RetrogeneDB ID:

retro_ptro_306

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:1:64434588..64435071(-)
Located in intron of:ENSPTRG00000024245
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CFL1
Ensembl ID:ENSPTRG00000003895
Aliases:None
Description:cofilin 1 (non-muscle) [Source:HGNC Symbol;Acc:1874]


Retrocopy-Parental alignment summary:






>retro_ptro_306
GTGTGGCTGTCTGATGGTGTCATGAACATGTTCAACGACATGAAGGTGCATAAGTCTTCAATGCCAGAGGAGGTGAAGAA
GCACAAGAAGGCGGTGCTCTTCTGCCTTAGTGAGGACAAGAAGAACATCATCCTGGAGGAGACCAAGAAGATCCTGGTGG
GCGATGTGAGCCAGACCATCGACGACCCCTACACCACCTTTGTCAGGATGCTGCCAGATAAGGACTGCCACTACACCCTC
TGTGACACAACCTACGAGACCAAGGAGAGCAAGGAGGAGGACCTGGTGTTTATCTTCTGGGTCCCTGAGTCTGCTCCCCT
TAAAAGCAAAATGATCTATGCCAGCTCCAAGGACACCGTCAAGAAGCTGACAGGGATCAAGCATGAATTACACACAAACT
GCTACAAGGAGGTCAAGGACCGCTGCACCCTGGCAGAGAAGCTGGGGGGCAGTGCGGTCATCTCCCTAGAGGACAAGCCT
TTG

ORF - retro_ptro_306 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.33 %
Parental protein coverage: 97.59 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalVAVSDGVIKVFNDMKVRKSSTPEEVKKRKKAVLFCLSEDKKNIILEEGKEILVGDVGQTVDDPYATFVKM
V..SDGV...FNDMKV.KSS.PEEVKK.KKAVLFCLSEDKKNIILEE.K.ILVGDV.QT.DDPY.TFV.M
RetrocopyVWLSDGVMNMFNDMKVHKSSMPEEVKKHKKAVLFCLSEDKKNIILEETKKILVGDVSQTIDDPYTTFVRM
ParentalLPDKDCRYALYDATYETKESKKEDLVFIFWAPESAPLKSKMIYASSKDAIKKKLTGIKHELQANCYEEVK
LPDKDC.Y.L.D.TYETKESK.EDLVFIFW.PESAPLKSKMIYASSKD...KKLTGIKHEL..NCY.EVK
RetrocopyLPDKDCHYTLCDTTYETKESKEEDLVFIFWVPESAPLKSKMIYASSKDTV-KKLTGIKHELHTNCYKEVK
ParentalDRCTLAEKLGGSAVISLEGKPL
DRCTLAEKLGGSAVISLE.KPL
RetrocopyDRCTLAEKLGGSAVISLEDKPL

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 403 .03 RPM
SRP007412_cerebellum 0 .00 RPM 306 .79 RPM
SRP007412_heart 0 .03 RPM 68 .29 RPM
SRP007412_kidney 0 .03 RPM 304 .15 RPM
SRP007412_liver 0 .00 RPM 324 .66 RPM
SRP007412_testis 0 .11 RPM 79 .88 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_306 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_306 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_306 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_400
Gorilla gorilla retro_ggor_397
Pongo abelii retro_pabe_316

Parental genes homology:
Parental genes homology involve 19 parental genes, and 73 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000173342 retrocopies
Canis familiaris ENSCAFG000000249556 retrocopies
Callithrix jacchus ENSCJAG000000019161 retrocopy
Equus caballus ENSECAG000000199001 retrocopy
Felis catus ENSFCAG000000132723 retrocopies
Homo sapiens ENSG000001727576 retrocopies
Gorilla gorilla ENSGGOG000000231835 retrocopies
Myotis lucifugus ENSMLUG000000246856 retrocopies
Macaca mulatta ENSMMUG000000190165 retrocopies
Mustela putorius furoENSMPUG000000115022 retrocopies
Nomascus leucogenys ENSNLEG000000058525 retrocopies
Oryctolagus cuniculus ENSOCUG000000256044 retrocopies
Otolemur garnettii ENSOGAG000000165038 retrocopies
Pongo abelii ENSPPYG000000030475 retrocopies
Pan troglodytes ENSPTRG00000003895 5 retrocopies
Pan troglodytes ENSPTRG000000132751 retrocopy
Rattus norvegicus ENSRNOG000000206602 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000279684 retrocopies
Tursiops truncatus ENSTTRG000000169312 retrocopies



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