RetrogeneDB ID:

retro_opri_914

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_44502:4408..5521(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ALDOA
Ensembl ID:ENSOPRG00000009760
Aliases:None
Description:aldolase A, fructose-bisphosphate [Source:HGNC Symbol;Acc:414]


Retrocopy-Parental alignment summary:






>retro_opri_914
GACCTTGCTGCCACCAGCACCATTCCCTACCCATATCCCAAGCTGACCCAAGGGCAGAAGAAGGAGCTGTCTGACATCAC
TCACCAGATTGTGGCCCCGGGCAAGGGCATCTTAGCTGCAGATGAGTCCACAAGTAGCATCGCCAAGAGGCTGCAGTCCA
TTGGCACGGAGAACACGGAGGAGAACCGGCGTTTCTACCTCCAGTTGCTGCTGACCGCTGATGACCGCGTGAACCCCCGC
ATCGGGGGCGTCATCCTCTTCCACGAGACCTTCTACCAGAAGGCTGATGATGGGCGTCCCTTCCAGCAAGTGATCAAGTC
CAAGGGCGGTGTCGTAGGCATCAAGGTGGACAAGGGCGTGGTACCCCTGGCAGGAACTAACGGTGAGACCACCACTGAAG
GACTGGATGAGCTGTCCGAGCGCTGTGCCCAGTACAAGGCAAACGGAGCCGACTTTGCCAAGTGGCGTTGAGTGCTGAAG
ATCGGGAAACATACCCCCTCAGCCCTGGCCATCATGGAGAATGCCAACGTTCTGGCCCATTATGCCAGCATCTGTCAGCA
GAATGGCATTGTGCCCATCGCGGAGCCGGAAATCCTCCCCGACGGGGGCCATGACCTGAAGCGCTGCCAGTATGTCACTG
AGAAGGTGCTGGCCGCCGTGTACAAGGCTCTGAGCGACCACCACATCTACCTGGAAGGCACCTTGCTGAAGTCCAACATA
GTGACCCCAAGATACACCTGCACCCAGAAGTATTCCCACGAGGAGGTTGCAATGGCAACCGTCATGGCACTGCGCCACAC
AGTGCCCCCCGCTGTTGCCGGAGTCACCTTCCTGTCTGGAGGCCAGAGTGAGGAGGAAGCGTCCATCAACCTCAATGCCA
TCAACAAGTGCCCCCTCCTGAAGCCATGGGCCCTGACCTTCTCTTATGGCCGCGCCCTGCAGGCCTCGGCCCTGAAGGGC
TGGGGTGGGAAGAAGGAAAACCTGAAGACAGCCCAGGAGGAGTACGTAAAGCGGACCCTGGCCAACAGCCTTGCCTGTCA
AGGAAAGTACACTCCAAGTGGCCAAGCCGGGGCCACCACCACCAAGTCCCTCTTCATCTCTAACCACACTTAC

