RetrogeneDB ID:

retro_sara_660

Retrocopy
location
Organism:Shrew (Sorex araneus)
Coordinates:scaffold_254281:45769..46279(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PSMB2
Ensembl ID:ENSSARG00000000409
Aliases:None
Description:proteasome (prosome, macropain) subunit, beta type, 2 [Source:HGNC Symbol;Acc:9539]


Retrocopy-Parental alignment summary:






>retro_sara_660
CCTGCCACCATGGAGTACCTCATCAGCATCCAGAGCCTTACCTGTGTGCTTGTCACCTCTGACAGGGGAGCCGCTAGCAG
TATTATGTAGATAAATAACACTCGTGACAGGATGTTTAAGATGAATGAGAACATTTTACCCCTGGTGTTGGTGAGGCTGG
AGACACTATACAGCTTGCAGAATATATTCAGGAAAAAAATGTGCAACTTTATAAGATGCGAAATGGTTATGAATCTGCTA
TCTGCCACAGCAGCAGCTAATTTTAAGTGTCAAAACTTAGCTGTCTTCGGAGTCAGAGCCTCAAGCATGTTAACCTCCTC
TTGGCTGGCAATGATAAACATGAGGGTCCTGCATTCTACCGTCTGGACTACCTGGCAGCCTTGGCCAAGAACCCCTTGGC
AACCCATGGCTATGGTGCCTTGCTGATTCCCAGTATCCTGGGCCAATATCATGCAACAAAGTATCACACGAGAAAGTGCA
GTGGGCCTTCTCAGGAAACATCTAGAGGAG

ORF - retro_sara_660 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 62.79 %
Parental protein coverage: 86.67 %
Number of stop codons detected: 3
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalPAAMEYLIGIQGLDFVLVASDRVAASNIVQMKDDHDKMFKMSEKILLLC-VGEAGDTVQFAEYIQ-KNVQ
PA.MEYLI.IQ.L..VLV.SDR.AAS.I.......D.MFKM.E.IL.L..VGEAGDT.Q.AEYIQ.KNVQ
RetrocopyPATMEYLISIQSLTCVLVTSDRGAASSIM*INNTRDRMFKMNENILPLV<VGEAGDTIQLAEYIQEKNVQ
ParentalLYKMRNGYELSPTAAANFTRRNLADCLRSRTPYHVNLLLAGYDEHEGPALYYMDYLAALAKAPFAAHGYG
LYKMRNGYE................CLRS....HVNLLLAG.D.HEGPA.Y..DYLAALAK.P.A.HGYG
RetrocopyLYKMRNGYESAICHSSS*F*VSKLSCLRSQSLKHVNLLLAGNDKHEGPAFYRLDYLAALAKNPLATHGYG
ParentalAFLTLSILDRYYTP-TITRENAVGLLRKCLEE
A.L..SIL..Y.....ITRE.AVGLLRK.LEE
RetrocopyALLIPSILGQYHAT>SITRESAVGLLRKHLEE

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






RNA-Seq - click to see more details

Sorex araneus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Sorex araneus was not studied using ChIP-Seq data.

EST - click to see more details

Sorex araneus was not studied using EST data.

TSS - click to see more details

Sorex araneus was not studied using FANTOM5 data.

Lab - click to see more details

retro_sara_660 was not experimentally validated.

Retrocopy orthology:
Sorex araneus 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 19 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000007151 retrocopy
retro_amel_743,
Canis familiaris ENSCAFG000000035431 retrocopy
retro_cfam_1291,
Callithrix jacchus ENSCJAG000000015471 retrocopy
retro_cjac_2110,
Dasypus novemcinctus ENSDNOG000000176631 retrocopy
retro_dnov_159,
Equus caballus ENSECAG000000216151 retrocopy
retro_ecab_769,
Echinops telfairi ENSETEG000000195111 retrocopy
retro_etel_1529,
Felis catus ENSFCAG000000308451 retrocopy
retro_fcat_1803,
Macropus eugenii ENSMEUG000000004211 retrocopy
retro_meug_1235,
Monodelphis domestica ENSMODG000000179021 retrocopy
retro_mdom_79,
Mustela putorius furoENSMPUG000000148911 retrocopy
retro_mputfur_1550,
Ochotona princeps ENSOPRG000000122592 retrocopies
retro_opri_76, retro_opri_762,
Pteropus vampyrus ENSPVAG000000018711 retrocopy
retro_pvam_909,
Sorex araneus ENSSARG00000000409 2 retrocopies
retro_sara_557, retro_sara_660 ,
Sarcophilus harrisii ENSSHAG000000169961 retrocopy
retro_shar_794,
Tupaia belangeri ENSTBEG000000052301 retrocopy
retro_tbel_4039,
Tarsius syrichta ENSTSYG000000056482 retrocopies
retro_tsyr_403, retro_tsyr_912,


Copyright © RetrogeneDB 2014-2017