RetrogeneDB ID:

retro_pcap_149

Retrocopy
location
Organism:Hyrax (Procavia capensis)
Coordinates:scaffold_11353:31698..32188(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSPCAG00000003203
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_pcap_149
AGTAGGAAGTCAAGCATGGCATCATCTTCCCAGCAAGAAGGGATGAGTTCCAAGCCTAAGCTCACTGAACAGCAGTGGCA
AGAAATCCATGATGCTTTCAATCTCTTTGATGATGATGGCACTGGAAGCATTGATGTCAGACAACTTAAGGTAGCTATGA
GGGCCTTGGGCTTTGAGCCGAAGAAAGAAGAGATTAAGAAGATGATAAGCGAAATTGATAAGGGAGGTACAGGAAAAATG
AACTTTGGTGAATTTTTGACTCTGATGACACAGAAAATGTCTGAGAGAGATACCCGAGAAGAAAATCTTGAAAGCTTTCA
AGCTCTTCAGTGATGATGAGACTGGAAAGATATCTTTTGACAATCTGAAACGTGTGGCCCAAGAGCTGGGTGAGAACCTC
ACTGATGAGGAGCTGAAGAAAATGATTAATGAGGCAGATCAAGATGGAGATGGGGAAGTCAACGAGAAAGAATTCCTGCG
CATCGTGAAG

ORF - retro_pcap_149 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 54.88 %
Parental protein coverage: 95.86 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalSSEDSRSTSSSQPTLTYKNVFPERLLQQIRQGFHLFDPDGNVSIDIRSLKVVLKTLGFEPRKE-MDIIVS
S...S...SS.Q.....K....E...Q.I...F.LFD.DG..SID.R.LKV....LGFEP.KE......S
RetrocopySRKSSMASSSQQEGMSSKPKLTEQQWQEIHDAFNLFDDDGTGSIDVRQLKVAMRALGFEPKKEEIKKMIS
ParentalIIDRKGTGKMNFSEFLYVITQKMLEKETEEE-LLKVFDLFDDDETGTISFANLKHVAEELGEDVTDEELQ
.ID..GTGKMNF.EFL...TQKM.E..T.EE..LK.F.LF.DDETG.ISF.NLK.VA.ELGE..TDEEL.
RetrocopyEIDKGGTGKMNFGEFLTLMTQKMSERDTREE>ILKAFKLFSDDETGKISFDNLKRVAQELGENLTDEELK
ParentalEMIDETAVDGEGEVSEHEFLEIIR
.MI.E...DG.GEV.E.EFL.I..
RetrocopyKMINEADQDGDGEVNEKEFLRIVK

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






RNA-Seq - click to see more details

Procavia capensis was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Procavia capensis was not studied using ChIP-Seq data.

EST - click to see more details

Procavia capensis was not studied using EST data.

TSS - click to see more details

Procavia capensis was not studied using FANTOM5 data.

Lab - click to see more details

retro_pcap_149 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 29 parental genes, and 45 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000003641 retrocopy
retro_amel_56,
Bos taurus ENSBTAG000000078441 retrocopy
retro_btau_170,
Canis familiaris ENSCAFG000000191701 retrocopy
retro_cfam_199,
Choloepus hoffmanni ENSCHOG000000102441 retrocopy
retro_chof_39,
Callithrix jacchus ENSCJAG000000163383 retrocopies
retro_cjac_106, retro_cjac_185, retro_cjac_316,
Cavia porcellus ENSCPOG000000120812 retrocopies
retro_cpor_1250, retro_cpor_21,
Equus caballus ENSECAG000000007961 retrocopy
retro_ecab_49,
Felis catus ENSFCAG000000049011 retrocopy
retro_fcat_47,
Homo sapiens ENSG000001474001 retrocopy
retro_hsap_71,
Gorilla gorilla ENSGGOG000000113781 retrocopy
retro_ggor_74,
Loxodonta africana ENSLAFG000000144241 retrocopy
retro_lafr_121,
Microcebus murinus ENSMICG000000058622 retrocopies
retro_mmur_122, retro_mmur_21,
Myotis lucifugus ENSMLUG000000145202 retrocopies
retro_mluc_320, retro_mluc_370,
Macaca mulatta ENSMMUG000000207432 retrocopies
retro_mmul_1127, retro_mmul_176,
Mustela putorius furoENSMPUG000000118581 retrocopy
retro_mputfur_386,
Mus musculus ENSMUSG000000313472 retrocopies
retro_mmus_107, retro_mmus_838,
Nomascus leucogenys ENSNLEG000000138601 retrocopy
retro_nleu_1221,
Oryctolagus cuniculus ENSOCUG000000078971 retrocopy
retro_ocun_180,
Otolemur garnettii ENSOGAG000000053011 retrocopy
retro_ogar_236,
Procavia capensis ENSPCAG00000003203 1 retrocopy
retro_pcap_149 ,
Procavia capensis ENSPCAG000000068541 retrocopy
retro_pcap_403,
Procavia capensis ENSPCAG000000077781 retrocopy
retro_pcap_364,
Pongo abelii ENSPPYG000000208331 retrocopy
retro_pabe_58,
Pan troglodytes ENSPTRG000000223891 retrocopy
retro_ptro_108,
Rattus norvegicus ENSRNOG000000170595 retrocopies
retro_rnor_2376, retro_rnor_2394, retro_rnor_2920, retro_rnor_304, retro_rnor_775,
Sus scrofa ENSSSCG000000127573 retrocopies
retro_sscr_1175, retro_sscr_57, retro_sscr_822,
Ictidomys tridecemlineatus ENSSTOG000000238532 retrocopies
retro_itri_636, retro_itri_91,
Tarsius syrichta ENSTSYG000000038312 retrocopies
retro_tsyr_1142, retro_tsyr_36,
Tursiops truncatus ENSTTRG000000012362 retrocopies
retro_ttru_32, retro_ttru_335,




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