RetrogeneDB ID:

retro_mdom_49

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:3:144396546..144399030(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMODG00000025040
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:TFIP11
Ensembl ID:ENSMODG00000010710
Aliases:TFIP11, STIP, STIP1
Description:Tuftelin-interacting protein 11 [Source:UniProtKB/Swiss-Prot;Acc:A4UMC6]


Retrocopy-Parental alignment summary:






>retro_mdom_49
ATGTCGCTGTCCCATCTCTACCGAGAGGGTAAAGGAGCCATTGATGAGGAAGAAGATGAGATGGAGAACTTTGAGATCAC
TGATTGGGACCTCCAGAATGAATTCAACCCAAACCGGCAATATCATTGGCAGACCAAGGAGGAGGCCACATATGGAGTAT
GGGCTGAGCATGAACGGGAAGATGAGCAGCCCGGTTATGGAGGCAAACGCTCCCGAGACTTTTTGGCTCCTGTAAATTTC
ATTAGTGCTGGCCTGAAGAAAGCAGACGAGGAGGATTCCAATGAGGACAAGAAGCCTATTAAGCAGCTGGATTTTCCTAA
AGATTTTGGCCCAAAGAAGTTACAAACAGGTGGCAATTTTAAACCCAGCCAGAAAGGCTGGGTGGGAGGAGCCAAATCTT
TCACAGGCTTGGGCAGCTGGGAAAGGCACACCAAAGGAATTGGGCAGAAGCTTTTGCAGAAGATGGGTTATGTTCCAGGG
AAGGGGCTTGGGAAGAAGGCACAAGGTATCATTCATCCAATTGAAGCTAAGGGGAGAAAAGGCCAGGCTGCTGGGGGAGC
CTCTGGCTCAGAAGGGACCGCTCAGTCAGTGCAAGATTTCCCTGGGCTTGACTCAGAAGAAGAGGAGGTTCAGAAGGAGC
TCAGCCAGAGGTGGAAAGACCTGAGTGGGGGCAGGAAGAAACCAAAATACTCCTCTCAGACAGTTGAAGAATTGAAGGCA
AAGGGTAGAATTGGAAAGAAACTCTCTGCTCCCCAGAAGGAGCTTTCCCAGGTTAAGGTTATCGACATGACAGGCCGGGA
ACAGAAGGTCTATTACGGTTACAGCCAAATTAGCCACAAGCACAACATACCAGAGGATGGACTTCAGCAGCAGCAGCTGC
CACTGTCTGGCAAACATGCCAAGCCACAGGCCTTTGCCCTGCCTGAGCTGGAGCACAACCTCCAGTTGCTCATTGATATC
ACTGAGCAGGAGATCATTCAGAATGACCGGCAGCTGCAGGAGGAGTCAGACAAGGTCCACAATCTGTCCCACGAGCTGGG
GAAAATGTCTGAGGTTCTGTCCCATGAAGAGACAGTGATCACCAACCTCAGGAAGGTCCTGGAGATGGTGGAGGAGTGTG
AGAGAAGGACGCAGCCAGACTGCAGCGATCCTCTCACACTGGATGAGTGTGCCAGAATATTTGAGACTCTCCAAGAGAAG
TACTATGAGGAATACCGCATGTCTGACCGCGTGGACCTGGCCGTGGCTATTGTCTACCCACTCGTGAAAGATTACTTCAA
GGCCTGGGATCCCCTCAAGGACTGCACTTATGGCACTGGCATCATTGCCAAGTGGAAAAGCCTTTTGACCAATGATCAGA
TCCTGTCTCATGGGGGCCAAGATCTTGCAGCAGATGCTTTCCACAGGATGATCTGGGAAATATGGATGCCTTTTGTTCGA
AATACTGTACCTCAGTGGCAGCCGAGGAACTGTGACCCAATGGTGGACTTTTTGGATAGCTGGGTCCATATTATTCCTGT
GTGGATCCTGGATCACATACTGGACCAGCTCATCTTCCCCAAACTGCAAAAGGAGGTTGAAAGCTGGAACCCTCTGACGG
ACATGGTTCCCATCCACTCATGGATACATCCCTGGCTTCCCCTTATGCAGTCACGCTTAGAGCCTTTGTACTCTCTGATC
CGGAACAAGTTATCCAGGGCTCTGCAGAAATGGCATCCCAGGGATTCCTCAGCCAAGCTTATCCTGCAGCCCTGGAAGGA
TGTGTTTACCCCTGGCTCCTGGGAGGCCTTCATGGTCAAAAATATTGTGCCCAAATTAGGAATGTGTCTTAATGAATTCA
TCATTAACCCTCACCAGCAGCACATGGATGCTTTCTATTGGGTGATTGACTGGGAAGGAATGATCTCAGTTTCCAGCCTA
GTAGGACTCCTCAAGAAGCATTTCTTTCCTAAGTGGCTTCACGTTCTCTGCTCCTGGCTCAGTAATAGTCCAAATTATGA
AGAGATCACCAAATGGTATTTGGGCTGGAAGTCCATGTTTACAGACCAGGTTTTGGCACATCCATCTATCAAGGACAAAT
TTAATGAAGCACTTGATATCATGAACAGGGCTGTTTCTTCCAATGTCGGGGCATATATGCAGCCAGGAGCTCGGGAGAAC
ATTGCCTATCTTACTCACACAGAGAGGAGGAAAGGCTTCCAGTATGAGGCCATGCAGCACTGCCGAGAAGCAGAGAACAT
GGCTCAGAGGGGCATAGGCATGGCAGCCAGCTCTGTGCCTATGAACTTCAAAGACCTCATTCAAACAAAGGCTGAAGAAC
ATAACATTGTTTTCCTGCCTGTTGTTGGGAAAAGGCATGAAGGGAAACAACTCTACACTTTTGGGCGGATTGTAGTCTAC
ATTGACCAGGGTGTTCTGTTTGTGCAAGGGGCAAAGACTTGGGTGCCAACATCCCTCCAAAGTCTGATCGATATGGCAAA
GTAG

