RetrogeneDB ID: retro_ptro_2013

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:129993886..129994156(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAT1
• Ensembl ID: ENSPTRG00000021741
• Aliases: SAT1, SAT
• Description: None

Sequence

>retro_ptro_2013
ATGGCTACATTTGTGATCCATCCTGCCATCACTGCTGACTCCAGTGGTATCTGTGGCTGATCAGGGAACTGGCTAAATAT
GAATATGTGGGAGACCAAGTAATATTAACTGAAAAAGATCTGCTAGAGAGTGGTTTCAGAGAGCATCCCTTCCACCACTG
TGTGGTTGCAGAGATGCCCAAGAAACACTGGACTCTGGAAAGAAAGAATTACTGTTGGTTTCACCATGTACCGTTGTACC
TATGACCCTTGAATTGGCAAGCTATTGTAC

Alignment

ORF - retro_ptro_2013 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.57 %
• Parental protein coverage: 52.63 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAKFVIRPATAADCSDI-LRLIKELAKYEYMEEQVILTEKDLLEDGFGEHPFYHCLVAEVPKEHWTPEGH
          MA.FVI.PA..AD.S.I.L.LI.ELAKYEY...QVILTEKDLLE.GF.EHPF.HC.VAE.PK.HWT.E..
Retrocopy MATFVIHPAITADSSGI<LWLIRELAKYEYVGDQVILTEKDLLESGFREHPFHHCVVAEMPKKHWTLERK

Parental  S-IVGFAMYYFTYDPWIGKLLY
          ...VGF.MY..TYDP.IGKLLY
Retrocopy N>TVGFTMYRCTYDP*IGKLLY

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	54.46 RPM
SRP007412_cerebellum	0.00 RPM	36.39 RPM
SRP007412_heart	0.00 RPM	64.21 RPM
SRP007412_kidney	0.00 RPM	271.56 RPM
SRP007412_liver	0.00 RPM	550.46 RPM
SRP007412_testis	0.00 RPM	57.54 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2013 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2013 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2013 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2979
Gorilla gorilla	retro_ggor_2063
Pongo abelii	retro_pabe_2470

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000004032	3 retrocopies	retro_fcat_1095, retro_fcat_332, retro_fcat_444,
Homo sapiens	ENSG00000130066	1 retrocopy	retro_hsap_2979,
Gorilla gorilla	ENSGGOG00000027873	1 retrocopy	retro_ggor_2063,
Myotis lucifugus	ENSMLUG00000004919	1 retrocopy	retro_mluc_2472,
Mustela putorius furo	ENSMPUG00000000112	1 retrocopy	retro_mputfur_264,
Mus musculus	ENSMUSG00000025283	2 retrocopies	retro_mmus_1621, retro_mmus_2639,
Pongo abelii	ENSPPYG00000020190	1 retrocopy	retro_pabe_2470,
Pan troglodytes	ENSPTRG00000021741	2 retrocopies	retro_ptro_2013 , retro_ptro_2934,