RetrogeneDB ID:

retro_mmus_788

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:11:48751869..48753714(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000082454
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Ddx5
Ensembl ID:ENSMUSG00000020719
Aliases:Ddx5, 2600009A06Rik, G17P1, HUMP68, Hlr1, p68
Description:DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 [Source:MGI Symbol;Acc:MGI:105037]


Retrocopy-Parental alignment summary:






>retro_mmus_788
ATGTCGAGTTATTCTAGTGACCGAGACCACAGCCGGGATCGAGGGTTTGGTGCACCTCGATTTGGAGGGAGTAGAACAGG
ACCCCTCTCTGGAAAGAAGTTTGGAAATCCTGGGGAGAAACTAGTTAAAAAGAAGTGGAATCTTGATGAGCTGCCCAAAT
TTGAGAAGAATTTTTATCAAGAACACCCTGATTTGGCAAGGCGCACCGCACAAGAGGTTGATACATACAGAAGAAGCAAG
GAAATTACAGTTAGAGGTCACAACTGTCCAAAACCTGTTCTGAAGTTTTATGAAGCAAACTTTCCTGCGAATGTCATGGA
CGTGATTGCAAGGCAGAACTTCACTGAACCCACTGCTATTCAAGCTCAGGGCTGGCCAGTTGCTCTCAGTGGATTGGATA
TGGTTGGAGTAGCTCAGACTGGATCTGGGAAAACACTATCTTATTTGCTGCCTGCCATTGTACACATAATCCACCAGCCA
TTCCTAGAGAGAGGTGATGGGCCTATTTGCTTGGTGCTGGCACCAACTCGAGAACTGGCACAGCAGGTGCAGCAAGTGGC
TGCTGAATATTGTAGAGCTTGTCGCTTGAAGTCTACTTGCATCTATGGTGGTGCTCCCAAAGGACCACAGATTCGTGATT
TGGAAAGAGGCGTGGAAATCTGTATTGCAACACCTGGAAGACTGATTGACTTTTTAGAGTGTGGGAAAACCAATCTGAGA
AGAACAACGTACCTTGTCCTCGATGAAGCTGATAGGATGCTTGATATGGGATTTGAACCCCAGATAAGGAAAATCGTGGA
TCAAATAAGACCTGATAGGCAAACACTAATGTGGAGTGCAACTTGGCCAAAAGAAGTAAGACAGCTTGCTGAAGATTTCC
TGAAAGACTATATTCATATCAATATTGGTGCGCTGGAACTGAGTGCAAACCATAACATTCTCCAGATTGTGGATGTATGT
CATGATGTCGAAAAGGATGAAAAGCTTATTCTTCTGATGGAAGAAATCATGAGTGAGAAGGAGAATAAAACCATTGTTTT
TGTTGAAACCAAAAGAAGATGTGATGAACTTACCAGAAAAATGAGGAGAGATGGGTGGCCTGCCATGGGCATCCATGGTG
ACAAGAGTCAGCAGGAACGTGACTGGGTTCTAAGTGAATTCAAACATGGAAAAGCTTCTATTCTGATTGCTACTGATGTG
GCCTCCAGAGGGCTAGATGTGGAAGATGTGAAATTTGTCATCAATTATGACTACCCTAACTCCTCAGAGGATTATATTCA
TCGAATTGGAAGAACTGCTCGCAGTACCAAAACAGGCACAGCATATACTTTCTTTACACCTAATAACATAAAGCAAGCGA
GCGACCTTATCTCTGTGCTTCGGGAAGCTAATCAAGCAATTAATCCCAAGTTGCTTCAGTTGGTCGAAGACAGAGGTTCA
GGTCGTTCCAGGGGTAGAGGAGGCATGAAGGACGATCGTCGTGACAGATACTCTGCAGGCAAAAGGGGTGGATTTAATAC
CTTTAGAGACAGGGAAAACTATGACAGAGGCTACTCTAATCTGCTTAAGAGAGATTTTGGGGCTAAAACTCAGAATGATG
TTTACAGTACTGCAAATTACACCAATGGGAGCTTTGGAAGTAATTTTGTATCTGCTGGCATACAGACCAGTTTTAGGACT
GGTAATCCAACAGGGACTTACCAGAACGATTATGATAGCACTCAGCAATATGGAAGTAATGTTGCAAATATGCACAATGG
TATGAACCAACAGGCATATGCGTATCCTGCTACCGCAGCTGCTGCGCCTATGATTGGCTATCCCGTGCCAACAGGGTATT
CTCAA