ORF - retro_mdom_49 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.89 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSLSHLYREGEGAIDEEEDEMENFEITDWDLQNEFNPNRQRHWQTKEEATYGVWAERELEDERPSFGGKR
MSLSHLYREG.GAIDEEEDEMENFEITDWDLQNEFNPNRQ.HWQTKEEATYGVWAE.E.EDE.P..GGKR
RetrocopyMSLSHLYREGKGAIDEEEDEMENFEITDWDLQNEFNPNRQYHWQTKEEATYGVWAEHEREDEQPGYGGKR
ParentalSRDFSAPVNFISAGLKKAADEADEEDSDEEEKPIKQEDFPKDFGPKKLKTGGNFKPSQKGFVGGAKSFTD
SRDF.APVNFISAGLKK....ADEEDS.E..KPIKQ.DFPKDFGPKKL.TGGNFKPSQKG.VGGAKSFT.
RetrocopySRDFLAPVNFISAGLKK----ADEEDSNEDKKPIKQLDFPKDFGPKKLQTGGNFKPSQKGWVGGAKSFTG
ParentalFGSWERHTKGIGQKLLQKMGYVPGKGLGKNAQGIINPIEAKQRKGKGAVGAYGSERTTQSVQDFPVVDSE
.GSWERHTKGIGQKLLQKMGYVPGKGLGK.AQGII.PIEAK.RKG..A.GA.GSE.T.QSVQDFP..DSE
RetrocopyLGSWERHTKGIGQKLLQKMGYVPGKGLGKKAQGIIHPIEAKGRKGQAAGGASGSEGTAQSVQDFPGLDSE
ParentalEEAEEEFQKELSQWRKDPSGGKKKPKYSYKTVEELKAKGRIGKKLSAPQKELSQVKVIDMTGREQKVYYS
...EEE.QKELSQ..KD.SGG.KKPKYS..TVEELKAKGRIGKKLSAPQKELSQVKVIDMTGREQKVYY.
Retrocopy---EEEVQKELSQRWKDLSGGRKKPKYSSQTVEELKAKGRIGKKLSAPQKELSQVKVIDMTGREQKVYYG
ParentalYSQISHKHNIPEDGLQQQQLPLPGKDAKPQAFALPELEHNLQLLIDITEQEIIQNDRQLQYERDMVVNLS
YSQISHKHNIPEDGLQQQQLPL.GK.AKPQAFALPELEHNLQLLIDITEQEIIQNDRQLQ.E.D.V.NLS
RetrocopyYSQISHKHNIPEDGLQQQQLPLSGKHAKPQAFALPELEHNLQLLIDITEQEIIQNDRQLQEESDKVHNLS
ParentalHELEKMSEVLSHEETVITNLSKVLEMVEECERRMQPDCSDPLTLDECARIFETLQEKYYEEYRMSDRVDL
HEL.KMSEVLSHEETVITNL.KVLEMVEECERR.QPDCSDPLTLDECARIFETLQEKYYEEYRMSDRVDL
RetrocopyHELGKMSEVLSHEETVITNLRKVLEMVEECERRTQPDCSDPLTLDECARIFETLQEKYYEEYRMSDRVDL
ParentalAVAIVYPLMKDYFKDWDPLKDCTYGTGIIAKWKSLLENDQILSHGGQDLAADAFHRLIWEMWMPFVRNIV
AVAIVYPL.KDYFK.WDPLKDCTYGTGIIAKWKSLL.NDQILSHGGQDLAADAFHR.IWE.WMPFVRN.V
