RetrogeneDB ID:

retro_dnov_1723

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_277094:186..811(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:FAM49B
Ensembl ID:ENSDNOG00000009323
Aliases:None
Description:family with sequence similarity 49, member B [Source:HGNC Symbol;Acc:25216]


Retrocopy-Parental alignment summary:






>retro_dnov_1723
AACTTGCAGTCTTATAGAGGAACTGACCGTGAAATACAAGAGGCAATCCAGCATCCAGCAGATGAGAAGTTGTAACACAA
GGCATGGAGGGCAGTTGTTCCACAAGCAGGTAAATTAAAGAAATTTTGTGAATTTTCTCAGAGGTTAGAAGCAGCATTAA
GAGGCCTTCTGGAAGCTTTGACAAATACCCCATATTCTCCCACCCAGCACCTAGAGCAAGAGCAGGCTGTTGTTAAACAG
TTTGCAGAAATTCTTCACTTCGCACTTGGTTTGATGAACTCAAGATAACAAATCTTGCCATACAGAATGATTTCAGCAAT
TATAGAAGAACATTGAGTTGTATGAGGATTAATAATGTTCCAGCAGGAGAAAATGAAGTAAATAGTGAATTGGCAAATCA
AATATCTTTATTTTATGCTGAGGCAACCCCAATACTGAAAACTTTAAGTGATGCCACAACAAAATTTGTATAAGAGAATA
AAAATTTACCAACAGAAAATACCACAGATTGTTTAAGCACCATAACTAGTGTGTGCAGAATCATCCTCGGATGCTGGAAT
ACAGAAGCAGGTTTACAAATGAGACGGTGTCCTGTTTGTGGGTCATGGTGGGTGTCTTCATCCTC

ORF - retro_dnov_1723 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.44 %
Parental protein coverage: 66.04 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalDLQSYRGAGHEIREAIQHPADEKLQEKAWGAVIPLVGKLKKFYEFSQRLETALRGLLGALTSTPYSPTQH
.LQSYRG...EI.EAIQHPADEKL..KAW.AV.P..GKLKKF.EFSQRLE.ALRGLL.ALT.TPYSPTQH
RetrocopyNLQSYRGTDREIQEAIQHPADEKL*HKAWRAVVPQAGKLKKFCEFSQRLEAALRGLLEALTNTPYSPTQH
ParentalLEREQALAKQFAEILHFTLR-FDELKMTNPAIQNDFSYYRRTLSRMRINNVPAEGENEVNNELANRMSLF
LE.EQA..KQFAEILHF.L..FDELK.TN.AIQNDFS.YRRTLS.MRINNVPA.GENEVN.ELAN..SLF
RetrocopyLEQEQAVVKQFAEILHFALG<FDELKITNLAIQNDFSNYRRTLSCMRINNVPA-GENEVNSELANQISLF
ParentalYAEATPMLKTLSDATTKFVSENKNLPIENTTDCLSTMASVCRVML-ETPEYRSRFTNEETVSFCLRVMVG
YAEATP.LKTLSDATTKFV.ENKNLP.ENTTDCLST..SVCR..L....EYRSRFTN.ETVS.CL.VMVG
RetrocopyYAEATPILKTLSDATTKFV*ENKNLPTENTTDCLSTITSVCRIIL<RMLEYRSRFTN-ETVS-CLWVMVG
ParentalVIIL
V.IL
RetrocopyVFIL

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 0 .00 RPM 44 .34 RPM
SRP012922_cerebellum 0 .14 RPM 48 .25 RPM
SRP012922_heart 0 .00 RPM 7 .19 RPM
SRP012922_kidney 0 .00 RPM 17 .25 RPM
SRP012922_liver 0 .00 RPM 13 .47 RPM
SRP012922_lung 0 .00 RPM 23 .06 RPM
SRP012922_quadricep_muscle 0 .17 RPM 26 .14 RPM
SRP012922_spleen 0 .11 RPM 58 .03 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_1723 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 7 parental genes, and 11 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG00000009323 3 retrocopies
retro_dnov_1596, retro_dnov_1723 , retro_dnov_896,
Dipodomys ordii ENSDORG000000051601 retrocopy
Echinops telfairi ENSETEG000000156471 retrocopy
Felis catus ENSFCAG000000156251 retrocopy
Oryctolagus cuniculus ENSOCUG000000136901 retrocopy
Procavia capensis ENSPCAG000000028663 retrocopies
Sus scrofa ENSSSCG000000059591 retrocopy



Copyright © RetrogeneDB 2014-2017