RetrogeneDB ID:

retro_dnov_727

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_10220:50783..51309(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ITGB1BP1
Ensembl ID:ENSDNOG00000008930
Aliases:None
Description:integrin beta 1 binding protein 1 [Source:HGNC Symbol;Acc:23927]


Retrocopy-Parental alignment summary:






>retro_dnov_727
TCTGTAGATTCCAGCCTTGGGGGACTTTCAGGATCGAGTACTGTAGCCAGCCTCGATACAGATTCTACGAGAAGCTCAGG
ACAAAGCAACAATAATTCAGATACCTGTGCAGAATTTCAAACAAAATACGTTGGTGCCATTGAGAAACTGAAAGTCTCTG
AGGAAAAAAGCCTTGAAGGGCCACTGGACCTGATAAATTATACAGATGTTGCCCAGCAAGATGGAAAGTTGCCTTTTGTT
CCTCTGGAGGAAGAATTTTTTATGGGAGTTTCCAAGTACGGTATAAAACTATCAACACCAGCTCAGTATGATGCGCTGCC
TAGCACGCTCTGTTTTAATCATCCGGATGGTGTGCTGTGGTGATGGTCTGGGGGCAGGAAAAAGCTTATTGGCTCTGAAA
ACGACAGATGCAGGCAATGACGCATACAGCCTACGGGTGTATCAGTGCAACGGCCTGCAACAAGCACAGGCAATTTGTAA
CGTTTTATCCACTGCTTTTGACTCTGTATTATTATCTGAGAAATCT

ORF - retro_dnov_727 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.96 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalSVDSSLGGLSRSSTVASLDTDSTRSSGQSNNNSDTCAEFRIKYVGAIEKLKVSEGKSLEGPLDLINYIDV
SVDSSLGGLS.SSTVASLDTDSTRSSGQSNNNSDTCAEF..KYVGAIEKLKVSE.KSLEGPLDLINY.DV
RetrocopySVDSSLGGLSGSSTVASLDTDSTRSSGQSNNNSDTCAEFQTKYVGAIEKLKVSEEKSLEGPLDLINYTDV
ParentalAQQDGKLPFVPLEEEFIMGVSKYGIKVSTSDQYDVLHR-HALY-LIIRMVCYDDGLGAGKSLLALKTTDA
AQQDGKLPFVPLEEEF.MGVSKYGIK.ST..QYD.L...HAL..LIIRMVC..DGLGAGKSLLALKTTDA
RetrocopyAQQDGKLPFVPLEEEFFMGVSKYGIKLSTPAQYDALPS<HALF<LIIRMVCCGDGLGAGKSLLALKTTDA
ParentalSNEEYSLWVYQCNSLXXAQAICKVLSTAFDSVLLSEKS
.N..YSL.VYQCN.L..AQAIC.VLSTAFDSVLLSEKS
RetrocopyGNDAYSLRVYQCNGLQQAQAICNVLSTAFDSVLLSEKS

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






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP012922_ascending_colon 3 .11 RPM 9 .72 RPM
SRP012922_cerebellum 3 .71 RPM 25 .57 RPM
SRP012922_heart 0 .70 RPM 7 .89 RPM
SRP012922_kidney 0 .55 RPM 11 .50 RPM
SRP012922_liver 0 .46 RPM 6 .81 RPM
SRP012922_lung 4 .58 RPM 20 .62 RPM
SRP012922_quadricep_muscle 1 .38 RPM 8 .83 RPM
SRP012922_spleen 3 .09 RPM 21 .86 RPM
Dasypus novemcinctus was not studied using ChIP-Seq data.
Dasypus novemcinctus was not studied using EST data.
Dasypus novemcinctus was not studied using FANTOM5 data.
retro_dnov_727 was not experimentally validated.

Retrocopy orthology:
Dasypus novemcinctus 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 19 parental genes, and 35 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000130632 retrocopies
Choloepus hoffmanni ENSCHOG000000136022 retrocopies
Callithrix jacchus ENSCJAG000000062503 retrocopies
Dasypus novemcinctus ENSDNOG00000008930 3 retrocopies
retro_dnov_1422, retro_dnov_2198, retro_dnov_727 ,
Homo sapiens ENSG000001191851 retrocopy
Gorilla gorilla ENSGGOG000000017541 retrocopy
Macropus eugenii ENSMEUG000000067611 retrocopy
Microcebus murinus ENSMICG000000023597 retrocopies
Myotis lucifugus ENSMLUG000000106292 retrocopies
Macaca mulatta ENSMMUG000000180361 retrocopy
Nomascus leucogenys ENSNLEG000000133221 retrocopy
Oryctolagus cuniculus ENSOCUG000000037261 retrocopy
Otolemur garnettii ENSOGAG000000016794 retrocopies
Procavia capensis ENSPCAG000000059761 retrocopy
Pongo abelii ENSPPYG000000126671 retrocopy
Pan troglodytes ENSPTRG000000116371 retrocopy
Sorex araneus ENSSARG000000097991 retrocopy
Tarsius syrichta ENSTSYG000000145371 retrocopy
Tursiops truncatus ENSTTRG000000008591 retrocopy



Copyright © RetrogeneDB 2014-2017