RetrogeneDB ID:

retro_pabe_1166

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:14:44354944..44355491(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:C11orf58
Ensembl ID:ENSPPYG00000003458
Aliases:None
Description:small acidic protein [Source:RefSeq peptide;Acc:NP_001125161]


Retrocopy-Parental alignment summary:






>retro_pabe_1166
ATGAGTGCTGCCAGAGAGTCTCACCTGCATGGGGTGAAGTGTTCAGCCTCCACAGATGACGATCTGGGATCTAGCAATTG
GGAGGCAGCAGACTTGGGTAATGAAGAGAAAAAACAAAAGTTCTTGAGACTTATGGGTGTAGGAAAGAAAAAACATACTG
GTCGTCTTATTATAGGAGATCGCAAATCAACATCACTCCTGAACGGGGGAAGAAGACAAGAAAATTAATGAAGAACTGGA
GACTCAATATCAGCAAAGTATGGACGGTAAATTATCAGGAAGATATCGGCGACATTGTGGACTTGGCTTCAATGAGGTAG
AAGATCATGATGGAGAAGGTGATGTGGCTGGAGTTGATGATGACGATGATGATGATTCACCTGATCCTGAAAGTCTAGAT
GATTCTGAAAGCGATTCAGAGTCAGAGAAAGAAGAATCTGCTGAAGAACTCCAAGCTGCTGAGCACCCTGATGAAATGGA
GGATCCCAAAAACAAAAAAGATGCAAAAAGCAATTATAAAATGATGTTTGTGAAATCCAGTGGTTCA

ORF - retro_pabe_1166 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.14 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMSAARESHPHGVKRSASPDDDLGSSNWEAADLGNEERKQKF-LRLMGAGK-KEHIDCLVLGDHKSTFHFR
MSAARESH.HGVK.SAS.DDDLGSSNWEAADLGNEE.KQKF.L...G..K....I....L.......H..
RetrocopyMSAARESHLHGVKCSASTDDDLGSSNWEAADLGNEEKKQKF<LETYGCRK<RKNILVVLL*EIANQHHS*
ParentalTGEEDKKINEELESQYQQSMDSKLSGRYRRHCGLGFSEVEDHDGEGDVAGDDDDDDDDSPDPESPDDSES
TGEEDKKINEELE.QYQQSMD.KLSGRYRRHCGLGF.EVEDHDGEGDVAG.DDDDDDDSPDPES.DDSES
RetrocopyTGEEDKKINEELETQYQQSMDGKLSGRYRRHCGLGFNEVEDHDGEGDVAGVDDDDDDDSPDPESLDDSES
ParentalDSESEKEESAEELQAAEHPDEVEDPKNKKDAKSNYKMMFVKSSGS
DSESEKEESAEELQAAEHPDE.ED.............MFVKSSGS
RetrocopyDSESEKEESAEELQAAEHPDEMEDXXXXXXXXXXXXXMFVKSSGS

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
SRP007412_brain_prefrontal_cortex 0 .61 RPM 71 .93 RPM
SRP007412_cerebellum 0 .49 RPM 39 .16 RPM
SRP007412_heart 0 .42 RPM 38 .56 RPM
SRP007412_kidney 0 .56 RPM 56 .05 RPM
SRP007412_liver 0 .31 RPM 36 .02 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1166 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1166 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1166 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1408

Parental genes homology:
Parental genes homology involve 15 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000302202 retrocopies
Callithrix jacchus ENSCJAG000000096261 retrocopy
Cavia porcellus ENSCPOG000000096792 retrocopies
Equus caballus ENSECAG000000117781 retrocopy
Felis catus ENSFCAG000000277471 retrocopy
Homo sapiens ENSG000001106962 retrocopies
Macropus eugenii ENSMEUG000000117951 retrocopy
Myotis lucifugus ENSMLUG000000015891 retrocopy
Monodelphis domestica ENSMODG000000071472 retrocopies
Mus musculus ENSMUSG000000306632 retrocopies
Nomascus leucogenys ENSNLEG000000177191 retrocopy
Otolemur garnettii ENSOGAG000000253352 retrocopies
Ochotona princeps ENSOPRG000000001541 retrocopy
Pongo abelii ENSPPYG00000003458 2 retrocopies
retro_pabe_1166 , retro_pabe_3178,
Rattus norvegicus ENSRNOG000000204361 retrocopy



Copyright © RetrogeneDB 2014-2017