RetrogeneDB ID:

retro_pcap_440

Retrocopy
location
Organism:Hyrax (Procavia capensis)
Coordinates:scaffold_88331:4008..5010(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GAPDH
Ensembl ID:ENSPCAG00000006928
Aliases:None
Description:glyceraldehyde-3-phosphate dehydrogenase [Source:HGNC Symbol;Acc:4141]


Retrocopy-Parental alignment summary:






>retro_pcap_440
ATGGTGAAGGTCGGAGTGAACGGGTTTGGCCGTATTGGATGCCTGCCCACCAGAGCTGCTTTTAACTCTGGCAAAGTGGA
CATTGTTTGCCATCAATGACCCCTTCATTGACCTCCACTACATGCTCTACATGTTCCAGTATGATTCCACTCACGGCAAG
TTCCATGGCACTGTCAAGGCTGAGAATGCAAAAGCTTGTCATTCAATGGGAACCACATCACTATCTTCCAGGAGTGAGAT
CCCGCCAACATCAAGTGGGGTGATGCTGGTGCTGAGTATGTTGTGGAATCTACCTGGTGTCTTTACAACCATGGAGAAGG
CTGGGGCTCACTTGAAGGGTGGTGCCAAGAGGGTGATCATATCTGCCCCTTCTGCCGATGCCCCCATGTTTGTGATGGGC
GTGAACCATGAGAAGTATGACAAGTCCCTCAAGATTGTCAGCAACGCCTCCTGCACTACCAACTGCTTGGCCCCCTTGGC
CAAGGTCATCCATGACAACTTTGGCATTGTGGAGGGACTCATGACCACAGTCCATGCCATCACTGCCACCCAGAAGACTG
TGATGGCCCCTCTGGGAAACTGTGTCGTGATGGCCGCGGGGCTGCCCAGAACATCATCCCCACATCTACTGGTGCTGCCA
AGGCTGTGGGCAAGGTCATCCCTGAGCTGAATGGGAAGCTCACTGGCATGGCCTTCCGTGTCCCTACCCCCAGTGTGTCA
GTGGTGGATCTGACCTGCCATCTACAGAAAGCTGCCAAATATGATGACATCAAGAAGGTGGTAAAGCAGGCATCAGAGGG
TCCCCTAAAGGGCATTCTGGGCTACACTGAGGACCAGGTTGTCTCTTGCGACTTTAACAGTGATACTCACTCTTCCACCT
TTGATGCTGAGGCTGGCATTGCCCTCAGTGACCACTTTGTCAAGCTCATCTCTTGGTATGACAATGAATTTGGCTACAGC
AACAGGGTGGTGGACCTTATGGTCCACATGGCCTCCAAGGAG

ORF - retro_pcap_440 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.67 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalMVKVGVNGFGRIGRLVTRAAFNSGKVDIV-AINDPFIDLHYMVYMFQYDSTHGKFHGTVKAENGK-LVI-
MVKVGVNGFGRIG.L.TRAAFNSGKVDIV.AINDPFIDLHYM.YMFQYDSTHGKFHGTVKAEN.K.LVI.
RetrocopyMVKVGVNGFGRIGCLPTRAAFNSGKVDIV>AINDPFIDLHYMLYMFQYDSTHGKFHGTVKAENAK>LVI>
ParentalNGKHITIFQERDPANIKWGDAGAEYVVEST-GVFTTMEKAGAHLKGGAKRVIISAPSADAPMFVMGVNHE
NG.HITIFQE.DPANIKWGDAGAEYVVEST.GVFTTMEKAGAHLKGGAKRVIISAPSADAPMFVMGVNHE
RetrocopyNGNHITIFQE*DPANIKWGDAGAEYVVEST>GVFTTMEKAGAHLKGGAKRVIISAPSADAPMFVMGVNHE
ParentalKYDKSLKIVSNASCTTNCLAPLAKVIHDNFGIVEGLMTTVHAITATQKTV-DGPSGKLWRDGRGAAQNII
KYDKSLKIVSNASCTTNCLAPLAKVIHDNFGIVEGLMTTVHAITATQKTV.DGPSGKL.RDGRGAAQNII
RetrocopyKYDKSLKIVSNASCTTNCLAPLAKVIHDNFGIVEGLMTTVHAITATQKTV<DGPSGKLCRDGRGAAQNII
ParentalPASTGAAKAVGKVIPELNGKLTGMAFRVPTPNVSVVDLTCRLEKAAKYDDIKKVVKQASEGPLKGILGYT
P.STGAAKAVGKVIPELNGKLTGMAFRVPTP.VSVVDLTC.L.KAAKYDDIKKVVKQASEGPLKGILGYT
RetrocopyPTSTGAAKAVGKVIPELNGKLTGMAFRVPTPSVSVVDLTCHLQKAAKYDDIKKVVKQASEGPLKGILGYT
ParentalEDQVVSCDFNSDTHSSTFDAGAGIALNDHFVKLISWYDNEFGYSNRVVDLMVHMASKE
EDQVVSCDFNSDTHSSTFDA.AGIAL.DHFVKLISWYDNEFGYSNRVVDLMVHMASKE
RetrocopyEDQVVSCDFNSDTHSSTFDAEAGIALSDHFVKLISWYDNEFGYSNRVVDLMVHMASKE

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






Procavia capensis was not studied using RNA-Seq expression data.
Procavia capensis was not studied using ChIP-Seq data.
Procavia capensis was not studied using EST data.
Procavia capensis was not studied using FANTOM5 data.
retro_pcap_440 was not experimentally validated.

