RetrogeneDB ID:

retro_mdom_1963

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:Un:56823226..56824816(+)
Located in intron of:ENSMODG00000000279
Retrocopy
information
Ensembl ID:ENSMODG00000017981
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PHTF1
Ensembl ID:ENSMODG00000000803
Aliases:None
Description:putative homeodomain transcription factor 1 [Source:HGNC Symbol;Acc:8939]


Retrocopy-Parental alignment summary:






>retro_mdom_1963
GAGAACGTTCCGGGCTGTCCCAGTCTGGGTACCAAGCAGAAACATTCCCAGCCGGAGGTGAGAATGTGGCCAGCCAAGGA
GAAAATGAACAATTCAGACGAAGGCAAGAATAAAGAAACATACCGTCTTCTGGGGAAAGGGTTTTCCGACGAGATATCCA
GTGAAGATTACTGTGAGGACCCCCCAGAGAAAGAGAGAAGCATAGAAGGGGCCTCCGGGGACAGCGACTTTGAAGTCAAG
AAGGAAAAGCCCTGGGTTTCCTCGAAACACGTCAGCAGCACTCAGGTAAAGAAGCCATCCCCTGCCAGGCGATGTCACGC
GGTGGGAGACTCCGAGACCCTGACTGAATCGGAGCTTGAGTCGGCCAGCCTTACTCGGGAGATCCTGAGAGATGGCAGTG
CCCGCTTTAGAAGCGGGAGCCTCAAGAACCTGAAAACCACCACCTTGGACACAGACCCCGAGGACGTGATGTGGGACGAA
CTTTTGCAGAACCAGTCATCATCGTCCACAAGAGACAGCAAGGAGGCAAGTGTGAAGACCCTCTGCCCCAGTACCAAGCA
GGAGCTGCAGAGTGATGTGCAACAGAACAGCGTGTTCTGTCACCAGAACAGCAAGAACTCTTCCTCAGAACTGGTGAATG
CAATTATTTGGGAAGACCGTGAATGCAAAAAGGTGACTCTGTCCGTTTTGGAACTCAGTGCCATCATCAAGAGAAGGGTT
AATGCATACCAACAGGGCAAAAACTACTGGATTCTGGGCAACCTCCTAACTCTGGGACTCGCATTTTTTCCATTCCTACA
CCGCCTCTTTCGTGAGAAGAACCCGTACCAACTACTATCCATTTCAGCCGAAGAACTTCTGAGTCTGTTTTGTGGGGCAC
CAACATCCGGATCAGTAATCATCTTAGCGACTGTGAACTTCTTCCAGCGCTTCTGTCTGATCTGGATATTCTTTTTTATG
ATGTGTGTAGCAGAGAGAACATACCAGCAACGCTTTCTATTCGCAAAACTCTTCAATCATATTACCTCTGCCAGAAAAGC
CAAGAAACACGAAATCCCCCATTTCAGACTCAGAAAGGTAGAGAACATCAAGATATGGCTGGCACTACATTCTTATTTAA
AGAGACAGAGTCCACAGCAGTCCATCGATGTGGTTGTTTCCTCAGTGTATTTATTGACCCTCTCTATCGCCTTTGTTTGC
TGCGCTCAGATCCTGCAAAACCACAAAACCTTTCTGGATCAAACTTACAATTGCGAATTCCTGATTTGGGAAACGGTCCT
GCTGCTCTTTTTATTGCATCTTGCATCCCTGGGGTCTGAAACAAGTAAGAAAAACAGGAACATCTCAGTGCTGCTCATGG
AGCAAATTAACTTATATTTTAAAATGGAAAAGAAGCCACACAAAAAAGACCAGCTCATTCTGGTGAACAACATGCTAAAG
CTATCGACCAAGTTACTAAAGGAGTTGAACACACCACCTAGGCTCTATGGCCTGACCACACATCCTCTGATCAGCAACAT
AACTCAAACAGTCATCCTTTTAGCCGTCCCCGGGATCGTAAGTAATCTACTGGGATTCAACATACACATG

