RetrogeneDB ID:

retro_mdom_516

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:1:125640690..125641737(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PTPN11
Ensembl ID:ENSMODG00000003120
Aliases:None
Description:protein tyrosine phosphatase, non-receptor type 11 [Source:HGNC Symbol;Acc:9644]


Retrocopy-Parental alignment summary:






>retro_mdom_516
CTTCCTCGTGGGGGAAAGCCAGAGCCACTCCGAGAATTTTATTCTTTCTGCACAGGGGACGATAAAGGCGAGAGTAATGA
TGGCAAATCAAAAATGACGCACTTCAAGATTCGCTGTCAGCATCTGAAATATGATGTTGGTGGAGGAGAGAAGTTTGCCT
CTTTAACAGACTTTGTAGAGCATTACAAGAAGAACCCTATGGTAGAAACTTTGGGTACAGTTCTACAGCTCAAGCAGCCT
CTGAATACAACTCGTATCAATGCTGCAGAGATTGAAAGCTGGGTGAGAGAATTAAGCTAATTAGCGGAGACCACAGATAA
AGTGAAACAAGGGTTTTGGGAAGAATTTGGGACTCTCCAACAGCAGGAATGCAAGCTCCTCTATAGTCGTAAAGAAGGTC
AGCAGCAAGAAAATAAAAACAAAAACATATATAAGAATATTTTGCCCTTTGATCATACCAGGGTCGTCCTACATGATGGG
GATCAAAATGAACCAGTTTCAGATTATATTAATGCAAATATTACCATTCCTGAATTTGAGACCAAATGCAACACAAAACC
CAAAAAGAATTATATTGCAACCCAAGGCTGTCTACAGAACACAGTAAACGACTTCTGGAGAATGGTGTTCCAGGAGAATT
CACGAGTTATTGCCATGACAATGAAAGAAGTAGAGAGAGGGAAGAGTAAATGTGTCAAGTACTGGCCTAATGAATATGCT
CTAAAGGAATATGGGACTATGCGTGTTAGGAATGTCAAAGAAAGTGCTTCTCATGTCCATACTTTTGGATAACTAAAACT
CTCTAAGTTTGGACAAGGGGACACTGAGAAAACTGTGTGGCAGTACCATTTTGGAACCTGGCCGGATCACGGTGTGCCCA
TTGACCCTAGGGGTCTTCTGGACTTTTTAGAAGCCATCCATAACAAGCAGGAGAGCATTCCTGATGCAGGCTCTGTGGTG
TTGTATTGCAGTGCTGGGATTGGCAGGACAGGAACTTTCATTGTGATTGACATCCTTATTGACATTATCAGAGAAAAAGG
TGTGGAT

ORF - retro_mdom_516 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.86 %
Parental protein coverage: 59.02 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQDLKYDVGGGEKFDSLTDLVEHYKKNPMVET
L.R.....P.....S..TGDDKGESNDGKSK.TH..IRCQ.LKYDVGGGEKF.SLTD.VEHYKKNPMVET
RetrocopyLPRGGKPEPLREFYSFCTGDDKGESNDGKSKMTHFKIRCQHLKYDVGGGEKFASLTDFVEHYKKNPMVET
ParentalLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETTDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKN
LGTVLQLKQPLNTTRINAAEIES.VRELS.LAETTDKVKQGFWEEF.TLQQQECKLLYSRKEGQ.QENKN
RetrocopyLGTVLQLKQPLNTTRINAAEIESWVRELS*LAETTDKVKQGFWEEFGTLQQQECKLLYSRKEGQQQENKN
ParentalKNRYKNILPFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMV
KN.YKNILPFDHTRVVLHDGD.NEPVSDYINANI..PEFETKC.N.KPKK.YIATQGCLQNTVNDFWRMV
RetrocopyKNIYKNILPFDHTRVVLHDGDQNEPVSDYINANITIPEFETKC-NTKPKKNYIATQGCLQNTVNDFWRMV
ParentalFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGAMRVRNVKESAAHDYTLRELKLSKVGQGNTERTV
FQENSRVI.MT.KEVERGKSKCVKYWP.EYALKEYG.MRVRNVKESA.H..T...LKLSK.GQG.TE.TV
RetrocopyFQENSRVIAMTMKEVERGKSKCVKYWPNEYALKEYGTMRVRNVKESASHVHTFG*LKLSKFGQGDTEKTV
ParentalWQYHFRTWPDHGVPTDPGGVLDFLEEVHHKQESIPDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVD
WQYHF.TWPDHGVP.DP.G.LDFLE..H.KQESIPDAG.VV..CSAGIGRTGTFIVIDILIDIIREKGVD
RetrocopyWQYHFGTWPDHGVPIDPRGLLDFLEAIHNKQESIPDAGSVVLYCSAGIGRTGTFIVIDILIDIIREKGVD

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 .33 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 .79 RPM 0 .00 RPM
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_516 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_516 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 5 parental genes, and 8 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000124641 retrocopy
Gorilla gorilla ENSGGOG000000106891 retrocopy
Macaca mulatta ENSMMUG000000132534 retrocopies
Monodelphis domestica ENSMODG00000003120 1 retrocopy
retro_mdom_516 ,
Monodelphis domestica ENSMODG000000214221 retrocopy



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