ORF - retro_opri_914 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.22 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 1
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalELATTSTMPYPYPALTPEQKKELSDIAHRIVAPGKGILAADESTGSIAKRLQSIGTENTEENRRFYRQLL
.LA.TST.PYPYP.LT..QKKELSDI.H.IVAPGKGILAADEST.SIAKRLQSIGTENTEENRRFY.QLL
RetrocopyDLAATSTIPYPYPKLTQGQKKELSDITHQIVAPGKGILAADESTSSIAKRLQSIGTENTEENRRFYLQLL
ParentalLTADDRVNPCIGGVILFHETLYQKADDGRPFPQVIKSKGGVVGIKVDKGVVPLAGTNGETTTQGLDGLSE
LTADDRVNP.IGGVILFHET.YQKADDGRPF.QVIKSKGGVVGIKVDKGVVPLAGTNGETTT.GLD.LSE
RetrocopyLTADDRVNPRIGGVILFHETFYQKADDGRPFQQVIKSKGGVVGIKVDKGVVPLAGTNGETTTEGLDELSE
ParentalRCAQYKKDGADFAKWRCVLKIGEHTPSALAIMENANVLARYASICQQNGIVPIVEPEILPDGDHDLKRCQ
RCAQYK..GADFAKWR.VLKIG.HTPSALAIMENANVLA.YASICQQNGIVPI.EPEILPDG.HDLKRCQ
RetrocopyRCAQYKANGADFAKWR*VLKIGKHTPSALAIMENANVLAHYASICQQNGIVPIAEPEILPDGGHDLKRCQ
ParentalYVTEKVLAAVYKALSDHHIYLEGTLLKPNMVTPGHACTQKYTHEEIAMATVTALRRTVPPAVTGVTFLSG
YVTEKVLAAVYKALSDHHIYLEGTLLK.N.VTP...CTQKY.HEE.AMATV.ALR.TVPPAV.GVTFLSG
RetrocopyYVTEKVLAAVYKALSDHHIYLEGTLLKSNIVTPRYTCTQKYSHEEVAMATVMALRHTVPPAVAGVTFLSG
ParentalGQSEEEASINLNAINKCPLLKPWALTFSYGRALQASALKAWGGKKENLKAAQEEYVKRALANSLACQGKY
GQSEEEASINLNAINKCPLLKPWALTFSYGRALQASALK.WGGKKENLK.AQEEYVKR.LANSLACQGKY
RetrocopyGQSEEEASINLNAINKCPLLKPWALTFSYGRALQASALKGWGGKKENLKTAQEEYVKRTLANSLACQGKY
ParentalTPSGQAGAAASESLFISNHAY
TPSGQAGA....SLFISNH.Y
RetrocopyTPSGQAGATTTKSLFISNHTY

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






RNA-Seq - click to see more details

Ochotona princeps was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ochotona princeps was not studied using ChIP-Seq data.

EST - click to see more details

Ochotona princeps was not studied using EST data.

TSS - click to see more details

Ochotona princeps was not studied using FANTOM5 data.

Lab - click to see more details

retro_opri_914 was not experimentally validated.

Retrocopy orthology:
Ochotona princeps 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 16 parental genes, and 30 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000082212 retrocopies
retro_cfam_190, retro_cfam_631,
Callithrix jacchus ENSCJAG000000068741 retrocopy
retro_cjac_1803,
Cavia porcellus ENSCPOG000000074341 retrocopy
retro_cpor_951,
Echinops telfairi ENSETEG000000192301 retrocopy
retro_etel_20,
Homo sapiens ENSG000001499251 retrocopy
retro_hsap_740,
Gorilla gorilla ENSGGOG000000139791 retrocopy
retro_ggor_621,
Myotis lucifugus ENSMLUG000000112103 retrocopies
retro_mluc_1172, retro_mluc_2634, retro_mluc_808,
Macaca mulatta ENSMMUG000000009831 retrocopy
retro_mmul_2596,
Monodelphis domestica ENSMODG000000156964 retrocopies
retro_mdom_1236, retro_mdom_1356, retro_mdom_528, retro_mdom_96,
Mus musculus ENSMUSG000000306953 retrocopies
retro_mmus_2160, retro_mmus_42, retro_mmus_90,
Nomascus leucogenys ENSNLEG000000021521 retrocopy
retro_nleu_133,
Oryctolagus cuniculus ENSOCUG000000063291 retrocopy
retro_ocun_1550,
Ochotona princeps ENSOPRG00000009760 1 retrocopy
retro_opri_914 ,
Pongo abelii ENSPPYG000000072441 retrocopy
retro_pabe_636,
Pan troglodytes ENSPTRG000000079831 retrocopy
retro_ptro_526,
Rattus norvegicus ENSRNOG000000236477 retrocopies
retro_rnor_1343, retro_rnor_1541, retro_rnor_1796, retro_rnor_1807, retro_rnor_226, retro_rnor_2791, retro_rnor_536,


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