RetrogeneDB ID: retro_ptro_99

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:70290415..70290898(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000042556
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPTRG00000000752
• Aliases: None
• Description: None

Sequence

>retro_ptro_99
ATGGGGAAAATCGCGCTGCAACTCAAAGCCACGCTGGAGAACATCACCAACCTCCGGCCCGTGGGCGAGGACTTCCGGTG
GTACCTGAAGATGAAATGTGGCAACTGTGGTGAGATTTCGGACAAGTGGCAGTACATCCGGCTGATGGACAGTGTGGCAC
TGAAGGGGGGCCGTGGCAGTGCTTCCATGGTCCAGAAGTGCAAGCTGTGTGCAAGAGAAAATTCCATCGAGATTTTAAGC
AGCACCATCAAGGCTTACAATGCTGAAGACAATGAGAACTTCAAGACAATAGTGGAGTTTGAGTGCCGGGGCCTTGAACC
AGTTGATTTCCAGCCGCAGGCTGGGTTTGCTGCTGAAGGTGTGGAGTCAGGGACAGCCTTCAGTGACATTAATCTGCAGG
AGAAGGACTGGACTGACTATGATGAAAAGGCCCAGGAGTCTGTGGGAATCTATGAGGTCACCCACCAGTTTGTGAAGTGC
TGA

Alignment

ORF - retro_ptro_99 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.38 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGKIALQLKATLENITNLRPVGEDFRWYLKMKCGNCGEISDKWQYIRLMDSVALKGGRGSASMVQKCKLC
          MGKIALQLKATLENITNLRPVGEDFRWYLKMKCGNCGEISDKWQYIRLMDSVALKGGRGSASMVQKCKLC
Retrocopy MGKIALQLKATLENITNLRPVGEDFRWYLKMKCGNCGEISDKWQYIRLMDSVALKGGRGSASMVQKCKLC

Parental  ARENSIEILSSTIKPYNAEDNENFKTIVEFECRGLEPVDFQPQAGFAAEGVESGTAFSDINLQEKDWTDY
          ARENSIEILSSTIK.YNAEDNENFKTIVEFECRGLEPVDFQPQAGFAAEGVESGTAFSDINLQEKDWTDY
Retrocopy ARENSIEILSSTIKAYNAEDNENFKTIVEFECRGLEPVDFQPQAGFAAEGVESGTAFSDINLQEKDWTDY

Parental  DEKAQESVGIYEVTHQFVKC
          DEKAQESVGIYEVTHQFVKC
Retrocopy DEKAQESVGIYEVTHQFVKC

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	17.89 RPM
SRP007412_cerebellum	0.00 RPM	10.43 RPM
SRP007412_heart	0.00 RPM	4.95 RPM
SRP007412_kidney	0.00 RPM	12.40 RPM
SRP007412_liver	0.00 RPM	7.17 RPM
SRP007412_testis	0.00 RPM	18.13 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_99 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_99 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_99 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004526	3 retrocopies	retro_cjac_2948, retro_cjac_3149, retro_cjac_3186,
Cavia porcellus	ENSCPOG00000011509	1 retrocopy	retro_cpor_1142,
Homo sapiens	ENSG00000162384	1 retrocopy	retro_hsap_192,
Gorilla gorilla	ENSGGOG00000004027	1 retrocopy	retro_ggor_271,
Microcebus murinus	ENSMICG00000006397	1 retrocopy	retro_mmur_1113,
Myotis lucifugus	ENSMLUG00000002439	1 retrocopy	retro_mluc_101,
Mus musculus	ENSMUSG00000028608	1 retrocopy	retro_mmus_975,
Nomascus leucogenys	ENSNLEG00000017988	1 retrocopy	retro_nleu_1001,
Oryctolagus cuniculus	ENSOCUG00000029317	1 retrocopy	retro_ocun_770,
Otolemur garnettii	ENSOGAG00000013324	1 retrocopy	retro_ogar_861,
Ochotona princeps	ENSOPRG00000009003	2 retrocopies	retro_opri_351, retro_opri_711,
Pongo abelii	ENSPPYG00000001336	1 retrocopy	retro_pabe_443,
Pan troglodytes	ENSPTRG00000000752	1 retrocopy	retro_ptro_99 ,
Rattus norvegicus	ENSRNOG00000012724	3 retrocopies	retro_rnor_1999, retro_rnor_2403, retro_rnor_2705,