RetrogeneDB ID:

retro_mmus_258

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:10:99757800..99759201(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000046934
Aliases:Csl, 1700007H16Rik
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Cs
Ensembl ID:ENSMUSG00000005683
Aliases:Cs, 2610511A05Rik, 9030605P22Rik, BB234005, Cis, ahl4
Description:citrate synthase [Source:MGI Symbol;Acc:MGI:88529]


Retrocopy-Parental alignment summary:






>retro_mmus_258
ATGGCTCTACTTACTGCGGCAGCCTGGTTCTTGGGAACCAAAAACCCACCCTGCCTTGTCCTTGCCGCCCGGCATGCCAG
TGCTTCTTCCACGAACTTGAAAGACGTGCTGAGGAATCTGATACCCAAGGAGCAAGCCAGAATTAAGACCTTCAGAAAGA
AACACGGGAAGACAGTTGTGGGCCAGATCACTGTGGACATGATGTACGGTGGCATGAGAGGCATGAAGGGACTTGTGTAT
GAGACATCGGTTCTTGATCCTGATGAGGGCATCCGTTTCCGAGGCTACAGTATCCCTGAGTGCCAGAAACTGCTGCCTAA
GGCTAAGGGTGGGAAAGAACCCCTGCCTGAGGGCTTATTTTGGCTGCTGGTAACTGGACAGATGCCCACAGAGGAACAGG
TATCTTGGCTCTCACAAGAATGGGTAAAAAGGGCAGCTCTACCTTCTCATGTCGTCACCATGCTGGACAATTTTCCGACC
AAATTGCACCCCATGTCTCAGCTCAGTGCAGCCATCACAGTCCTCAACAATGAAAGCAACTTTGCCCGGGCATATGCGCA
GGGAATGAACCGAACTAAGTACTGGGAGCTCACCTATGAAGACTGTATGGACCTGCTTGCCAAGCTTCCGTGTGTTGCAG
CAAAGATCTACCGGAATCTGTACCGGGAAGATAGGAATATTGAGGCCATTGACTCTAAGCTGGACTGGTCCCACAATTTT
ACCAACATGTTAGGCTACACGGACCCTCAGTTCACCGAGCTCATGCGTTTGTACCTCACCATCCACAGTGACCATGAGGG
TGGTAATGTAAGTGCCCACACCAGCCATTTGGTGGGCAGTGCCCTTTCTGATCCTTACCTGTCCTTTGCAGCAGCCTTGA
ATGGGCTGGCGGGGCCTCTCCATGGGCTAGCAAATCAGGAGGTGCTTGTCTGGCTGACACAGCTACAGAAGGAAGTTGGC
GAAGATGCATCAGATGAGAAGTTAAAAAACTACATCTGGAACACACTCAACTCAGGACGGGTTGTCCCAGGCTATGGCCA
TGCAGTACTGAGGAAGACTGACCCTCGCTATTCCTGTCAGCGAGAGTTTGCTCTGAAACATCTGCCTAAGGATCCCATGT
TCAAGCTGGTTGGTCAGCTGTACAAGATTGTACCCGATATCCTCTTAGAGCAAGGGAAGGCTAAGAACCCTTGGCCCAAC
GTAGACGCTCACAGTGGGGTGCTGCTCCAGTACTACGGCATGAGGGAGATGAATTACTACACAGTCCTGTTCGGAGTGTC
GCGGGCACTGGGCGTTCTGTCCCAGCTCATCTGGAGCAGAGCCCTAGGCTTCCCTCTGGAAAGGCCCAAGTCCATGAGCA
CGGATGCTCTGATGAAGTTTGTGAACTCTGAGTCAGGATAA

