RetrogeneDB ID:

retro_ogar_3259

Retrocopy
location
Organism:Bushbaby (Otolemur garnettii)
Coordinates:GL873758.1:1429656..1430552(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOGAG00000028467
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SDCBP
Ensembl ID:ENSOGAG00000013462
Aliases:None
Description:syndecan binding protein (syntenin) [Source:HGNC Symbol;Acc:10662]


Retrocopy-Parental alignment summary:






>retro_ogar_3259
ATTTCTCTCTATCCATCTTTTGAAGACTTGAAGGTAGATAAAGTAATTCAGGTTCAGACTGCCTTTTCTGCAAATCCTGC
CAACCCAGCAATTTTCTCAGAAGCTTCTGCTCCTGTCTCTCAAGATGGAAATCTCTATCCTAAACTGTATCCAGAGCTCT
CTCAGAACATGGGTGTGAGTTTAAATGAAGAAGAAATACGTGAAAATATGGCCATGGTCCCTGGAGCATCAGTTCAGGGG
CAATTGTTAGCAAAGCCTTCCAGTATGAGTTATATGGTAGCTCCTATAACTGGTAATGATGTTGGAATTTGTAGAGCAGA
AATTAAGCAAAGGATTCATGAAGTCATTTTTGTGTAAGCATCAAGATGGAAAAATTAGACTCAGGCTTAAATTGATAGAT
AATGGTATATTTTGTTCAGCTGATCCAGGCTAATTCTCCATCCTCTTTGGTTGGTCTGAGAGTTGAGGACCAGGTACTCC
AGATCATTGGTGAAAACTGTGCTGGCTGGAGCTCTGATAAAGCACACTATGTGCTCAAACAGGCTTTTGGAGAGAAGATT
ATTATGACCATTTGTGACAGGCCCTTTGAACGGACAATCACCATGCACAAAGATAGCAGTGGACATGTTGGCTTTATCTT
TAAAAATGGAAAAATAACATCCATAGTCAAAGATAGTTCTGCAGCCAGAAATGGCCCTCTCACGGAACACAACATCTGTG
AAATAAATGGGCAGAATGTCATTGTTTTGAAGGACTCTCAAATTGCAGACATACTGTCAACAGCTGGAACTTTAGTTACC
ATTATAATCATGCCTGCTTTTATCTTTGAACATATCATTAAATGGATGGCGCCAAGCATTATGAAAAGCCTGATGGACCA
CACCATTCCTGAAGTT

ORF - retro_ogar_3259 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.67 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalMSLYPSLEDLKVDKVIQAQTAFSANPANPAILSEASAPVSQDGNLYPKLYPELSQYMGLSLNEEEIFANM
.SLYPS.EDLKVDKVIQ.QTAFSANPANPAI.SEASAPVSQDGNLYPKLYPELSQ.MG.SLNEEEI..NM
RetrocopyISLYPSFEDLKVDKVIQVQTAFSANPANPAIFSEASAPVSQDGNLYPKLYPELSQNMGVSLNEEEIRENM
ParentalVLVGGAPAQGQLVARPSSMSYMVAPVTGNDVGIRRAEIKQGIREVI-LCKDQDGKIGLRLKSIDNGIF-V
..V.GA..QGQL.A.PSSMSYMVAP.TGNDVGI.RAEIKQ.I.EVI.LCK.QDGKI.LRLK.IDNGIF.V
RetrocopyAMVPGASVQGQLLAKPSSMSYMVAPITGNDVGICRAEIKQRIHEVI>LCKHQDGKIRLRLKLIDNGIF>V
ParentalQLVQANSPASLVGLRFGDQVLQINGENCAGWSSDKAHKVLKQAFGEKITMTIRDRPFERTITMHKDSSGH
QL.QANSP.SLVGLR..DQVLQI.GENCAGWSSDKAH.VLKQAFGEKI.MTI.DRPFERTITMHKDSSGH
RetrocopyQLIQANSPSSLVGLRVEDQVLQIIGENCAGWSSDKAHYVLKQAFGEKIIMTICDRPFERTITMHKDSSGH
ParentalVGFIFKNGKITSIVKDSSAARNGLLTEHNICEINGQNVIGLKDSQIADILSTARTVVTITVMPTFIFEHI
VGFIFKNGKITSIVKDSSAARNG.LTEHNICEINGQNVI.LKDSQIADILSTA.T.VTI..MP.FIFEHI
RetrocopyVGFIFKNGKITSIVKDSSAARNGPLTEHNICEINGQNVIVLKDSQIADILSTAGTLVTIIIMPAFIFEHI
ParentalIKRMAPSIMKSLMDHTIPEV
IK.MAPSIMKSLMDHTIPEV
RetrocopyIKWMAPSIMKSLMDHTIPEV

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






RNA-Seq - click to see more details

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Otolemur garnettii was not studied using ChIP-Seq data.

EST - click to see more details

Otolemur garnettii was not studied using EST data.

TSS - click to see more details

Otolemur garnettii was not studied using FANTOM5 data.

Lab - click to see more details

retro_ogar_3259 was not experimentally validated.

Retrocopy orthology:
Otolemur garnettii 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 18 parental genes, and 33 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000061611 retrocopy
retro_amel_654,
Bos taurus ENSBTAG000000199102 retrocopies
retro_btau_1035, retro_btau_383,
Canis familiaris ENSCAFG000000071121 retrocopy
retro_cfam_112,
Choloepus hoffmanni ENSCHOG000000035655 retrocopies
retro_chof_1063, retro_chof_1151, retro_chof_1910, retro_chof_713, retro_chof_970,
Equus caballus ENSECAG000000150531 retrocopy
retro_ecab_439,
Homo sapiens ENSG000001375752 retrocopies
retro_hsap_3971, retro_hsap_4810,
Gorilla gorilla ENSGGOG000000090192 retrocopies
retro_ggor_2666, retro_ggor_2995,
Loxodonta africana ENSLAFG000000107571 retrocopy
retro_lafr_1044,
Microcebus murinus ENSMICG000000039681 retrocopy
retro_mmur_170,
Myotis lucifugus ENSMLUG000000048071 retrocopy
retro_mluc_12,
Macaca mulatta ENSMMUG000000172961 retrocopy
retro_mmul_2564,
Mustela putorius furoENSMPUG000000103395 retrocopies
retro_mputfur_1055, retro_mputfur_1340, retro_mputfur_292, retro_mputfur_829, retro_mputfur_933,
Nomascus leucogenys ENSNLEG000000014082 retrocopies
retro_nleu_2185, retro_nleu_2525,
Otolemur garnettii ENSOGAG00000013462 1 retrocopy
retro_ogar_3259 ,
Procavia capensis ENSPCAG000000164321 retrocopy
retro_pcap_186,
Pongo abelii ENSPPYG000000186123 retrocopies
retro_pabe_3265, retro_pabe_3266, retro_pabe_3738,
Pan troglodytes ENSPTRG000000202772 retrocopies
retro_ptro_2696, retro_ptro_3200,
Tupaia belangeri ENSTBEG000000139651 retrocopy
retro_tbel_2142,


Copyright © RetrogeneDB 2014-2017