RetrogeneDB ID:

retro_ptro_2872

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:9:6827323..6827599(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPTRG00000039609
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SNRPEL1
Ensembl ID:ENSPTRG00000030224
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_2872
ATGGCATACAGTGGCCAGGGCCAGAAAGTGCAGAAGGTTATGGTGCAGCCCATCAACCTCATCTTCAGATACTTACAAAA
TAGATCGCGGATTCAGGTGTGGCTCTATGAGCAAGTGAATATGCAGATAGAAGGCTGTATCATTGGTTTTGATGAGTATA
TGAACCTTGTATTAGATGATGCAGAAGAGATTCATTCTAAAACAAAGTCAAGAAAACAACTGGGTCGGATCATGCTAAAA
GGAGATAATATTACTCTGCTACAAAGTGTCTCCAAC

ORF - retro_ptro_2872 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.83 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAYRGQGQKVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKS
MAY.GQGQKVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNM.IEGCIIGFDEYMNLVLDDAEEIHSKTKS
RetrocopyMAYSGQGQKVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMQIEGCIIGFDEYMNLVLDDAEEIHSKTKS
ParentalRKQLGRIMLKGDNITLLQSVSN
RKQLGRIMLKGDNITLLQSVSN
RetrocopyRKQLGRIMLKGDNITLLQSVSN

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain_prefrontal_cortex 0 .52 RPM 11 .39 RPM
SRP007412_cerebellum 0 .18 RPM 6 .20 RPM
SRP007412_heart 0 .20 RPM 4 .78 RPM
SRP007412_kidney 0 .58 RPM 10 .41 RPM
SRP007412_liver 0 .43 RPM 5 .30 RPM
SRP007412_testis 0 .21 RPM 4 .85 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2872 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2872 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2872 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_4228
Gorilla gorilla retro_ggor_91
Pongo abelii retro_pabe_20

Parental genes homology:
Parental genes homology involve 13 parental genes, and 115 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000091586 retrocopies
Callithrix jacchus ENSCJAG000000067351 retrocopy
Dasypus novemcinctus ENSDNOG0000000449024 retrocopies
Echinops telfairi ENSETEG0000001401524 retrocopies
Felis catus ENSFCAG000000008732 retrocopies
Homo sapiens ENSG0000018200410 retrocopies
Gorilla gorilla ENSGGOG000000007557 retrocopies
Microcebus murinus ENSMICG000000155373 retrocopies
Monodelphis domestica ENSMODG000000283943 retrocopies
Mustela putorius furoENSMPUG000000116427 retrocopies
Pongo abelii ENSPPYG000000003268 retrocopies
Pan troglodytes ENSPTRG00000030224 11 retrocopies
Sorex araneus ENSSARG000000033119 retrocopies



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