RetrogeneDB ID: retro_ptro_2554

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:97968858..97969125(+)
• 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_2554
AATGTGCAGATATGCTGTGCTACTGTGAATCAGGGCAATGAACTAACTGCCCTAGAAACAATTCATCATTACATGGAATT
ACTTAAGTATTTTGGCAGTGTGTGTGAACTTGATGTCGTCTTTAATTTTGAAGAGGTTTATTTTATTTTGGATGAGTTAT
TTTTGGAGGGGAAGTTAGGAAACCTCCAAGAAAAGGCAATTGCACAGGCTGATCTACCTCAGGAGGAAGCTTAAACCCCA
CACAGAGTTGTCCAAGAAATTGGACTG

Alignment

ORF - retro_ptro_2554 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.13 %
• Parental protein coverage: 59.87 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SLYFCCAIEGQDNELITLELIHRYVELLDKYFGSVCELDIIFNFEKAYFILDEFLMGGDVQDTSKKSVLK
          ....CCA...Q.NEL..LE.IH.Y.ELL.KYFGSVCELD..FNFE..YFILDE....G.......K....
Retrocopy NVQICCATVNQGNELTALETIHHYMELL-KYFGSVCELDVVFNFEEVYFILDELFLEGKLGNLQEKAI--

Parental  AIEQADLLQEEDESPRSVLEEMGL
          ...QADL.QEE...P..V..E.GL
Retrocopy --AQADLPQEEA*TPHRVVQEIGL

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	0.00 RPM	107.00 RPM
SRP007412_cerebellum	0.00 RPM	29.79 RPM
SRP007412_heart	0.00 RPM	4.43 RPM
SRP007412_kidney	0.00 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_2554 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2554 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2554 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3765

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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 ,