RetrogeneDB ID: retro_ptro_2258

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:45301317..45301665(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP1S3
• Ensembl ID: ENSPTRG00000012979
• Aliases: None
• Description: adaptor-related protein complex 1, sigma 3 subunit [Source:HGNC Symbol;Acc:18971]

Sequence

>retro_ptro_2258
AAAAAGATCACAAGAGAACTTGTTCAGACCGTTTTAGCACGGAAACCTAAAATGTGCAGCTTCCTTGAGTGGCGAGATCT
GAAGATTGTTTACAAAAGATATGCTAGTCTGTATTTTTGCTGTGCTATTGAGGATCAGGACAATGAACTAATTACCCTGG
AAATAATTCATCGTTATGTGGAATTACTTGACAAGTATTTCGGCAGTGTCTGTGAACTAGATATCATCTTTAATTTTGAG
AAGGCTTATTTTATTTTGGATGAGTTTCTTTTGGGAGGGGAAGTTCAGGAAACATCCAAGAAAAATGTCCTTAAAGCAAT
TGAGCAGGCCGATCTACTATAGGAGAGT

Alignment

ORF - retro_ptro_2258 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.0 %
• Parental protein coverage: 75.32 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKITREIVQIILSRGHRTSSFVDWKELKLVYKRYASLYFCCAIENQDNELLTLEIVHRYVELLDKYFGNV
          KKITRE.VQ..L.R.....SF..W..LK.VYKRYASLYFCCAIE.QDNEL.TLEI.HRYVELLDKYFG.V
Retrocopy KKITRELVQTVLARKPKMCSFLEWRDLKIVYKRYASLYFCCAIEDQDNELITLEIIHRYVELLDKYFGSV

Parental  CELDIIFNFEKAYFILDEFIIGGEIQETSKKIAVKAIEDSDMLQET
          CELDIIFNFEKAYFILDEF..GGE.QETSKK...KAIE..D.L.E.
Retrocopy CELDIIFNFEKAYFILDEFLLGGEVQETSKKNVLKAIEQADLL*ES

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	0.11 RPM	0.38 RPM
SRP007412_cerebellum	0.04 RPM	0.54 RPM
SRP007412_heart	0.00 RPM	0.03 RPM
SRP007412_kidney	0.00 RPM	4.18 RPM
SRP007412_liver	0.00 RPM	3.18 RPM
SRP007412_testis	0.00 RPM	0.53 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2258 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2258 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2258 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011939	5 retrocopies	retro_chof_113, retro_chof_1230, retro_chof_1299, retro_chof_1949, retro_chof_2099,
Callithrix jacchus	ENSCJAG00000012352	2 retrocopies	retro_cjac_3187, retro_cjac_3903,
Macropus eugenii	ENSMEUG00000016580	11 retrocopies	retro_meug_1074, retro_meug_1342, retro_meug_1488, retro_meug_168, retro_meug_1864, retro_meug_289, retro_meug_318, retro_meug_361, retro_meug_816, retro_meug_909, retro_meug_938,
Microcebus murinus	ENSMICG00000014406	1 retrocopy	retro_mmur_1492,
Monodelphis domestica	ENSMODG00000021198	1 retrocopy	retro_mdom_1427,
Mus musculus	ENSMUSG00000054702	3 retrocopies	retro_mmus_2202, retro_mmus_2799, retro_mmus_487,
Ochotona princeps	ENSOPRG00000013358	1 retrocopy	retro_opri_443,
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,
Sarcophilus harrisii	ENSSHAG00000010973	1 retrocopy	retro_shar_695,