RetrogeneDB ID:

retro_opri_154

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:GeneScaffold_2970:49227..49716(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOPRG00000013234
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SBDS
Ensembl ID:ENSOPRG00000008721
Aliases:None
Description:Shwachman-Bodian-Diamond syndrome [Source:HGNC Symbol;Acc:19440]


Retrocopy-Parental alignment summary:






>retro_opri_154
TTGACGAAAGGAGAACTTCAGTGTCAGATTAGGGAGAGGCCCACACAGCTGGAGCAGATGTGTAGGGACATTGGCAACCG
ATTGTAGCCGACACATGTGTGACCCTGAAACAAAGAGACCATACATCGTTATTCTCATAGAGAGAGCCGTGAAAGGACAT
CCTCTATTCGGTCAAAACCAACAAGAGCACGAAACAGCGGCTTTGGAAGTGATCACGCAGCTGAGGGAGAAAATGAGGAT
AGAGCGCGCCCACGTGAGACTGCGGTTAATCCTCCTGGTGAATGAGGGCTACACGCTGAAGCAAAAGCTCAAGCAGCTCC
GCAAGGTCGTGGCAAGTGAGGACTGCTGTCAGCAGCTGGAAATGGTGTGCCTCATTGACCCCGCTGCTTCCTAGAAATCG
ATGAGCTCATAAAGAAGGAAGCCAAAGGCAGAGGTTCCTTGGAGGTGCTCAATCTCAAAGTCGTGGAAGAAGGCAACGAG
AAATTTGAA

ORF - retro_opri_154 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.33 %
Parental protein coverage: 65.2 %
Number of stop codons detected: 0
Number of frameshifts detected 6


Retrocopy - Parental Gene Alignment:

ParentalLTKGELQVSDKERHTQLEQMFRD-IAT-IVADKCV-NPETKRPYTVILIERAMK-DIHYSVKTNKSTKQQ
LTKGELQ....ER.TQLEQM.RD..AT.IVAD.CV..PETKRPY.VILIERA.K.DI.YSVKTNKSTKQ.
RetrocopyLTKGELQCQIRERPTQLEQMCRD>LAT>IVADTCV<DPETKRPYIVILIERAVK>DILYSVKTNKSTKQR
Parental-ALEVIKQLKEKMKIERAHMRLRFILPVNEGKKLKEKLKPLIKVVESEDYSQQVEMVCLIDPG-CFREID
.ALEVI.QL.EKM.IERAH.RLR.IL.VNEG..LK.KLK.L.KVV.SED..QQ.EMVCLIDP..CF.EID
Retrocopy<ALEVITQLREKMRIERAHVRLRLILLVNEGYTLKQKLKQLRKVVASEDCCQQLEMVCLIDPA<CFLEID
ParentalELIKKETKGRGSLEVLSLKDVEEGDEKFE
ELIKKE.KGRGSLEVL.LK.VEEG.EKFE
RetrocopyELIKKEAKGRGSLEVLNLKVVEEGNEKFE

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






Ochotona princeps was not studied using RNA-Seq expression data.
Ochotona princeps was not studied using ChIP-Seq data.
Ochotona princeps was not studied using EST data.
Ochotona princeps was not studied using FANTOM5 data.
retro_opri_154 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 10 parental genes, and 16 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000037952 retrocopies
Callithrix jacchus ENSCJAG000000042831 retrocopy
Dasypus novemcinctus ENSDNOG000000169041 retrocopy
Loxodonta africana ENSLAFG000000087631 retrocopy
Monodelphis domestica ENSMODG000000066441 retrocopy
Mus musculus ENSMUSG000000253371 retrocopy
Otolemur garnettii ENSOGAG000000090111 retrocopy
Ochotona princeps ENSOPRG00000008721 6 retrocopies
Rattus norvegicus ENSRNOG000000008881 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000222031 retrocopy



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