RetrogeneDB ID:

retro_mdom_671

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:2:60760369..60761090(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMODG00000002936
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CXorf38
Ensembl ID:ENSMODG00000021100
Aliases:None
Description:chromosome X open reading frame 38 [Source:HGNC Symbol;Acc:28589]


Retrocopy-Parental alignment summary:






>retro_mdom_671
CAGTTGTGCACAAAATGAAAAAGGGAGATTCTGAAACATCACACCAACAGAAATGGAGACATCTACTGGGGAAATTGTGA
ACCTGAGAGCTGGTCTTTTGACCCCTGGGAACTGGCAAAGGCCTTTATGCCCTGGGGATTGGCAGACAAAAAAGTTCCTG
AGGAATGTGATGCGGTTGCCAGTTCTAAGTCTTATAACCTCCTGTGATCACTTCAGGATTGATGGAAAGAAAGCCATAGA
GGTGATTAAATGTCGTAATGAAATAACGCACTCTTCAGAAATGAAAGTCTCTTCTTCATGGCTGCAAGATTTTCAGATGA
AGATTCAAAGTTTTTTGAATGAGTTCAGGAATATCCCAGAGGTTGCCGCCACAAGTGCCAGAATAGAAAAGCTATTGACA
TTTGATCGGGCAGTCCATATTCCTGGGGATGATCAGCTGGATGGACCTAAAAGTGACACCAAGATTTATCTCAGTGAAAG
TGAAATCAGTGAAATTGAAATGGAATTATTAAGAGAAAAGCTTCAAGAGAGTTATCTTCAAGCAGAAGGACAAGCAGTGC
CACCTGAGGAGGTGGTAAAGCATGTGGAGGCCATGAAGATCTTCCTGAAGAACAACAAGGATCTTAGAAGCAGCTTTGAA
AAAGAAATGCAGAAGTTGGAAGACTTTCATCTCCTGCATCAGACCATGTGTGCGGAGGAAGCCGGGAAAGGGAGGCTGAA
G

ORF - retro_mdom_671 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.31 %
Parental protein coverage: 75. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalQLCTEWKREILKHHTNRNGDIYWGNCKPERWPFDPWELAKAFMPRGLADKKGPEECDAVA-LLSLINSCD
QLCT..KREILKHHTNRNGDIYWGNC.PE.W.FDPWELAKAFMP.GLADKK.PEECDAVA..LSLI.SCD
RetrocopyQLCTK*KREILKHHTNRNGDIYWGNCEPESWSFDPWELAKAFMPWGLADKKVPEECDAVA>VLSLITSCD
ParentalHFRIDRKKVIEVIKCRNEIMHSSEMKVSSSWLQDFQMKIQSFLNEFRNIPEIAATSARIEKLLTFDWAVH
HFRID.KK.IEVIKCRNEI.HSSEMKVSSSWLQDFQMKIQSFLNEFRNIPE.AATSARIEKLLTFD.AVH
RetrocopyHFRIDGKKAIEVIKCRNEITHSSEMKVSSSWLQDFQMKIQSFLNEFRNIPEVAATSARIEKLLTFDRAVH
ParentalIPGDDQLDGPKSDTKIYLSESEISEIEMELLREKLQESYLQAEGQAIPPEEVAKHVEAMKIFLKNNKDLG
IPGDDQLDGPKSDTKIY...........ELLREKLQESYLQAEGQA.PPEEV.KHVEAMKIFLKNNKDL.
RetrocopyIPGDDQLDGPKSDTKIYXXXXXXXXXXXELLREKLQESYLQAEGQAVPPEEVVKHVEAMKIFLKNNKDLR
ParentalSSFEEEMQKLEDFHLQHQTVRAEEAGKGRLK
SSFE.EMQKLEDFHL.HQT..AEEAGKGRLK
RetrocopySSFEKEMQKLEDFHLLHQTMCAEEAGKGRLK

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(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

ChIP-Seq - click to see more details

Monodelphis domestica was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_mdom_671 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_671 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 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Monodelphis domestica ENSMODG00000021100 1 retrocopy
retro_mdom_671 ,


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