RetrogeneDB ID:

retro_mdom_864

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:2:244558523..244560476(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMODG00000000274
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CCNT2
Ensembl ID:ENSMODG00000000727
Aliases:None
Description:cyclin T2 [Source:HGNC Symbol;Acc:1600]


Retrocopy-Parental alignment summary:






>retro_mdom_864
ATGGCGTCGGGCCGTGGGGCTTCTTCTCGCTGGTTCTTCAGCCGGGAGCAGCTGGAGAACACGCCGAGCCGCCGCTGCGG
GGTGGAGGCGGATAAAGAGCTCTCGTACCGCCAGCAGGCGGCCAACTTTATCCAAGATATGGGGCAGCGTCTCAATGTCT
CTCAACTTACAATAAATACTGCAATTGTTTACATGCACAGGTTTTATATGCACCATTCTTTCACAAAGTTTAACAGAAAT
ATAATAGCACCTACTGCATTATTCTTGGCTGCAAAAGTAGAAGAACAGCCAAGAAAACTTGAACATGTCATCAAAGTAGC
ACATGCCTGTCTTCATCAAGAGCTACTGTTGGACACAAAGAGTGAAGCATACCTTCAGCAGACCCAAGAACTGGTTATAC
TTGAAACTATAATGCTACAAACTCTGGGTTTTGAGATCACCATTGAACACCCACATACAGATGTGGTGAAATGTACCCAG
TTAGTGAGAGCAAGCAAGGATTTGGCACAGACATCCTATTTCATGGCTACCAACAGTCTACATCTTACTACCTTCTGCCT
TCAATATAAACCAACAGTGATAGCATGTGTGTGCATTCATTTGGCTTGCAAGTGGTCCAATTGGGAGATTCCTGTATCTA
CTGATGGAAAGCATTGGTGGGAATATGTGGATCCATCAGTTACCTTAGAATTACTAGATGAATTAACTCACGAGTTCCTA
CAAATTTTGGAGAAAACTCCTAATAGATTGAAGAGGATACGAAACTGGAGGGCTACTCAGGCGGCTAGAAAACCTAAAGG
GGATGGACAGGTGTCTGAAACAGCTCTTCTTGGTTCATCTCTGGTACAGAATTCCATTTTAGTAGATAGTGTTACTGGTG
TGACTACAAATGCAAGCTTTCAAAAACCATCTACATCAGCATTTCCTGCACCAGTACCTCTGAATTCAGGAAATATTTCT
GTTCAAGATACTCATGCATCTGATAATTTGACAATACTAACCACAGGAATGCCAAGTACCTCATACAGTTTGGCATCACA
CCAAGAATGGCCTCAGCATCAAGAACCAACAAGGACAGAACAAATATATTCACAGAAACAGGAGGCTCCGATGTCTGGTA
GTCAATACAACATCAACTTCCAGCAAGGACCTGCTGGGCCATTACATTCAGGATTACATCACAGGTCTGACAAACTGTCT
GATCATTCTTCAGTTAAACAAGAATATACTCACAAGGCAGGAAGCAGCAAACACCATGGGCCAGTTTCTGCTGCTCCTGT
AATAGTTCCTCAGAAAATGTCGTTAGATAAATATAGAGAGAAACGAAAGCTAGAAACACTTGAACTGGATGTAAGGGAAC
ACTATGTAGCTGCCCAAACAGAGCAGCCCCACAAAAAGCACATGCAATTGCAGGCAGCCAGCAGCAGTTCTGTAACTTCT
CCCATTAAAATGAAAATTCCTATTGCGAATGCAGAGAAACCGGAAAAATACATGTTGGATAAAAAAGAAAAGAGTGGATC
ACTTAAACTGCGTATTCCAATTCCCCCCACTGATAAAATTTCTAGTAAAGAAGAACTGAAAATGAAAATAAAAGTTTCTT
CCTCGGAAAGACACAGCTCTTCTGATGAGGGCAGTGGAAAGAGCAAGCATTCAAGCCCACATGTGAGTAAAGACCACAAA
GAAAAGCACAAGGAACATTCCTCCAACCGCCATCACAGTAGCAGCCACAAGCATTCCCATTCACATAGTGGCAGCAGTAG
TAGTGGCAGTAAGCATAGTACTGACGGAATACCACCCACGGTTCTGAGGAGTCCTGTTGGCCTGAGTAGTGATGGTGGTA
ATTCCTCTAGTTCCAGTGCTGCAAGAAAGAAGTTGCACATCAATGATGCGTCTCACAACCACCACTCCAAAATGAGCAAA
AGTTCCAAAAGTTCAGGTGGGCTACGGACATCT