Retrocopy orthology:
Procavia capensis 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 23 parental genes, and 390 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000066755 retrocopies
Ailuropoda melanoleuca ENSAMEG0000001432935 retrocopies
Canis familiaris ENSCAFG000000150774 retrocopies
Callithrix jacchus ENSCJAG000000082341 retrocopy
Cavia porcellus ENSCPOG000000263501 retrocopy
Equus caballus ENSECAG0000002205111 retrocopies
Felis catus ENSFCAG0000000687417 retrocopies
Gorilla gorilla ENSGGOG0000000955330 retrocopies
Loxodonta africana ENSLAFG000000027803 retrocopies
Myotis lucifugus ENSMLUG0000001432018 retrocopies
Macaca mulatta ENSMMUG0000001867933 retrocopies
Monodelphis domestica ENSMODG0000001806641 retrocopies
Mustela putorius furoENSMPUG0000001689128 retrocopies
Mus musculus ENSMUSG00000057666109 retrocopies
retro_mmus_1029, retro_mmus_1082, retro_mmus_1136, retro_mmus_1193, retro_mmus_1249, retro_mmus_1319, retro_mmus_1328, retro_mmus_136, retro_mmus_1365, retro_mmus_1371, retro_mmus_1467, retro_mmus_1474, retro_mmus_1480, retro_mmus_1615, retro_mmus_1692, retro_mmus_1721, retro_mmus_1728, retro_mmus_1886, retro_mmus_1922, retro_mmus_1957, retro_mmus_1983, retro_mmus_1985, retro_mmus_2009, retro_mmus_2020, retro_mmus_2030, retro_mmus_2100, retro_mmus_211, retro_mmus_2119, retro_mmus_2122, retro_mmus_2148, retro_mmus_2158, retro_mmus_2175, retro_mmus_2206, retro_mmus_2216, retro_mmus_2248, retro_mmus_2298, retro_mmus_2370, retro_mmus_2371, retro_mmus_2389, retro_mmus_2463, retro_mmus_2477, retro_mmus_2481, retro_mmus_2512, retro_mmus_2556, retro_mmus_2587, retro_mmus_2623, retro_mmus_2626, retro_mmus_2647, retro_mmus_2681, retro_mmus_2755, retro_mmus_2761, retro_mmus_2764, retro_mmus_2848, retro_mmus_2872, retro_mmus_2911, retro_mmus_2912, retro_mmus_2913, retro_mmus_2914, retro_mmus_2915, retro_mmus_2920, retro_mmus_2932, retro_mmus_2943, retro_mmus_300, retro_mmus_3036, retro_mmus_3064, retro_mmus_3120, retro_mmus_3137, retro_mmus_3140, retro_mmus_3148, retro_mmus_3151, retro_mmus_3188, retro_mmus_3193, retro_mmus_3197, retro_mmus_3216, retro_mmus_3228, retro_mmus_3306, retro_mmus_3335, retro_mmus_3336, retro_mmus_3357, retro_mmus_3377, retro_mmus_3445, retro_mmus_3514, retro_mmus_3575, retro_mmus_3650, retro_mmus_3658, retro_mmus_3693, retro_mmus_3716, retro_mmus_3814, retro_mmus_416, retro_mmus_437, retro_mmus_48, retro_mmus_553, retro_mmus_608, retro_mmus_619, retro_mmus_628, retro_mmus_635, retro_mmus_698, retro_mmus_745, retro_mmus_765, retro_mmus_766, retro_mmus_787, retro_mmus_811, retro_mmus_893, retro_mmus_914, retro_mmus_921, retro_mmus_946, retro_mmus_952, retro_mmus_976, retro_mmus_996,
Ornithorhynchus anatinus ENSOANG000000044921 retrocopy
Ochotona princeps ENSOPRG0000001251410 retrocopies
Procavia capensis ENSPCAG00000006928 9 retrocopies
Pteropus vampyrus ENSPVAG0000001257014 retrocopies
Rattus norvegicus ENSRNOG000000186304 retrocopies
Rattus norvegicus ENSRNOG000000306382 retrocopies
Sarcophilus harrisii ENSSHAG000000149534 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000075389 retrocopies
Xenopus tropicalis ENSXETG000000339751 retrocopy



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