RetrogeneDB ID: retro_ptro_1757

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:12542581..12542853(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PFDN1
• Ensembl ID: ENSPTRG00000017310
• Aliases: None
• Description: prefoldin subunit 1 [Source:HGNC Symbol;Acc:8866]

Sequence

>retro_ptro_1757
ATAGTGATTGAACAGCTAAACAGAACGAAAAAGCATGCACATCTTACAGATACAGAGATCATGACTTTGGTAGATGAGAC
TAACATGTATGAAGGTGTAGGAAGAATGTTTATTCTTCAGTCCAAGGAAGCAATTCACAATCAGCTGTTAGAGAAGCAGC
AAATAGCGAAGAAAAAATTAAAGAACTAGAACAGAAAAAGTCCTACCTGGAGCGGAGCGTTAAGGAAGCTGAGAACAACA
TCCGGGAGATGCTGATGGCACGAAGGGCCCAG

Alignment

ORF - retro_ptro_1757 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.65 %
• Parental protein coverage: 74.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IQIEQLNRTKKHAHLTDTEIMTLVDETNMYEGVGRMFILQSKEAIHNQLLEKQKIA-EEKIKELEQKKSY
          I.IEQLNRTKKHAHLTDTEIMTLVDETNMYEGVGRMFILQSKEAIHNQLLEKQ.IA.EEKIKELEQKKSY
Retrocopy IVIEQLNRTKKHAHLTDTEIMTLVDETNMYEGVGRMFILQSKEAIHNQLLEKQQIA<EEKIKELEQKKSY

Parental  LERSVKEAEDNIREMLMARRAQ
          LERSVKEAE.NIREMLMARRAQ
Retrocopy LERSVKEAENNIREMLMARRAQ

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	0.25 RPM	50.83 RPM
SRP007412_cerebellum	0.04 RPM	23.80 RPM
SRP007412_heart	0.06 RPM	25.97 RPM
SRP007412_kidney	0.03 RPM	27.38 RPM
SRP007412_liver	0.00 RPM	9.79 RPM
SRP007412_testis	0.00 RPM	10.54 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1757 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1757 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1757 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2606

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005742	8 retrocopies	retro_cfam_1742, retro_cfam_1893, retro_cfam_1943, retro_cfam_251, retro_cfam_276, retro_cfam_417, retro_cfam_788, retro_cfam_997,
Equus caballus	ENSECAG00000011843	1 retrocopy	retro_ecab_53,
Echinops telfairi	ENSETEG00000019281	1 retrocopy	retro_etel_1629,
Homo sapiens	ENSG00000113068	1 retrocopy	retro_hsap_2606,
Macropus eugenii	ENSMEUG00000002726	3 retrocopies	retro_meug_380, retro_meug_686, retro_meug_801,
Otolemur garnettii	ENSOGAG00000003376	6 retrocopies	retro_ogar_1025, retro_ogar_1216, retro_ogar_1412, retro_ogar_2217, retro_ogar_3129, retro_ogar_89,
Pan troglodytes	ENSPTRG00000017310	1 retrocopy	retro_ptro_1757 ,