RetrogeneDB ID:

retro_mdom_1148

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:3:252763334..252763780(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CLTA
Ensembl ID:ENSMODG00000002610
Aliases:None
Description:clathrin, light chain A [Source:HGNC Symbol;Acc:2090]


Retrocopy-Parental alignment summary:






>retro_mdom_1148
GGCAGTGGCTAATCGGACCTCAGCAGCAATGAAGATGTGGACACCACTGCCTTCCTGGCTCATCAGGAGAACCACATTAC
AGGCATCTAGAAGGATAAAGAGCTTCAATATCCTGCACAACTGGGGTGTGCTTGCCTCCCTGCAAGGGGAGCCCCTTGAG
CCCCAGATGCTATTGATGGAGTGATGAATAGAGAATACTATCAGAAAAGTAATGGTCCAACAAGTAGTTATGCAGCTATA
TCACAAGTGGATCAATTAATGTCAGAACCTGAGAGTATTCCTAGAAGGAGAGAAGATCAAATGGAATGTCTGCAAGTCCT
TGATTCTTGGAATCAGGAAGCATAAAGGAAAGAAAAAAGCAATAAAAGAATTGGAAGAATGGTATGCAAGGCAATATGAA
CAACTACTAAACCCAAAGTGTATAACAGGCAGCTGAAGAAGCTTTT

ORF - retro_mdom_1148 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 62.82 %
Parental protein coverage: 59.68 %
Number of stop codons detected: 3
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalGNGVASGGSSEEDPAAAFLAQQESEIAGIENDE-GFSILDTGSVPASLQGEP-PGGPDAIDAVMNGEYYQ
G.G.....S.E.....AFLA.QE..I.GI..D...F.IL....V.ASLQGEP.P..PDAID.VMN.EYYQ
RetrocopyGSG*SDLSSNEDVDTTAFLAHQENHITGI*KDK>SFNILHNWGVLASLQGEP<P*APDAIDGVMNREYYQ
ParentalESNGPTDSYAAISQVDRLQSEPESIRKWREEQMERLEVLDANSRKQEA-EWKEKAIKELEEWYARQDEQL
.SNGPT.SYAAISQVD.L.SEPESI...RE.QME.L.VLD..S..QEA...K.KAIKELEEWYARQ.EQL
RetrocopyKSNGPTSSYAAISQVDQLMSEPESIPRRREDQMECLQVLD--SWNQEA>KGKKKAIKELEEWYARQYEQL
Parental-QKTKVNNR-VADEAF
..K.KV.NR..A.EAF
Retrocopy<TKPKVYNR<AAEEAF

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 0 .00 RPM 0 .00 RPM
SRP007412_cerebellum 0 .00 RPM 0 .00 RPM
SRP007412_heart 0 .00 RPM 0 .00 RPM
SRP007412_kidney 0 .00 RPM 0 .00 RPM
SRP007412_liver 0 .00 RPM 0 .00 RPM
SRP007412_testis 0 .00 RPM 0 .00 RPM
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_1148 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1148 was not experimentally validated.

Retrocopy orthology:
Monodelphis domestica 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 9 parental genes, and 11 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000011371 retrocopy
Homo sapiens ENSG000001227052 retrocopies
Macropus eugenii ENSMEUG000000108581 retrocopy
Macaca mulatta ENSMMUG000000061322 retrocopies
Monodelphis domestica ENSMODG00000002610 1 retrocopy
retro_mdom_1148 ,
Monodelphis domestica ENSMODG000000051901 retrocopy
Nomascus leucogenys ENSNLEG000000038741 retrocopy
Pongo abelii ENSPPYG000000190691 retrocopy
Pan troglodytes ENSPTRG000000209301 retrocopy



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