RetrogeneDB ID:

retro_ptro_2541

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:7:63488888..63489305(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:FAM162B
Ensembl ID:ENSPTRG00000018538
Aliases:None
Description:family with sequence similarity 162, member B [Source:HGNC Symbol;Acc:21549]


Retrocopy-Parental alignment summary:






>retro_ptro_2541
TGTGCCCCTGGGAAGCCTCTAGAAGCCACACAGAGGCCCATAGCAACTCTCATGCCTTGGAGGGTCTCACCAGCCACTCC
AGTGATGGGCCCTCCAGTAGCTCTGGGACCCAAGCAGGGATGATTCACAAAGTCCCTACCAAGCACAGGCCTTCACAGTT
CAACAAGAAAATCCTACTGTTGACTGGATTTTTAAAAATCAGTGGAGGAGATCACACTAGAAATGATAGATACTGCAAGA
AACAAAGCTTGAGTGAAAGCTTGTTACCGTAATGAATGGACTCACACATATCACTGCTTTGCAGTGATAGCATCAGCCAA
AAAGGCTGCAGAACATGAATCATTAACAAGTTGAAATATGTCAAAGATGGCTGTGTGGTGTGAAGAAGCTGCATTAGCTG
CACAGGCTAAGCCTAAA

ORF - retro_ptro_2541 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.43 %
Parental protein coverage: 88.89 %
Number of stop codons detected: 2
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalCGPGAPLEATRRP-APALPPR-GLPCYSSGGAPSNSGPQGHGEIHRVPTQRRPSQFDKKILLWTGRFK-S
C.PG.PLEAT.RP.A...P.R.GL...SS.G..S.SG.Q..G.IH.VPT..RPSQF.KKILL.TG..K.S
RetrocopyCAPGKPLEATQRPIATLMPWR<GLTSHSSDGPSSSSGTQA-GMIHKVPTKHRPSQFNKKILLLTGFLK>S
ParentalMEEIPPRIPPEMIDTARNKARVKACY-IMIGLTIIA-CFAVIVSAKRAVERHESLTSWNLAKKAKWREEA
.EE....I..EMIDTARNKA.VKACY..M.GLT.I..CFAVI.SAK.A.E.HESLTS.N..K.A.W.EEA
RetrocopyVEE----ITLEMIDTARNKA*VKACY>VMNGLTHIT<CFAVIASAKKAAE-HESLTS*NMSKMAVWCEEA
ParentalALAAQAKAK
ALAAQAK.K
RetrocopyALAAQAKPK

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 .00 RPM 1 .34 RPM
SRP007412_cerebellum 0 .00 RPM 0 .25 RPM
SRP007412_heart 0 .00 RPM 2 .48 RPM
SRP007412_kidney 0 .00 RPM 3 .01 RPM
SRP007412_liver 0 .00 RPM 0 .72 RPM
SRP007412_testis 0 .00 RPM 1 .58 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2541 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2541 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2541 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3744
Pan troglodytes retro_ptro_2542
Pan troglodytes retro_ptro_2994

Parental genes homology:
Parental genes homology involve 5 parental genes, and 9 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG000001838072 retrocopies
Gorilla gorilla ENSGGOG000000020451 retrocopy
Microcebus murinus ENSMICG000000145551 retrocopy
Mus musculus ENSMUSG000000199091 retrocopy
Pan troglodytes ENSPTRG00000018538 4 retrocopies



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