RetrogeneDB ID: retro_ptro_1234

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 17:58819011..58819356(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP1S1
• Ensembl ID: ENSPTRG00000019520
• Aliases: None
• Description: Adaptor-related protein complex 1, sigma 1 subunit [Source:UniProtKB/TrEMBL;Acc:K7B188]

Sequence

>retro_ptro_1234
AGAGAACTTGTTCAGACCGTTTTAGCACGGAAACCTAAAATGTGCAGCTTCCTTGAGTGGCGAGATCTGAAGATTGTTTA
CAAAAGATACGCTAGTCTGTATTTTTGCTGTGCTATTGAGGATCAGGACAATGAACTAATTACCCTGGAAATAATTCATC
GTTATGTGGAATTACTTGACAAGTATTTCGGCAGTGTCTGTGAACTAGATATCATCTTTAATTTTGAGAAGGCTTATTTT
ATTCTGGATGAGTTTCTTTTGGGAGGGGAAGTTCAGGAAACATCCAAGAAAAATGTTCTTAAAGCAATTGAGCAGGCCGA
TCTACTGCAGGAGAAAACAGAGACT

Alignment

ORF - retro_ptro_1234 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.57 %
• Parental protein coverage: 73.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RELMQVVLARKPKMCSFLEWRDLKVVYKRYASLYFCCAIEGQDNELITLELIHRYVELLDKYFGSVCELD
          REL.Q.VLARKPKMCSFLEWRDLK.VYKRYASLYFCCAIE.QDNELITLE.IHRYVELLDKYFGSVCELD
Retrocopy RELVQTVLARKPKMCSFLEWRDLKIVYKRYASLYFCCAIEDQDNELITLEIIHRYVELLDKYFGSVCELD

Parental  IIFNFEKAYFILDEFLMGGDVQDTSKKSVLKAIEQADLLQEEDES
          IIFNFEKAYFILDEFL.GG.VQ.TSKK.VLKAIEQADLLQE..E.
Retrocopy IIFNFEKAYFILDEFLLGGEVQETSKKNVLKAIEQADLLQEKTET

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	0.04 RPM	107.00 RPM
SRP007412_cerebellum	0.07 RPM	29.79 RPM
SRP007412_heart	0.03 RPM	4.43 RPM
SRP007412_kidney	0.03 RPM	87.61 RPM
SRP007412_liver	0.00 RPM	45.34 RPM
SRP007412_testis	0.00 RPM	6.43 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1234 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1234 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1234 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1849

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002673	1 retrocopy	retro_amel_210,
Felis catus	ENSFCAG00000029169	1 retrocopy	retro_fcat_152,
Homo sapiens	ENSG00000106367	1 retrocopy	retro_hsap_3765,
Macropus eugenii	ENSMEUG00000016245	3 retrocopies	retro_meug_1011, retro_meug_154, retro_meug_2051,
Microcebus murinus	ENSMICG00000005406	2 retrocopies	retro_mmur_1026, retro_mmur_1368,
Myotis lucifugus	ENSMLUG00000009898	2 retrocopies	retro_mluc_1493, retro_mluc_2061,
Mustela putorius furo	ENSMPUG00000015867	1 retrocopy	retro_mputfur_1184,
Pan troglodytes	ENSPTRG00000006239	1 retrocopy	retro_ptro_2368,
Pan troglodytes	ENSPTRG00000012979	1 retrocopy	retro_ptro_2258,
Pan troglodytes	ENSPTRG00000019520	3 retrocopies	retro_ptro_1234 , retro_ptro_24, retro_ptro_2554,