ORF - retro_mmus_788 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 98.05 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSSYSSDRDRGRDRGFGAPRFGGSRTGPLSGKKFGNPGEKLVKKKWNLDELPKFEKNFYQEHPDLARRTA
MSSYSSDRD..RDRGFGAPRFGGSRTGPLSGKKFGNPGEKLVKKKWNLDELPKFEKNFYQEHPDLARRTA
RetrocopyMSSYSSDRDHSRDRGFGAPRFGGSRTGPLSGKKFGNPGEKLVKKKWNLDELPKFEKNFYQEHPDLARRTA
ParentalQEVDTYRRSKEITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQT
QEVDTYRRSKEITVRGHNCPKPVL.FYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQT
RetrocopyQEVDTYRRSKEITVRGHNCPKPVLKFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQT
ParentalGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQ
GSGKTLSYLLPAIVHI.HQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQ
RetrocopyGSGKTLSYLLPAIVHIIHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQ
ParentalIRDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSA
IRDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSA
RetrocopyIRDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSA
ParentalTWPKEVRQLAEDFLKDYIHINIGALELSANHNILQIVDVCHDVEKDEKLIRLMEEIMSEKENKTIVFVET
TWPKEVRQLAEDFLKDYIHINIGALELSANHNILQIVDVCHDVEKDEKLI.LMEEIMSEKENKTIVFVET
RetrocopyTWPKEVRQLAEDFLKDYIHINIGALELSANHNILQIVDVCHDVEKDEKLILLMEEIMSEKENKTIVFVET
ParentalKRRCDELTRKMRRDGWPAMGIHGDKSQQERDWVLNEFKHGKAPILIATDVASRGLDVEDVKFVINYDYPN
KRRCDELTRKMRRDGWPAMGIHGDKSQQERDWVL.EFKHGKA.ILIATDVASRGLDVEDVKFVINYDYPN
RetrocopyKRRCDELTRKMRRDGWPAMGIHGDKSQQERDWVLSEFKHGKASILIATDVASRGLDVEDVKFVINYDYPN
ParentalSSEDYIHRIGRTARSTKTGTAYTFFTPNNIKQVSDLISVLREANQAINPKLLQLVEDRGSGRSRGRGGMK
SSEDYIHRIGRTARSTKTGTAYTFFTPNNIKQ.SDLISVLREANQAINPKLLQLVEDRGSGRSRGRGGMK
RetrocopySSEDYIHRIGRTARSTKTGTAYTFFTPNNIKQASDLISVLREANQAINPKLLQLVEDRGSGRSRGRGGMK
ParentalDDRRDRYSAGKRGGFNTFRDRENYDRGYSNLLKRDFGAKTQNGVYSAANYTNGSFGSNFVSAGIQTSFRT
DDRRDRYSAGKRGGFNTFRDRENYDRGYSNLLKRDFGAKTQN.VYS.ANYTNGSFGSNFVSAGIQTSFRT
RetrocopyDDRRDRYSAGKRGGFNTFRDRENYDRGYSNLLKRDFGAKTQNDVYSTANYTNGSFGSNFVSAGIQTSFRT
ParentalGNPTGTYQNGYDSTQQYGSNVANMHNGMNQQAYAYPATAAAAPMIGYPMPTGYSQ
GNPTGTYQN.YDSTQQYGSNVANMHNGMNQQAYAYPATAAAAPMIGYP.PTGYSQ
RetrocopyGNPTGTYQNDYDSTQQYGSNVANMHNGMNQQAYAYPATAAAAPMIGYPVPTGYSQ

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 1 .50 RPM 645 .89 RPM
SRP007412_cerebellum 1 .52 RPM 930 .74 RPM
SRP007412_heart 1 .12 RPM 347 .91 RPM
SRP007412_kidney 1 .81 RPM 579 .55 RPM
SRP007412_liver 0 .66 RPM 372 .57 RPM
SRP007412_testis 1 .78 RPM 661 .48 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_788 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_788 retrocopy.

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_12942149 libraries311 libraries564 libraries38 libraries10 libraries
TSS #2 TSS_12943207 libraries455 libraries381 libraries21 libraries8 libraries

The graphical summary, for retro_mmus_788 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_mmus_788 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_788 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Echinops telfairi ENSETEG000000199501 retrocopy
retro_etel_1009,
Felis catus ENSFCAG000000035121 retrocopy
retro_fcat_172,
Myotis lucifugus ENSMLUG000000094964 retrocopies
retro_mluc_1136, retro_mluc_1499, retro_mluc_1845, retro_mluc_2208,
Monodelphis domestica ENSMODG000000037434 retrocopies
retro_mdom_1519, retro_mdom_1520, retro_mdom_1955, retro_mdom_1956,
Mus musculus ENSMUSG000000200752 retrocopies
retro_mmus_582, retro_mmus_662,
Mus musculus ENSMUSG000000200761 retrocopy
retro_mmus_3362,
Mus musculus ENSMUSG00000020719 1 retrocopy
retro_mmus_788 ,
Pteropus vampyrus ENSPVAG000000019321 retrocopy
retro_pvam_1267,
Rattus norvegicus ENSRNOG000000306801 retrocopy
retro_rnor_1277,
Tupaia belangeri ENSTBEG000000094901 retrocopy
retro_tbel_4260,
Tarsius syrichta ENSTSYG000000121491 retrocopy
retro_tsyr_1269,
Tursiops truncatus ENSTTRG000000087931 retrocopy
retro_ttru_1662,




Copyright © RetrogeneDB 2014-2017