RetrogeneDB ID:

retro_mmus_67

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:9:6265140..6266367(-)
Located in intron of:ENSMUSG00000032006
Retrocopy
information
Ensembl ID:ENSMUSG00000047619
Aliases:Ddi1, 1700011N24Rik
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Ddi2
Ensembl ID:ENSMUSG00000078515
Aliases:None
Description:DNA-damage inducible protein 2 [Source:MGI Symbol;Acc:MGI:1917244]


Retrocopy-Parental alignment summary:






>retro_mmus_67
ATGCTGATCACTGTGTATTGTGTGCGTAGGGACCTCACAGAGGTAACCTTTTCCCTCCAGGTCAACCCTGACTTTGAGCT
CTCAAACTTCAGAGTCCTCTGTGAGCTTGAGTCTGGTGTGCCTGCTGAGGAGGCCCAGATCGTTTACATGGAACAGCTCC
TCACAGATGACCACTGCTCCCTGGGCTCCTATGGACTCAAAGATGGTGACATGGTTGTACTTCTTCAGAAGGATAATGTT
GGACTTCGGACTCCAGGAAGGACTCCAAACCATCCTCGAGCAGATTTCACTGGGTCTGGGTCGGCCGTGCCTGGAACATC
AAGTTCCCGACACCCGCATCAGCATCAACACCATTATCACCATCATCAACGTATACCATCAACACAGCAAGCCCACGGAT
TAGCCTCTGGAGAGAATATGACCTTTGCTCAGGAACTCGACAGCCCTGCCCTGATTCGAAGCATGCTGCTTTCCAACCCC
CATGATCTGTCCCTGTTGAAGGAACGGAATCCTGCTTTGGCTGAAGCTCTGCTTAGTGGAAACCTTGAGACATTTTCTCA
GGTCCTGATGGAGCAGCAGAGAGAAAGGACCTTGAGAGAGCAAGAGATGTTTCGTCTTTACTCTACTAACCCATTTGATC
AGGAAACTCAGGCTAGAATAGAAGAAGAAATCCGACAACAGAATATTGAAGAAAATATGAACATAGCTATGGAAGAGGCT
CCGGAGAGTTTTGGACAAGTCGCTATGCTCTATATTAACTGCAAAGTGAATGGGCATCCTTTAAAGGCTTTTGTTGACTC
TGGTGCCCAGATGACTATCATGAGCCAAGCTTGTGCTGAGAGATGTAATATTATGAGACTGGTAGACCGACGGTGGGGTG
GGGTTGCTAAGGGAGTAGGCACACAGAGGATTATGGGCCGCGTTCATCTGGCTCAGATTCAAATTGAAGGTGATTTCTTA
CAGTGCTCTTTCTCTATACTTGAAGAGCAGCCCATGGATATCCTTCTAGGGCTTGATATGCTCAGGAGGCACCAGTGTTC
CATCGACCTAAAGAAAAATGTGCTGGTGATTGGCACTACCGGCTCACAGACTCACTTCCTTCCTGAAGGAGAGTTGCCCT
TGTGTGCTAAACTGTTGAGTGGAACTGTACAAGAAGAGTCTTCAGACAGGGAAGTAGGAGGTACTATCAAACACCCTGTC
AAGGGTCCTGGACGTAAAAAGCATTGA

ORF - retro_mmus_67 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.67 %
Parental protein coverage: 67.42 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalRQLPRTQAQHS-SPGEMASSPQGLDNPALLRDMLLANPHELSLLKERNPPLAEALLSGDLEKFSRVLVEQ
...P.TQ..H....GE.....Q.LD.PAL.R.MLL.NPH.LSLLKERNP.LAEALLSG.LE.FS.VL.EQ
RetrocopyQRIPSTQQAHGLASGENMTFAQELDSPALIRSMLLSNPHDLSLLKERNPALAEALLSGNLETFSQVLMEQ
ParentalQQDRARREQERIRLFSADPFDLEAQAKIEEDIRQQNIEENMTIAMEEAPESFGQVAMLYINCRVNGHPVK
Q..R..REQE..RL.S..PFD.E.QA.IEE.IRQQNIEENM.IAMEEAPESFGQVAMLYINC.VNGHP.K
RetrocopyQRERTLREQEMFRLYSTNPFDQETQARIEEEIRQQNIEENMNIAMEEAPESFGQVAMLYINCKVNGHPLK
ParentalAFVDSGAQMTIMSQACAERCNIMRLVDRRWAGIAKGVGTQKIIGRVHLAQVQIEGDFLACSFSILEEQPM
AFVDSGAQMTIMSQACAERCNIMRLVDRRW.G.AKGVGTQ.I.GRVHLAQ.QIEGDFL.CSFSILEEQPM
RetrocopyAFVDSGAQMTIMSQACAERCNIMRLVDRRWGGVAKGVGTQRIMGRVHLAQIQIEGDFLQCSFSILEEQPM
ParentalDMLLGLDMLKRHQCSIDLKKNVLVIGTTGSQTTFLPEGELPECARLAYGTGREDIRPEEI
D.LLGLDML.RHQCSIDLKKNVLVIGTTGSQT.FLPEGELP.CA.L..GT..E.....E.
RetrocopyDILLGLDMLRRHQCSIDLKKNVLVIGTTGSQTHFLPEGELPLCAKLLSGTVQEESSDREV