ORF - retro_mmus_258 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.81 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMALLTAATRLLGAKNSSCLVLAARHASASSTNLKDVLSNLIPKEQARIKTFKQQHGKTVVGQITVDMMYG
MALLTAA...LG.KN..CLVLAARHASASSTNLKDVL.NLIPKEQARIKTF...HGKTVVGQITVDMMYG
RetrocopyMALLTAAAWFLGTKNPPCLVLAARHASASSTNLKDVLRNLIPKEQARIKTFRKKHGKTVVGQITVDMMYG
ParentalGMRGMKGLVYETSVLDPDEGIRFRGYSIPECQKMLPKAKGGEEPLPEGLFWLLVTGQMPTEEQVSWLSRE
GMRGMKGLVYETSVLDPDEGIRFRGYSIPECQK.LPKAKGG.EPLPEGLFWLLVTGQMPTEEQVSWLS.E
RetrocopyGMRGMKGLVYETSVLDPDEGIRFRGYSIPECQKLLPKAKGGKEPLPEGLFWLLVTGQMPTEEQVSWLSQE
ParentalWAKRAALPSHVVTMLDNFPTNLHPMSQLSAAITALNSESNFARAYAEGMNRAKYWELIYEDCMDLIAKLP
W.KRAALPSHVVTMLDNFPT.LHPMSQLSAAIT.LN.ESNFARAYA.GMNR.KYWEL.YEDCMDL.AKLP
RetrocopyWVKRAALPSHVVTMLDNFPTKLHPMSQLSAAITVLNNESNFARAYAQGMNRTKYWELTYEDCMDLLAKLP
ParentalCVAAKIYRNLYREGSSIGAIDSRLDWSHNFTNMLGYTDPQFTELMRLYLTIHSDHEGGNVSAHTSHLVGS
CVAAKIYRNLYRE...I.AIDS.LDWSHNFTNMLGYTDPQFTELMRLYLTIHSDHEGGNVSAHTSHLVGS
RetrocopyCVAAKIYRNLYREDRNIEAIDSKLDWSHNFTNMLGYTDPQFTELMRLYLTIHSDHEGGNVSAHTSHLVGS
ParentalALSDPYLSFAAAMNGLAGPLHGLANQEVLVWLTQLQKEVGKDVSDEKLRDYIWNTLNSGRVVPGYGHAVL
ALSDPYLSFAAA.NGLAGPLHGLANQEVLVWLTQLQKEVG.D.SDEKL..YIWNTLNSGRVVPGYGHAVL
RetrocopyALSDPYLSFAAALNGLAGPLHGLANQEVLVWLTQLQKEVGEDASDEKLKNYIWNTLNSGRVVPGYGHAVL
ParentalRKTDPRYSCQREFALKHLPKDPMFKLVAQLYKIVPNILLEQGKAKNPWPNVDAHSGVLLQYYGMTEMNYY
RKTDPRYSCQREFALKHLPKDPMFKLV.QLYKIVP.ILLEQGKAKNPWPNVDAHSGVLLQYYGM.EMNYY
RetrocopyRKTDPRYSCQREFALKHLPKDPMFKLVGQLYKIVPDILLEQGKAKNPWPNVDAHSGVLLQYYGMREMNYY
ParentalTVLFGVSRALGVLAQLIWSRALGFPLERPKSMSTDGLMKFVDSK
TVLFGVSRALGVL.QLIWSRALGFPLERPKSMSTD.LMKFV.S.
RetrocopyTVLFGVSRALGVLSQLIWSRALGFPLERPKSMSTDALMKFVNSE

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 .19 RPM 239 .66 RPM
SRP007412_cerebellum 0 .13 RPM 209 .59 RPM
SRP007412_heart 0 .47 RPM 1205 .45 RPM
SRP007412_kidney 0 .23 RPM 434 .64 RPM
SRP007412_liver 0 .05 RPM 98 .69 RPM
SRP007412_testis 154 .69 RPM 60 .51 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_258 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_258 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_77611062 libraries4 libraries2 libraries0 libraries4 libraries
TSS #2 TSS_77621064 libraries2 libraries2 libraries0 libraries4 libraries
TSS #3 TSS_77631065 libraries3 libraries0 libraries1 library3 libraries
TSS #4 TSS_77641066 libraries2 libraries1 library2 libraries1 library
TSS #5 TSS_77651064 libraries3 libraries1 library1 library3 libraries
TSS #6 TSS_77661066 libraries1 library1 library1 library3 libraries
TSS #7 TSS_77671064 libraries2 libraries2 libraries0 libraries4 libraries
TSS #8 TSS_77681066 libraries1 library1 library2 libraries2 libraries

The graphical summary, for retro_mmus_258 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_258 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_258 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Rattus norvegicus retro_rnor_2518
Parental genes homology:
Parental genes homology involve 21 parental genes, and 29 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000043711 retrocopy
retro_btau_386,
Canis familiaris ENSCAFG000000001151 retrocopy
retro_cfam_765,
Choloepus hoffmanni ENSCHOG000000003971 retrocopy
retro_chof_1803,
Callithrix jacchus ENSCJAG000000112751 retrocopy
retro_cjac_2031,
Dasypus novemcinctus ENSDNOG000000109072 retrocopies
retro_dnov_205, retro_dnov_468,
Echinops telfairi ENSETEG000000120351 retrocopy
retro_etel_584,
Homo sapiens ENSG000000624852 retrocopies
retro_hsap_1972, retro_hsap_3621,
Gorilla gorilla ENSGGOG000000090962 retrocopies
retro_ggor_1432, retro_ggor_2445,
Macropus eugenii ENSMEUG000000056572 retrocopies
retro_meug_1078, retro_meug_1304,
Microcebus murinus ENSMICG000000176592 retrocopies
retro_mmur_1322, retro_mmur_394,
Macaca mulatta ENSMMUG000000024832 retrocopies
retro_mmul_1502, retro_mmul_1840,
Mus musculus ENSMUSG00000005683 1 retrocopy
retro_mmus_258 ,
Nomascus leucogenys ENSNLEG000000175142 retrocopies
retro_nleu_1201, retro_nleu_809,
Oryctolagus cuniculus ENSOCUG000000072161 retrocopy
retro_ocun_1183,
Pongo abelii ENSPPYG000000046541 retrocopy
retro_pabe_2972,
Rattus norvegicus ENSRNOG000000235201 retrocopy
retro_rnor_2518,
Sorex araneus ENSSARG000000100932 retrocopies
retro_sara_360, retro_sara_628,
Sus scrofa ENSSSCG000000210911 retrocopy
retro_sscr_321,
Sus scrofa ENSSSCG000000228581 retrocopy
retro_sscr_322,
Tupaia belangeri ENSTBEG000000064251 retrocopy
retro_tbel_4652,
Tarsius syrichta ENSTSYG000000044831 retrocopy
retro_tsyr_1659,


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