RetrogeneDB ID: retro_ptro_104

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:34270009..34270435(-)
• Located in intron of: ENSPTRG00000020158

Retrocopy information

• Ensembl ID: ENSPTRG00000039627
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPTRG00000022224
• Aliases: None
• Description: None

Sequence

>retro_ptro_104
CCTGAAGGCATTGAACTACAGTACAGAAAGAAATGTGCAAAGTGTGGACTGCTGCTCTTCTACCAATCCCAGCCGAAGAA
TGCTCCCATTACCTTCATTGTGGATGGAGCAGTAGTCAAGTTTGGCCAGGGCTTTGGGAAAACGAACATATATACTCAGA
AACAAGAGCCTCCTAAGAAGGTGATGATGACCAAACGGACCAAAGACATGGGCAAGTTCAGTTCTGTCACTGTGTCTACC
ATTGATGAAGAGGAAGAGGAGATTGAGGCTAGGGAAGTTGCTGACTCGTATGCACAGAATGCCAAAGTGATTGAAAAACA
GCTGGAGCGCAAAGGCATGAGCAAGAGGCCACTGCAAGAGCTGGCTGAATGGGAAGCCAAGAAAGTGAAAATGAAGGGGA
CCTTGATTGACAACCAGTTCAAATAA

Alignment

ORF - retro_ptro_104 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.62 %
• Parental protein coverage: 84.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PEGIERQYRKKCAKCGLPLFYQSQPKNAPVTFIVDGAVVKFGQGFGKTNIYTQKQEPPKKVMMTKRTKDM
          PEGIE.QYRKKCAKCGL.LFYQSQPKNAP.TFIVDGAVVKFGQGFGKTNIYTQKQEPPKKVMMTKRTKDM
Retrocopy PEGIELQYRKKCAKCGLLLFYQSQPKNAPITFIVDGAVVKFGQGFGKTNIYTQKQEPPKKVMMTKRTKDM

Parental  GKFSSVTVSTIDEEEEEIEAAEL
          GKFSSVTVSTIDEEEEEIEA.E.
Retrocopy GKFSSVTVSTIDEEEEEIEAREV

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	2.54 RPM	2.29 RPM
SRP007412_cerebellum	3.84 RPM	2.62 RPM
SRP007412_heart	2.56 RPM	1.75 RPM
SRP007412_kidney	3.71 RPM	3.50 RPM
SRP007412_liver	1.67 RPM	1.83 RPM
SRP007412_testis	6.01 RPM	1.69 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_104 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_104 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_104 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4044
Gorilla gorilla	retro_ggor_2711
Pongo abelii	retro_pabe_177

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000018610	1 retrocopy	retro_hsap_4044,
Gorilla gorilla	ENSGGOG00000013324	1 retrocopy	retro_ggor_2711,
Latimeria chalumnae	ENSLACG00000012468	1 retrocopy	retro_lcha_59,
Myotis lucifugus	ENSMLUG00000015751	1 retrocopy	retro_mluc_72,
Macaca mulatta	ENSMMUG00000022665	1 retrocopy	retro_mmul_2333,
Mus musculus	ENSMUSG00000006423	1 retrocopy	retro_mmus_1715,
Nomascus leucogenys	ENSNLEG00000014862	1 retrocopy	retro_nleu_2057,
Otolemur garnettii	ENSOGAG00000012474	1 retrocopy	retro_ogar_145,
Pongo abelii	ENSPPYG00000020670	1 retrocopy	retro_pabe_177,
Pan troglodytes	ENSPTRG00000022224	1 retrocopy	retro_ptro_104 ,
Sorex araneus	ENSSARG00000003163	1 retrocopy	retro_sara_5,
Sarcophilus harrisii	ENSSHAG00000006319	1 retrocopy	retro_shar_16,
Ictidomys tridecemlineatus	ENSSTOG00000011579	1 retrocopy	retro_itri_103,
Tarsius syrichta	ENSTSYG00000008043	1 retrocopy	retro_tsyr_634,
Tursiops truncatus	ENSTTRG00000013101	2 retrocopies	retro_ttru_231, retro_ttru_77,