.00 RPM	75.03 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2846 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2846 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2846 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007181	2 retrocopies	retro_chof_1089, retro_chof_1847,
Callithrix jacchus	ENSCJAG00000011811	2 retrocopies	retro_cjac_4214, retro_cjac_4215,
Homo sapiens	ENSG00000170515	6 retrocopies	retro_hsap_1930, retro_hsap_2413, retro_hsap_2868, retro_hsap_3646, retro_hsap_4191, retro_hsap_4895,
Pan troglodytes	ENSPTRG00000005076	6 retrocopies	retro_ptro_1289, retro_ptro_1389, retro_ptro_1940, retro_ptro_2471, retro_ptro_2846 , retro_ptro_3263,
Sus scrofa	ENSSSCG00000022666	2 retrocopies	retro_sscr_1143, retro_sscr_337,
Vicugna pacos	ENSVPAG00000009523	1 retrocopy	retro_vpac_2,