RetrogeneDB ID:

retro_ptro_3080

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:GL394737.1:15555..15964(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ACP1
Ensembl ID:ENSPTRG00000011605
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_3080
GAACAGGGGCCCGTAGTGGGGCTGTTTGTGTGTTCTGGGTGACATCTGGCAATCCCCCACTGCAGAGGCAATTTTAAGAA
AATCTGCAGATAATAAAAACGTTTCCGGTAATTGGATCGTTGACAGCGGAGCGGCCTTGGACTGAGAATGTGGGCTAGCC
CTTAAAAGCAAGAGCTCTAAGCTGCCTAAGAAACTGTGGCATTACCAGGCCATCAAATAAGTCAGGATTATCAAAGACAT
CTTCCTTGCTTGTGATTATATATAATACATGGATGAAAGCAAACTGGGAGATTGGAACAGAAAAGGTAATTAAGTTAAAA
AATGCAAAGCTAAAATTGAACTCCTTGGGAGGTAGGAGCCACAAATGTAACTTATAACTGAAAAGCCCTATTAAGGTAAT
GATTCAGAT

ORF - retro_ptro_3080 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 56.12 %
Parental protein coverage: 86.08 %
Number of stop codons detected: 7
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalEQATKSVLFVC-LGNICRSPIAEAVFRKLVTDQNISENWVIDSGAVSD-WNVGRSPDPRAVSCLRNHGI-
EQ.....LFVC.LG.I..SP.AEA..RK.....N.S.NW..DSGA..D..NVG.....RA.SCLRN.GI.
RetrocopyEQGPVVGLFVC>LGDIWQSPTAEAILRKSADNKNVSGNWIVDSGAALD>ENVG*PLKARALSCLRNCGI<
ParentalHTAHKARQITKEDFATFDYILCMDESNLRDLNRKSNQVKTCKAKIELLGSYDPQKQLIIEDPYYGNDSD
..A.K...I.K..F...DYI..MDES.L.D.NRK.N.VK.CKAKIELLG...PQ..LI.E.PY.GNDSD
RetrocopyYQAIK*VRIIKDIFLACDYI*YMDESKLGDWNRKGN*VKKCKAKIELLGR*EPQM*LITEKPY*GNDSD

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 .02 RPM 37 .13 RPM
SRP007412_cerebellum 0 .04 RPM 37 .57 RPM
SRP007412_heart 0 .00 RPM 29 .58 RPM
SRP007412_kidney 0 .03 RPM 74 .22 RPM
SRP007412_liver 0 .00 RPM 55 .94 RPM
SRP007412_testis 0 .00 RPM 50 .58 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_3080 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_3080 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_3080 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 30 parental genes, and 270 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000095542 retrocopies
Bos taurus ENSBTAG000000204984 retrocopies
Canis familiaris ENSCAFG000000300971 retrocopy
Choloepus hoffmanni ENSCHOG0000000389194 retrocopies
retro_chof_1010, retro_chof_1053, retro_chof_1073, retro_chof_1099, retro_chof_1100, retro_chof_1144, retro_chof_119, retro_chof_1190, retro_chof_121, retro_chof_1259, retro_chof_1265, retro_chof_1275, retro_chof_1330, retro_chof_1351, retro_chof_1359, retro_chof_1389, retro_chof_1390, retro_chof_1412, retro_chof_142, retro_chof_1444, retro_chof_1447, retro_chof_1508, retro_chof_1567, retro_chof_1570, retro_chof_1593, retro_chof_1632, retro_chof_1633, retro_chof_1658, retro_chof_1684, retro_chof_169, retro_chof_1698, retro_chof_17, retro_chof_1716, retro_chof_174, retro_chof_1799, retro_chof_1802, retro_chof_1815, retro_chof_1833, retro_chof_1838, retro_chof_1864, retro_chof_1941, retro_chof_1956, retro_chof_1993, retro_chof_2012, retro_chof_2041, retro_chof_2044, retro_chof_2091, retro_chof_2165, retro_chof_2192, retro_chof_2208, retro_chof_2228, retro_chof_2259, retro_chof_2344, retro_chof_2378, retro_chof_2384, retro_chof_2443, retro_chof_245, retro_chof_2478, retro_chof_2512, retro_chof_2532, retro_chof_2542, retro_chof_2551, retro_chof_261, retro_chof_262, retro_chof_2622, retro_chof_2636, retro_chof_2643, retro_chof_2653, retro_chof_2654, retro_chof_2678, retro_chof_2701, retro_chof_2705, retro_chof_2707, retro_chof_319, retro_chof_377, retro_chof_460, retro_chof_598, retro_chof_603, retro_chof_649, retro_chof_650, retro_chof_66, retro_chof_727, retro_chof_80, retro_chof_803, retro_chof_83, retro_chof_842, retro_chof_934, retro_chof_939, retro_chof_958, retro_chof_962, retro_chof_986, retro_chof_991, retro_chof_994, retro_chof_999,
Callithrix jacchus ENSCJAG000000116635 retrocopies
Cavia porcellus ENSCPOG000000028624 retrocopies
Dasypus novemcinctus ENSDNOG0000001738232 retrocopies
Dipodomys ordii ENSDORG000000164696 retrocopies
Equus caballus ENSECAG000000100791 retrocopy
Echinops telfairi ENSETEG0000001376418 retrocopies
Felis catus ENSFCAG000000267171 retrocopy
Homo sapiens ENSG000001437275 retrocopies
Gorilla gorilla ENSGGOG000000155775 retrocopies
Loxodonta africana ENSLAFG000000029664 retrocopies
Macropus eugenii ENSMEUG000000107333 retrocopies
Myotis lucifugus ENSMLUG000000177074 retrocopies
Macaca mulatta ENSMMUG000000170972 retrocopies
Monodelphis domestica ENSMODG000000257643 retrocopies
Mustela putorius furoENSMPUG000000127872 retrocopies
Mus musculus ENSMUSG0000004457311 retrocopies
Nomascus leucogenys ENSNLEG000000083596 retrocopies
Oryctolagus cuniculus ENSOCUG0000001287611 retrocopies
Otolemur garnettii ENSOGAG000000003015 retrocopies
Pongo abelii ENSPPYG000000126946 retrocopies
Pan troglodytes ENSPTRG00000011605 5 retrocopies
Pteropus vampyrus ENSPVAG000000133875 retrocopies
Rattus norvegicus ENSRNOG0000000526011 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000025203 retrocopies
Tarsius syrichta ENSTSYG000000048647 retrocopies
Tursiops truncatus ENSTTRG000000107704 retrocopies



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