RetrogeneDB ID: retro_ptro_1624

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:98542035..98542563(-)
• Located in intron of: ENSPTRG00000012265

Retrocopy information

• Ensembl ID: ENSPTRG00000038685
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: VPS25
• Ensembl ID: ENSPTRG00000009220
• Aliases: None
• Description: Pan troglodytes vacuolar protein sorting 25 homolog (S. cerevisiae) (VPS25), mRNA. [Source:RefSeq mRNA;Acc:NM_001252014]

Sequence

>retro_ptro_1624
ATGGCGATGAGTTTCGAGTGGCCGTGGCAGTATCGCTTCCCACCCTTCTTTACGTTACAACCGAATGTGGACACTCGGCA
GAAGCAGCTGGCCGCCTGGTGCTCGCTGGTCCTGTCCTTCTGCCGCCTGCACAAACAGTCCAGCATGACGGTGATGGAAG
CTCAGGAGAGCCCGCTCTTCAACAACGTCAAGCTACAGCGAAAGCTTCCTGTGGAGTCGATCCAGATTGTATTAGAGGAA
CTGAGGAAGAAAGGGAACCTCGAGTGGTTGGATAAGAGCAAGTCCAGCTTCCTGATCATGTGGCGGAGGCCAGAAGAATG
GGGGAAACTCATCTATCAGTGGGTTTCCAGGAGTGGCCAGAACAACTCCATCTTTACCCTGTATGAACTGACTAATGGGG
AAGACACAGAGGATGAGGAGTTCCATGGGCTGGATGAAGCCACTCTACTGCGGGCTCTGCAGGCCCTACAGCAGGAGCAC
AAGGCCGAGATCATCACCGTCAGCGATGGCCGAGGTGTCAAGTTCTTC

Alignment

ORF - retro_ptro_1624 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.43 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAMSFEWPWQYRFPPFFTLQPNVDTRQKQLAAWCSLVLSFCRLHKQSSMTVMEAQESPLFNNVKLQRKLP
          MAMSFEWPWQYRFPPFFTLQPNVDTRQKQLAAWCSLVLSFCRLHKQSSMTVMEAQESPLFNNVKLQRKLP
Retrocopy MAMSFEWPWQYRFPPFFTLQPNVDTRQKQLAAWCSLVLSFCRLHKQSSMTVMEAQESPLFNNVKLQRKLP

Parental  VESIQIVLEELRKKGNLEWLDKSKSSFLIMWRRPEEWGKLIYQWVSRSGQNNSVFTLYELTNGEDTEDEE
          VESIQIVLEELRKKGNLEWLDKSKSSFLIMWRRPEEWGKLIYQWVSRSGQNNS.FTLYELTNGEDTEDEE
Retrocopy VESIQIVLEELRKKGNLEWLDKSKSSFLIMWRRPEEWGKLIYQWVSRSGQNNSIFTLYELTNGEDTEDEE

Parental  FHGLDEATLLRALQALQQEHKAEIITVSDGRGVKFF
          FHGLDEATLLRALQALQQEHKAEIITVSDGRGVKFF
Retrocopy FHGLDEATLLRALQALQQEHKAEIITVSDGRGVKFF

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	0.32 RPM	5.77 RPM
SRP007412_cerebellum	0.00 RPM	3.84 RPM
SRP007412_heart	0.00 RPM	2.89 RPM
SRP007412_kidney	0.03 RPM	9.91 RPM
SRP007412_liver	0.13 RPM	5.92 RPM
SRP007412_testis	0.32 RPM	3.37 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1624 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1624 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1624 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013276	1 retrocopy	retro_cjac_2959,
Homo sapiens	ENSG00000131475	1 retrocopy	retro_hsap_213,
Gorilla gorilla	ENSGGOG00000016041	1 retrocopy	retro_ggor_284,
Macropus eugenii	ENSMEUG00000011611	2 retrocopies	retro_meug_1247, retro_meug_1681,
Macaca mulatta	ENSMMUG00000002149	1 retrocopy	retro_mmul_406,
Nomascus leucogenys	ENSNLEG00000011797	1 retrocopy	retro_nleu_1862,
Ochotona princeps	ENSOPRG00000012574	1 retrocopy	retro_opri_1071,
Pongo abelii	ENSPPYG00000008377	1 retrocopy	retro_pabe_427,
Pan troglodytes	ENSPTRG00000009220	2 retrocopies	retro_ptro_1624 , retro_ptro_334,