RetrogeneDB ID:

retro_cpor_614

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_2:65258912..65259262(-)
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:ENSCPOG00000002862
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_614
ATTGACAGCGGTGCTGTTTTGGACTGGAACATGGGTCAGGCCCCAGCCCCAGGCCCTGCAAGTCGCCCAGGAAACAGTGG
CATGAGCACAGCCTACACATCAGGCAGGACAGCCTTACTGAAGAGGGCTTTGCAGTGTTTGACCACATGCTGAGTACGGA
GAAAAACACTCAGAGAGGTGAACAGAGAAAGTAATCAAGTCAAAACCAGCAAAGCTAACACTGAACACCTGAGGAGCCGT
GGTCCACAAAGCAGCTCATCACTGAAGGTCCCCACTACGGGCCTGAGTCTGACTTCTCGCTGCAGGACCGGCAGTGCATC
CTCCATTGCAGAGCCTTCTTGGACAAGGCC

ORF - retro_cpor_614 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 54.55 %
Parental protein coverage: 73.42 %
Number of stop codons detected: 0
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalIDSGAVSDWNVGRAPDPRAVSCLRNHGISTAHKA-RQ--VTKEDFATFDYMLCMDESN-LRDLTRKSNQV
IDSGAV.DWN.G.AP.P...S...N.G.STA....RQ...T.E.FA.FD.ML...E.N.LR...R.SNQV
RetrocopyIDSGAVLDWNMGQAPAPGPASRPGNSGMSTAYTS<RQDSLTEEGFAVFDHMLST-EKN>LREVNRESNQV
ParentalKNCKARIELLGSYDPQ-KQLIIEDPYYGNESDFEQVYQQCVRCCKAFLEKA
K..KA..E.L.S..PQ.KQLI.E.P.YG.ESDF.....QC...C.AFL.KA
RetrocopyKTSKANTEHLRSRGPQ<KQLITEGPHYGPESDFSLQDRQCILHCRAFLDKA

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
SRP017611_brain 0 .00 RPM 16 .97 RPM
SRP017611_kidney 0 .00 RPM 14 .87 RPM
SRP017611_liver 0 .00 RPM 12 .19 RPM
SRP040447_lung 0 .00 RPM 14 .80 RPM
SRP040447_skeletal_muscle 0 .00 RPM 13 .28 RPM
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_614 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_614 was not experimentally validated.

Retrocopy orthology:
Cavia porcellus 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 20 parental genes, and 215 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000095542 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,
Cavia porcellus ENSCPOG00000002862 4 retrocopies
Dasypus novemcinctus ENSDNOG0000001738232 retrocopies
Dipodomys ordii ENSDORG000000164696 retrocopies
Echinops telfairi ENSETEG0000001376418 retrocopies
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
Nomascus leucogenys ENSNLEG000000083596 retrocopies
Otolemur garnettii ENSOGAG000000003015 retrocopies
Pan troglodytes ENSPTRG000000116055 retrocopies
Pteropus vampyrus ENSPVAG000000133875 retrocopies
Tarsius syrichta ENSTSYG000000048647 retrocopies
Tursiops truncatus ENSTTRG000000107704 retrocopies



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