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 53 .90 RPM
SRP007412_cerebellum 0 .00 RPM 55 .36 RPM
SRP007412_heart 0 .00 RPM 49 .81 RPM
SRP007412_kidney 0 .04 RPM 96 .25 RPM
SRP007412_liver 0 .03 RPM 189 .49 RPM
SRP007412_testis 145 .72 RPM 16 .92 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_67 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_67 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_1520491064 libraries2 libraries3 libraries0 libraries3 libraries
TSS #2 TSS_1520501060 libraries4 libraries2 libraries0 libraries6 libraries

The graphical summary, for retro_mmus_67 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_67 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_67 has 11 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_96
Pan troglodytes retro_ptro_570
Gorilla gorilla retro_ggor_143
Pongo abelii retro_pabe_158
Macaca mulatta retro_mmul_231
Callithrix jacchus retro_cjac_196
Oryctolagus cuniculus retro_ocun_249
Bos taurus retro_btau_15
Sus scrofa retro_sscr_6
Canis familiaris retro_cfam_193
Equus caballus retro_ecab_110
Parental genes homology:
Parental genes homology involve 24 parental genes, and 25 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000118731 retrocopy
retro_amel_10,
Bos taurus ENSBTAG000000187182 retrocopies
retro_btau_15, retro_btau_650,
Canis familiaris ENSCAFG000000162201 retrocopy
retro_cfam_193,
Callithrix jacchus ENSCJAG000000086251 retrocopy
retro_cjac_196,
Cavia porcellus ENSCPOG000000208851 retrocopy
retro_cpor_88,
Equus caballus ENSECAG000000007621 retrocopy
retro_ecab_110,
Homo sapiens ENSG000001973121 retrocopy
retro_hsap_96,
Gorilla gorilla ENSGGOG000000135371 retrocopy
retro_ggor_143,
Macropus eugenii ENSMEUG000000061481 retrocopy
retro_meug_1364,
Myotis lucifugus ENSMLUG000000306691 retrocopy
retro_mluc_68,
Macaca mulatta ENSMMUG000000199121 retrocopy
retro_mmul_231,
Monodelphis domestica ENSMODG000000035151 retrocopy
retro_mdom_282,
Mustela putorius furoENSMPUG000000163321 retrocopy
retro_mputfur_1509,
Mus musculus ENSMUSG00000078515 1 retrocopy
retro_mmus_67 ,
Oryctolagus cuniculus ENSOCUG000000238911 retrocopy
retro_ocun_249,
Otolemur garnettii ENSOGAG000000277091 retrocopy
retro_ogar_4,
Ochotona princeps ENSOPRG000000184481 retrocopy
retro_opri_4,
Pongo abelii ENSPPYG000000018411 retrocopy
retro_pabe_158,
Pan troglodytes ENSPTRG000000240591 retrocopy
retro_ptro_570,
Pteropus vampyrus ENSPVAG000000050841 retrocopy
retro_pvam_420,
Rattus norvegicus ENSRNOG000000122741 retrocopy
retro_rnor_2606,
Sus scrofa ENSSSCG000000034621 retrocopy
retro_sscr_6,
Ictidomys tridecemlineatus ENSSTOG000000194471 retrocopy
retro_itri_93,
Tarsius syrichta ENSTSYG000000025221 retrocopy
retro_tsyr_1120,


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