ORF - retro_mdom_1963 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.43 %
Parental protein coverage: 69.99 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalDNNPTILNLNPKKKHPRSEMRMWQAREKAKLSDGEKSHEGYRRLGNGISDELSSEDDCEEQTQMILLRRS
.N.P....L..K.KH...E.RMW.A.EK...SD..K..E.YR.LG.G.SDE.SSED.CE.........RS
RetrocopyENVPGCPSLGTKQKHSQPEVRMWPAKEKMNNSDEGKNKETYRLLGKGFSDEISSEDYCEDPPEK---ERS
ParentalVEGASSDNGYEIKNEKPSVSSKHASS-QVKKNSTSRWCRMVRDSDSLAESELESVAFSQESRSGISGGSR
.EGAS.D...E.K.EKP.VSSKH.SS.QVKK.S..R.C..V.DS..L.ESELES.....E.....S...R
RetrocopyIEGASGDSDFEVKKEKPWVSSKHVSSTQVKKPSPARRCHAVGDSETLTESELESASLTREILRDGSARFR
ParentalSCSRRDSESTRHDSETEDMLWDDLLHGPECRSSATSDSEEGNVKALPPGAKRDPKEDVFQQNHLFWLQNT
S.S......T..D...ED..WD.LL......SS.T.DS.E..VK.L.P..K.....DV.QQN..F..QN.
RetrocopySGSLKNLKTTTLDTDPEDVMWDELLQNQS--SSSTRDSKEASVKTLCPSTKQELQSDV-QQNSVFCHQNS
Parental-SPASERVSAIIWEGNECKKMDMSVLEISGIIMSRVNAYQQGAGYQMLGNIVTIGLAFFPFLHRLFHEKN
....SE.V.AIIWE..ECKK...SVLE.S.II..RVNAYQQG..Y..LGN..T.GLAFFPFLHRLF.EKN
RetrocopyKNSSSELVNAIIWEDRECKKVTLSVLELSAIIKRRVNAYQQGKNYWILGNLLTLGLAFFPFLHRLFREKN
ParentalMDQIRSISTNEILTLFCGAPPSVAIIILSAVNFLERLCLTWMFFFMMCVAERTYKQRFLFAKLFSHITSA
..Q..SIS..E.L.LFCGAP.S...IIL..VNF..R.CL.W.FFFMMCVAERTY.QRFLFAKLF.HITSA
RetrocopyPYQLLSISAEELLSLFCGAPTSGSVIILATVNFFQRFCLIWIFFFMMCVAERTYQQRFLFAKLFNHITSA
ParentalRKARKYEIPHFRLKKVENIKIWLSLRSYLKRRGPQRSVDVVVSSVFLLTLSIAFICCAQVLQGHKTFLDD
RKA.K.EIPHFRL.KVENIKIWL.L.SYLKR..PQ.S.DVVVSSV.LLTLSIAF.CCAQ.LQ.HKTFLD.
RetrocopyRKAKKHEIPHFRLRKVENIKIWLALHSYLKRQSPQQSIDVVVSSVYLLTLSIAFVCCAQILQNHKTFLDQ
ParentalAYNWEFLIWETALLLFLLRLASLGSETNKKYSNISVLLTEQINLYLKMEKKPNKKEQLTLVNNVLKLSTK
.YN.EFLIWET.LLLFLL.LASLGSET.KK..NISVLL.EQINLY.KMEKKP.KK.QL.LVNN.LKLSTK
RetrocopyTYNCEFLIWETVLLLFLLHLASLGSETSKKNRNISVLLMEQINLYFKMEKKPHKKDQLILVNNMLKLSTK
ParentalLLKELDTPFRLYGLTMNPLIYNITRVVILSAVSGVISDLLGFNIRL
LLKEL.TP.RLYGLT..PLI.NIT..VIL.AV.G..S.LLGFNI..
RetrocopyLLKELNTPPRLYGLTTHPLISNITQTVILLAVPGIVSNLLGFNIHM

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_1963 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_1963 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 2 parental genes, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Monodelphis domestica ENSMODG00000000803 1 retrocopy
retro_mdom_1963 ,
Sarcophilus harrisii ENSSHAG000000119371 retrocopy
retro_shar_63,


Copyright © RetrogeneDB 2014-2017