RetrocopyAVAIVYPLVKDYFKAWDPLKDCTYGTGIIAKWKSLLTNDQILSHGGQDLAADAFHRMIWEIWMPFVRNTV
ParentalTQWQPRNCDPMVDFLDSWVHIIPVWILDNILDQLIFPKLQKEVENWNPLTDTVPIHSWIHPWLPLMQSRL
.QWQPRNCDPMVDFLDSWVHIIPVWILD.ILDQLIFPKLQKEVE.WNPLTD.VPIHSWIHPWLPLMQSRL
RetrocopyPQWQPRNCDPMVDFLDSWVHIIPVWILDHILDQLIFPKLQKEVESWNPLTDMVPIHSWIHPWLPLMQSRL
ParentalEPLYSPIRNKLSSALQKWHPSDSSAKLILQPWKDVFTPGSWEAFMVKNIVPKLGMCLNELIINPHQQHMD
EPLYS.IRNKLS.ALQKWHP.DSSAKLILQPWKDVFTPGSWEAFMVKNIVPKLGMCLNE.IINPHQQHMD
RetrocopyEPLYSLIRNKLSRALQKWHPRDSSAKLILQPWKDVFTPGSWEAFMVKNIVPKLGMCLNEFIINPHQQHMD
ParentalAFYWVIDWEGMISVSSLVGLLEKHFFPKWLQVLCSWLSNSPNYEEITKWYLGWKSMFSDQVLAHPSIKDK
AFYWVIDWEGMISVSSLVGLL.KHFFPKWL.VLCSWLSNSPNYEEITKWYLGWKSMF.DQVLAHPSIKDK
RetrocopyAFYWVIDWEGMISVSSLVGLLKKHFFPKWLHVLCSWLSNSPNYEEITKWYLGWKSMFTDQVLAHPSIKDK
ParentalFNEALDIMNRAVSSNVGAYMQPGARENIAYLTHTERRKDFQYEAMQERREAENMAQRGIGMAASSVPMNF
FNEALDIMNRAVSSNVGAYMQPGARENIAYLTHTERRK.FQYEAMQ..REAENMAQRGIGMAASSVPMNF
RetrocopyFNEALDIMNRAVSSNVGAYMQPGARENIAYLTHTERRKGFQYEAMQHCREAENMAQRGIGMAASSVPMNF
ParentalKDLIQTKAEEHNIVFMPVIGKRHEGKQLYTFGRIVVYIDRGVVFVQGEKTWVPTSLQSLIDMAK
KDLIQTKAEEHNIVF.PV.GKRHEGKQLYTFGRIVVYID.GV.FVQG.KTWVPTSLQSLIDMAK
RetrocopyKDLIQTKAEEHNIVFLPVVGKRHEGKQLYTFGRIVVYIDQGVLFVQGAKTWVPTSLQSLIDMAK

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_49 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_49 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 3 parental genes, and 3 retrocopies.

Species Parental gene accession Retrocopies number
Equus caballus ENSECAG000000162421 retrocopy
retro_ecab_65,
Myotis lucifugus ENSMLUG000000080151 retrocopy
retro_mluc_1721,
Monodelphis domestica ENSMODG00000010710 1 retrocopy
retro_mdom_49 ,




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