RetrogeneDB ID:

retro_cfam_2018

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:AAEX03020959.1:26019..26670(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCAFG00000014359
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:LGALS3
Ensembl ID:ENSCAFG00000015013
Aliases:LGALS3, CBP 35, Gal-3, Galectin-3
Description:Canis lupus familiaris lectin, galactoside-binding, soluble, 3 (LGALS3), mRNA. [Source:RefSeq mRNA;Acc:NM_001197043]


Retrocopy-Parental alignment summary:






>retro_cfam_2018
CCTCAAGGATGGCCTGGTCCATGGGGAAACCAGCCTGCTGGAGCAGGGGGATACTCAGGGGCCTCTTATCCTGGTGCCTA
CCCTGGCCAGGCACCTCCCGGCGGCTACCCTGGCCCCACAGCACCTGCTTATCCTGGCCCAACAGCACCAGGAGCCCAAC
CTGGGCAACCGAGTGGACCTGGGGCCTACCCGCCTCCTGGACAACCAAGCGCTTCGGGAACCTACCCTGCTGCTGGTCCC
TTTGGCATCCCTACTGGACCACTGACTGTGCCTTATGACCTGCCTTTGCCTGGAGGAGTCAAGCCTCGCATGCTGATAAC
AATTCTGGGCACAGTAAGGCCCAGTGAAAACAGACTTGCTTTAGATTTCAAGAGAGGGAATGATGTTGCCTTCCACTTTA
ACCCACGCTTCAATGAAGACAAGAGAGTCATTGTTTGCAATACCAAGCTGGATAATATCTGGGGAAAGGAAGAAAGGCAG
GCGGCTTTCCCATTTGAAAATGGTAAACCATTCAAAATACAAGTGCTGGTTGATTCTGACCACTTCAAGGTTGCGGTCAG
TGATGTCCATTTGTTGCAGTACAATCATCGTCTGAAAAATCTCCCAGAAATCAGCAAATTGGGTATTTCTGATGACATAG
ATCTCACCAGC

ORF - retro_cfam_2018 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.94 %
Parental protein coverage: 74.25 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalPGGYPGQAPPGGYPGQAPPGGYPGQAPPGGYPGQAPPGTYPGPTAPAYPGPTAPGTQPGQPSGPGAYPPP
P.G.PG..P.G..P..A..GGY.G...PG.YPGQAPPG.YPGPTAPAYPGPTAPG.QPGQPSGPGAYPPP
RetrocopyPQGWPG--PWGNQPAGA--GGYSGASYPGAYPGQAPPGGYPGPTAPAYPGPTAPGAQPGQPSGPGAYPPP
ParentalGQPSAPGAYPAAGPFGIPAGPLTVPYDLPLPGGVKPRMLITILGTVRPSANRLALDFKRGNDVAFHFNPR
GQPSA.G.YPAAGPFGIP.GPLTVPYDLPLPGGVKPRMLITILGTVRPS.NRLALDFKRGNDVAFHFNPR
RetrocopyGQPSASGTYPAAGPFGIPTGPLTVPYDLPLPGGVKPRMLITILGTVRPSENRLALDFKRGNDVAFHFNPR
ParentalFNEDNKRVIVCNTKLDNIWGKEERQAAFPFESGKPFKIQVLVESDHFKVAVNDAHLLQYNHRMKNLPEIS
FNED.KRVIVCNTKLDNIWGKEERQAAFPFE.GKPFKIQVLV.SDHFKVAV.D.HLLQYNHR.KNLPEIS
RetrocopyFNED-KRVIVCNTKLDNIWGKEERQAAFPFENGKPFKIQVLVDSDHFKVAVSDVHLLQYNHRLKNLPEIS
ParentalKLGISGDIDLTS
KLGIS.DIDLTS
RetrocopyKLGISDDIDLTS

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
SRP012049_cerebellum 0 .13 RPM 6 .85 RPM
SRP017611_brain 0 .32 RPM 7 .38 RPM
SRP017611_kidney 1 .19 RPM 45 .10 RPM
SRP017611_liver 0 .00 RPM 1 .38 RPM
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_2018 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_2018 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_2018 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 5 parental genes, and 9 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG00000015013 1 retrocopy
retro_cfam_2018 ,
Canis familiaris ENSCAFG000000241911 retrocopy
Mustela putorius furoENSMPUG000000057252 retrocopies
Pteropus vampyrus ENSPVAG000000160671 retrocopy
Tarsius syrichta ENSTSYG000000090204 retrocopies



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