RetrogeneDB ID:

retro_ptro_1490

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:22:37833693..37834253(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:FUNDC2
Ensembl ID:ENSPTRG00000041852
Aliases:None
Description:Pan troglodytes FUN14 domain containing 2 (FUNDC2), mRNA. [Source:RefSeq mRNA;Acc:NM_001251911]


Retrocopy-Parental alignment summary:






>retro_ptro_1490
TCTGTCCCACGTGCCGGAAGCCAACCGGTGGTGATGACTCTGTGTGCCACTCCGCCTCCTACAGCGCGGATCCTCTGCGT
GTGTCCTCGCAAGACAAGCTCGATGAAATGGCCGAGTCCAGTCAAGCAAACTTTGAGGGAAATTTTGAGTCGCTGGACCT
TGTGGAATTTGCTAAGAAACAGCCATGGTGGTGTAAGCTGTTCGGGCAGGAATCTGGACCTTCGCCGAAAAGTGAAGGGT
GGCAACTCAGCCGTTCATTGGGGGTGTCACGGAATGGTGCACGGGTTTCATATCCCAGAAGGTTGGAAAGTTGGCTGTAA
CAGTTGTGGGAGGTGTTTTTTTTTTTCTCTTTCAGCTTGCAAATCATACTGGGTACATCAAAGTTGACTGGCAATGAGTG
GAGAAAGATATAAAGAAAGCCAAAGAGCTGCTGAAGATCCCTTAAGAGCAATCAGATACCTACCAAGGTCAGGAGCAAAG
CTGAGGAGGTGGTGTCATTTGTGAAGAATGTTCTAGTGACTGGGGGATTTTTCGGAGGCTTTCTGTTTGGCATGGCATCC

ORF - retro_ptro_1490 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.63 %
Parental protein coverage: 98.41 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalSAPRAGSQ-VVATTAR-HSAAYRADPLRVASRDKLTEMAASSQGNFEGNFESLDLAEFAKKQPWWRKLFG
S.PRAGSQ.VV.T....HSA.Y.ADPLRV.S.DKL.EMA.SSQ.NFEGNFESLDL.EFAKKQPWW.KLFG
RetrocopySVPRAGSQPVVMTLCA<HSASYSADPLRVSSQDKLDEMAESSQANFEGNFESLDLVEFAKKQPWWCKLFG
ParentalQESGPS-AEKYSVATQLFIGGVTGWCTGFIFQKVGKLAATAVGG-GFFLLQLANHTGYIKVDWQRVEKDM
QESGPS.AEK..VATQ.FIGGVT.WCTGFI.QKVGKLA.T.VGG....L.QLANHTGYIKVDWQ.VEKD.
RetrocopyQESGPS<AEK*RVATQPFIGGVTEWCTGFISQKVGKLAVTVVGGXXXXLFQLANHTGYIKVDWQ*VEKDI
ParentalKKAKEQLKI-RKSNQIPTEVRSKAEEVVSFVKKNVLVTGGFFGGFLLGMAS
KKAKE.LKI..KSNQIPT.VRSKAEEVVSFV.KNVLVTGGFFGGFL.GMAS
RetrocopyKKAKELLKI>LKSNQIPTKVRSKAEEVVSFV-KNVLVTGGFFGGFLFGMAS

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 28 .81 RPM
SRP007412_cerebellum 0 .04 RPM 26 .78 RPM
SRP007412_heart 0 .12 RPM 48 .38 RPM
SRP007412_kidney 0 .08 RPM 33 .24 RPM
SRP007412_liver 0 .13 RPM 9 .43 RPM
SRP007412_testis 0 .11 RPM 31 .40 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1490 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1490 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1490 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2560

Parental genes homology:
Parental genes homology involve 20 parental genes, and 50 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000169771 retrocopy
Choloepus hoffmanni ENSCHOG0000000430611 retrocopies
Callithrix jacchus ENSCJAG000000042873 retrocopies
Dipodomys ordii ENSDORG000000131561 retrocopy
Echinops telfairi ENSETEG000000138172 retrocopies
Homo sapiens ENSG000001657753 retrocopies
Loxodonta africana ENSLAFG000000152891 retrocopy
Myotis lucifugus ENSMLUG000000077761 retrocopy
Macaca mulatta ENSMMUG000000102481 retrocopy
Monodelphis domestica ENSMODG000000164841 retrocopy
Mus musculus ENSMUSG000000311982 retrocopies
Nomascus leucogenys ENSNLEG000000144435 retrocopies
Otolemur garnettii ENSOGAG000000334613 retrocopies
Pongo abelii ENSPPYG000000208974 retrocopies
Pan troglodytes ENSPTRG000000218211 retrocopy
Pan troglodytes ENSPTRG00000041852 4 retrocopies
Pteropus vampyrus ENSPVAG000000135521 retrocopy
Rattus norvegicus ENSRNOG000000240662 retrocopies
Sus scrofa ENSSSCG000000128171 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000078012 retrocopies



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