ORF - retro_mdom_864 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 99.23 %
Parental protein coverage: 88.69 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMASGRGASSRWFFSREQLENTPSRRCGVEADKELSYRQQAANFIQDMGQRLNVSQLTINTAIVYMHRFYM
MASGRGASSRWFFSREQLENTPSRRCGVEADKELSYRQQAANFIQDMGQRLNVSQLTINTAIVYMHRFYM
RetrocopyMASGRGASSRWFFSREQLENTPSRRCGVEADKELSYRQQAANFIQDMGQRLNVSQLTINTAIVYMHRFYM
ParentalHHSFTKFNRNIIAPTALFLAAKVEEQPRKLEHVIKVAHACLHQELLLDTKSEAYLQQTQELVILETIMLQ
HHSFTKFNRNIIAPTALFLAAKVEEQPRKLEHVIKVAHACLHQELLLDTKSEAYLQQTQELVILETIMLQ
RetrocopyHHSFTKFNRNIIAPTALFLAAKVEEQPRKLEHVIKVAHACLHQELLLDTKSEAYLQQTQELVILETIMLQ
ParentalTLGFEITIEHPHTDVVKCTQLVRASKDLAQTSYFMATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEI
TLGFEITIEHPHTDVVKCTQLVRASKDLAQTSYFMATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEI
RetrocopyTLGFEITIEHPHTDVVKCTQLVRASKDLAQTSYFMATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEI
ParentalPVSTDGKHWWEYVDPSVTLELLDELTHEFLQILEKTPNRLKRIRNWRATQAARKPKGDGQVSETALLGSS
PVSTDGKHWWEYVDPSVTLELLDELTHEFLQILEKTPNRLKRIRNWRATQAARKPKGDGQVSETALLGSS
RetrocopyPVSTDGKHWWEYVDPSVTLELLDELTHEFLQILEKTPNRLKRIRNWRATQAARKPKGDGQVSETALLGSS
ParentalLVQNSILVDSVTGVTTNASFQKPSTSAFPAPVPLNSGNISVQDTHASDNLTILTTGMPSTSYSLASHQEW
LVQNSILVDSVTGVTTNASFQKPSTSAFPAPVPLNSGNISVQDTHASDNLTILTTGMPSTSYSLASHQEW
RetrocopyLVQNSILVDSVTGVTTNASFQKPSTSAFPAPVPLNSGNISVQDTHASDNLTILTTGMPSTSYSLASHQEW
ParentalPQHQEPTRTEQIYSQKQEAPMSGSQYNINFQQGPAGPLHSGLHHRSDKLSDHSSVKQEYTHKAGSSKHHG
PQHQEPTRTEQIYSQKQEAPMSGSQYNINFQQGPAGPLHSGLHHRSDKLSDHSSVKQEYTHKAGSSKHHG
RetrocopyPQHQEPTRTEQIYSQKQEAPMSGSQYNINFQQGPAGPLHSGLHHRSDKLSDHSSVKQEYTHKAGSSKHHG
ParentalPVSAAPVIVPQKMSLDKYREKRKLETLELDVREHYVAAQTEQPHKKHMQLQAASSSSVTSPIKMKIPIAN
PVSAAPVIVPQKMSLDKYREKRKLETLELDVREHYVAAQTEQPHKKHMQLQAASSSSVTSPIKMKIPIAN
RetrocopyPVSAAPVIVPQKMSLDKYREKRKLETLELDVREHYVAAQTEQPHKKHMQLQAASSSSVTSPIKMKIPIAN
ParentalAEKPEKYMLDKKEKSGSLKLRIPIPPTDKSSSKEELKMKIKVSSSERHSSSDEGSGKSKHSSPHVSKDHK
AEKPEKYMLDKKEKSGSLKLRIPIPPTDK.SSKEELKMKIKVSSSERHSSSDEGSGKSKHSSPHVSKDHK
RetrocopyAEKPEKYMLDKKEKSGSLKLRIPIPPTDKISSKEELKMKIKVSSSERHSSSDEGSGKSKHSSPHVSKDHK
ParentalEKHKEHSSNRHHSSSHKHSHSHSGSSSSGSKHSTDGIPPTVLRSPVGLSSDGGNSSSSSAARKKLHINDA
EKHKEHSSNRHHSSSHKHSHSHSGSSSSGSKHSTDGIPPTVLRSPVGLSSDGGNSSSSSAARKKLHINDA
RetrocopyEKHKEHSSNRHHSSSHKHSHSHSGSSSSGSKHSTDGIPPTVLRSPVGLSSDGGNSSSSSAARKKLHINDA
ParentalSHNHHSKMSKSSKSSGSSSSS
SHNHHSKMSKSSKSSG....S
RetrocopySHNHHSKMSKSSKSSGGLRTS

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_864 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_864 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 2 retrocopies.

Species Parental gene accession Retrocopies number
Monodelphis domestica ENSMODG00000000727 2 retrocopies
retro_mdom_1109, retro_mdom_864 ,


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