RetrogeneDB ID:

retro_ogar_3169

Retrocopy
location
Organism:Bushbaby (Otolemur garnettii)
Coordinates:GL873734.1:481247..481955(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PTCD2
Ensembl ID:ENSOGAG00000008390
Aliases:None
Description:pentatricopeptide repeat domain 2 [Source:HGNC Symbol;Acc:25734]


Retrocopy-Parental alignment summary:






>retro_ogar_3169
CTCATCAAAGACCAGTGTCCACCAGGTTTTTCTCAGATATGACATCATACAATATTTTGATGGATATGTTATTATCAAGA
GTAAATATGAAAGTGCTTCAGAAGTATTGGTGGAGATGAAAAACTAAGATGTGAAGTTCATCAAAGATACCTATGTCCTT
GCTTGTGGAATTTTCTACAAACTGAATATCTCTGAATCTCTCAAAATCTGTACTATGTTTAGAGAAGAATCCCTAATCAA
AGGAGAAGCTCTCTCCAGGGAAGCATACTGTTTTGCTGTGACATCAGTTCTGAATCATAACCAGTGGAAAAAACTATGTC
CATTTTCTCTCAAATCATGGATCCAGAAAGCATAGCCTGCACTGATTTAAATATTATATTCCATATCCAGTCAAATATGT
TGGAAACCCCCATAAAGATACTAACAGATGCTGCAGAAGGAAATGTATGAAGATTTGTGAAAAGACATGTGTTCTCAGAA
GAAGTGCTGGCCAAAGTGAGGGAAAAAGTGAAGGGTGTGCCTGCCTTTTTGGCCAAATTTGATGAGATCTATGGGAAACT
GCACATCACTGGCCATGTCACCACTTGGACTTTAGATGACTTGCTCTGCTATACCCTCAGGGATAAGAAATCCCCCATGT
TGTCACTGAAGAAGAATACAGTCAGCCAGAGGACCCTCCAGCCACTCAGCAAGCCCCTGCTGGCTGAG

ORF - retro_ogar_3169 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75. %
Parental protein coverage: 61.08 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalLIKDQSLRGF-FSDSTSYNILMDMLF-MKGEYESASEVLIEMKNQDVKFSKDTYVLAFAIFYKLNSPESL
LIKDQ...GF.FSD.TSYNILMDML...K..YESASEVL.EMKN.DVKF.KDTYVLA..IFYKLN..ESL
RetrocopyLIKDQCPPGF<FSDMTSYNILMDMLL<IKSKYESASEVLVEMKN*DVKFIKDTYVLACGIFYKLNISESL
ParentalKMCTMLREEALIKGDVLSRRASCFAVALALNQNQ-VEKATSFYSQIMNPESIACANLKIIIHIQSNMLET
K.CTM.REE.LIKG..LSR.A.CFAV...LN.NQ.VEK..S..SQIM.PESIAC..L.II.HIQSNMLET
RetrocopyKICTMFREESLIKGEALSREAYCFAVTSVLNHNQ<VEKTMSIFSQIMDPESIACTDLNIIFHIQSNMLET
ParentalLIKELADAAEGNVSRFVKRHVFSEEVLAKVREKVKAIPALLDRFDEIYGKLHITGHVTTQTLDDLLCHIP
.IK.L.DAAEGNV.RFVKRHVFSEEVLAKVREKVK..PA.L..FDEIYGKLHITGHVTT.TLDDLLC...
RetrocopyPIKILTDAAEGNV*RFVKRHVFSEEVLAKVREKVKGVPAFLAKFDEIYGKLHITGHVTTWTLDDLLCYTL
ParentalKDKKSPMLFLNKRRISRRTLQPLNKSLLAE
.DKKSPML.L.K...S.RTLQPL.K.LLAE
RetrocopyRDKKSPMLSLKKNTVSQRTLQPLSKPLLAE

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






Otolemur garnettii was not studied using RNA-Seq expression data.
Otolemur garnettii was not studied using ChIP-Seq data.
Otolemur garnettii was not studied using EST data.
Otolemur garnettii was not studied using FANTOM5 data.
retro_ogar_3169 was not experimentally validated.

Retrocopy orthology:
Otolemur garnettii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

Parental genes homology:
Parental genes homology involve 8 parental genes, and 12 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000163641 retrocopy
Homo sapiens ENSG000000498832 retrocopies
Gorilla gorilla ENSGGOG000000106952 retrocopies
Macaca mulatta ENSMMUG000000179081 retrocopy
Nomascus leucogenys ENSNLEG000000045162 retrocopies
Otolemur garnettii ENSOGAG00000008390 1 retrocopy
retro_ogar_3169 ,
Pan troglodytes ENSPTRG000000169682 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000065961 retrocopy



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