RetrogeneDB ID: retro_ptro_107

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 19:23653827..23654748(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000039971
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPTRG00000009065
• Aliases: None
• Description: None

Sequence

>retro_ptro_107
ATGGCAGCCCCCATACCTCAAGGGTTCTCTTGTTTATCGAGGGTTTTGGGCTGGTGGTCTCGGCAGCCAGTTCTGGTGAC
TCAGTCCTCAGCTATAGTTCCAGTAAGAACTAAAAAACGTTTCACACCTCCTATTTATCAACCTAAATTTAAAACAGAAA
AGGAGTTTATGCAACATGCCCGGAAAGCAGGATTGGTTATTCCTCCAGAAAAATCGAACCGTTCCATACATCTGGCCTGT
ACAGCTGGTATATTTGATGCCTATGTTCCTCCTGAGGGTGATGCACGCATATCATCTCTTTCAAAGGAGGGACTGATAGA
GAGAACTGAACGAATGAAGAAGACTATGGCATCACAAGTGTCAATCCGGAGGATAAAAGACTATGATGCCAACTTTAAAA
TAAAGGACTTCCCTGAAAAAGCTAAGGATATCTTTATTGAAGCTCACCTTTGTCTAAACAACTCAGACCATGACCGACTT
CATACCTTGGTAACTGAACACTGTTTTCCAGACATGACCTGGGACATCAAATATAAGACCGTCCGCTGGAGCTTTGTGGA
ATCTTTAGAGCCCTCCCATGTTGTTCAAGTTCGCTGTTCAAGTATGATGAACCAGGGCAACGTGTACGGCCAGATCACCG
TACGCATGCACACCCGGCAGACTCTGGCCATCTATGACCGGTTTGGCCGGTTGATGTATGGACAGGAAGATGTACCCAAG
GATGTCCTGGAGTATGTTGTATTCGAAAAGCAGTTGACAAACCCCTATGGAAGCTGGAGAATGCATACCAAGATCGTTCC
CCCATGGGCACCCCCTAAGCAGCCCATCCTTAAGACGGTGATGATCCCTGGCCCTCAGCTGAAACCAGAAGAAGAATATG
AAGAGGCACAAGGAGAGGCCCAGAAGCCTCAGCTAGCCTGA

Alignment

ORF - retro_ptro_107 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.71 %
• Parental protein coverage: 99.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAPIPQGFSCLSRVLGWWSRQPVLVTQSSAIVPVRTKKRFTPPIYQPKFKTEKEFMQHARKAGLVIPPE
          MAAPIPQGFSCLSRVLGWWSRQPVLVTQSSAIVPVRTKKRFTPPIYQPKFKTEKEFMQHARKAGLVIPPE
Retrocopy MAAPIPQGFSCLSRVLGWWSRQPVLVTQSSAIVPVRTKKRFTPPIYQPKFKTEKEFMQHARKAGLVIPPE

Parental  KSDRSIHLACTAGIFDAYVPPEGDARISSLSKEGLIERTERMKKTMASQVSIRRIKDYDANFKIKDFPEK
          KS.RSIHLACTAGIFDAYVPPEGDARISSLSKEGLIERTERMKKTMASQVSIRRIKDYDANFKIKDFPEK
Retrocopy KSNRSIHLACTAGIFDAYVPPEGDARISSLSKEGLIERTERMKKTMASQVSIRRIKDYDANFKIKDFPEK

Parental  AKDIFIEAHLCLNNSDHDRLHTLVTEHCFPDMTWDIKYKTVRWSFVESLEPSHVVQVRCSSMMNQGNVYG
          AKDIFIEAHLCLNNSDHDRLHTLVTEHCFPDMTWDIKYKTVRWSFVESLEPSHVVQVRCSSMMNQGNVYG
Retrocopy AKDIFIEAHLCLNNSDHDRLHTLVTEHCFPDMTWDIKYKTVRWSFVESLEPSHVVQVRCSSMMNQGNVYG

Parental  QITVRMHTRQTLAIYDRFGRLMYGQEDVPKDVLEYVVFQKQLTNPYGSWRMHTKIVPPWAPPKQPILKTV
          QITVRMHTRQTLAIYDRFGRLMYGQEDVPKDVLEYVVF.KQLTNPYGSWRMHTKIVPPWAPPKQPILKTV
Retrocopy QITVRMHTRQTLAIYDRFGRLMYGQEDVPKDVLEYVVFEKQLTNPYGSWRMHTKIVPPWAPPKQPILKTV

Parental  MIPGPQLKEEPE---AQGEAQKPQLA
          MIPGPQLK.E.E...AQGEAQKPQLA
Retrocopy MIPGPQLKPEEEYEEAQGEAQKPQLA

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	4.24 RPM	3.11 RPM
SRP007412_cerebellum	3.87 RPM	1.18 RPM
SRP007412_heart	5.10 RPM	1.17 RPM
SRP007412_kidney	5.86 RPM	2.51 RPM
SRP007412_liver	3.01 RPM	1.18 RPM
SRP007412_testis	4.95 RPM	1.05 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_107 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_107 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_107 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000005808	2 retrocopies	retro_fcat_1677, retro_fcat_283,
Monodelphis domestica	ENSMODG00000012560	1 retrocopy	retro_mdom_403,
Nomascus leucogenys	ENSNLEG00000000530	1 retrocopy	retro_nleu_1967,
Otolemur garnettii	ENSOGAG00000015816	1 retrocopy	retro_ogar_1029,
Pan troglodytes	ENSPTRG00000009065	1 retrocopy	retro_ptro_107 ,
Ictidomys tridecemlineatus	ENSSTOG00000000304	2 retrocopies	retro_itri_102, retro_itri_1575,
Tupaia belangeri	ENSTBEG00000000585	1 retrocopy	retro_tbel_4621,
Vicugna pacos	ENSVPAG00000004977	1 retrocopy	retro_vpac_512,