RetrogeneDB ID:

retro_mmus_69

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:2:152687270..152687816(+)
Located in intron of:ENSMUSG00000019188
Retrocopy
information
Ensembl ID:ENSMUSG00000042814
Aliases:Mcts2, 2400002F11Rik
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Mcts1
Ensembl ID:ENSMUSG00000000355
Aliases:Mcts1, 1500019M23Rik, MCT-1
Description:malignant T cell amplified sequence 1 [Source:MGI Symbol;Acc:MGI:1916245]


Retrocopy-Parental alignment summary:






>retro_mmus_69
ATGTTCAAGAAATTTGACGAGAAGGAAAGTGTGTCCAACTGCATCCAACTGAAAACTTCCGTTATTAAGGGTATTAAGAG
CCAACTGACTGAGCAGTTTCCAGGTATCGAGCCGTGGCTTAATCAAATCATGCCTAAGAAAGATCCCGTCAAAATAGTGA
GATGCCATGAACACATGGAAATCCTTACAGTCAACGGAGAATTACTGTTTTTCAGGCAGAGAAAAGGACCTTTTTATCCA
ACGCTAAGACTACTTCACAAATACCCGTTTATCCTGCCACACCAGCAGGTCGACAAAGGAGCCATCAAATTTGTGCTCAG
TGGTGCAAATATCATGTGCCCGGGTTTAACGTCTCCTGGAGCGAAGCTCTACACTGCTGCAGTAGATACCATCGTGGCGG
TCATGGCAGAGGGGAAAGAGCATGCCCTGTGTGTCGGAGTCATGAAGATGGCTGCAGCAGACATTGAGAAAATCAACAAG
GGGATCGGCATTGAGAATATCCATTATCTAAATGACGGGCTGTGGCACATGAAGACATATAAGTGA

ORF - retro_mmus_69 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.92 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMFKKFDEKENVSNCIQLKTSVIKGIKNQLLEQFPGIEPWLNQIMPKKDPVKIVRCHEHIEILTVNGELLF
MFKKFDEKE.VSNCIQLKTSVIKGIK.QL.EQFPGIEPWLNQIMPKKDPVKIVRCHEH.EILTVNGELLF
RetrocopyMFKKFDEKESVSNCIQLKTSVIKGIKSQLTEQFPGIEPWLNQIMPKKDPVKIVRCHEHMEILTVNGELLF
ParentalFRQREGPFYPTLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPGAKLYPAAVDTIVAIMAEGKQ
FRQR.GPFYPTLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPGAKLY.AAVDTIVA.MAEGK.
RetrocopyFRQRKGPFYPTLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPGAKLYTAAVDTIVAVMAEGKE
ParentalHALCVGVMKMSAEDIEKVNKGIGIENIHYLNDGLWHMKTYK
HALCVGVMKM.A.DIEK.NKGIGIENIHYLNDGLWHMKTYK
RetrocopyHALCVGVMKMAAADIEKINKGIGIENIHYLNDGLWHMKTYK

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 5 .65 RPM 27 .01 RPM
SRP007412_cerebellum 4 .86 RPM 14 .46 RPM
SRP007412_heart 3 .83 RPM 8 .44 RPM
SRP007412_kidney 3 .93 RPM 14 .51 RPM
SRP007412_liver 2 .32 RPM 14 .53 RPM
SRP007412_testis 15 .55 RPM 1 .69 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_mmus_69 in 1 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF001XVA POLR2A 2:152686732..152687364

EST - click to see more details

1 EST(s) were mapped to retro_mmus_69 retrocopy
EST ID Start End Identity Match Mis-match Score
AA839136 152687293 152687486 98 189 4 185

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_81659840 libraries226 libraries3 libraries1 library2 libraries
TSS #2 TSS_81660314 libraries82 libraries542 libraries115 libraries19 libraries
TSS #3 TSS_81661276 libraries61 libraries161 libraries394 libraries180 libraries
TSS #4 TSS_81662289 libraries57 libraries191 libraries366 libraries169 libraries

The graphical summary, for retro_mmus_69 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_69 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_69 has 6 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2422
Pan troglodytes retro_ptro_1396
Gorilla gorilla retro_ggor_1507
Pongo abelii retro_pabe_1786
Macaca mulatta retro_mmul_626
Rattus norvegicus retro_rnor_1841
Parental genes homology:
Parental genes homology involve 26 parental genes, and 35 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000349921 retrocopy
retro_btau_116,
Canis familiaris ENSCAFG000000185451 retrocopy
retro_cfam_94,
Cavia porcellus ENSCPOG000000055021 retrocopy
retro_cpor_1411,
Equus caballus ENSECAG000000145971 retrocopy
retro_ecab_697,
Erinaceus europaeus ENSEEUG000000072581 retrocopy
retro_eeur_197,
Echinops telfairi ENSETEG000000154621 retrocopy
retro_etel_19,
Felis catus ENSFCAG000000084482 retrocopies
retro_fcat_1009, retro_fcat_310,
Homo sapiens ENSG000002321191 retrocopy
retro_hsap_2422,
Gorilla gorilla ENSGGOG000000094201 retrocopy
retro_ggor_1507,
Macropus eugenii ENSMEUG000000143281 retrocopy
retro_meug_1518,
Myotis lucifugus ENSMLUG000000151011 retrocopy
retro_mluc_16,
Macaca mulatta ENSMMUG000000090431 retrocopy
retro_mmul_626,
Monodelphis domestica ENSMODG000000103541 retrocopy
retro_mdom_203,
Mustela putorius furoENSMPUG000000014071 retrocopy
retro_mputfur_98,
Mus musculus ENSMUSG00000000355 3 retrocopies
retro_mmus_2504, retro_mmus_2505, retro_mmus_69 ,
Nomascus leucogenys ENSNLEG000000150211 retrocopy
retro_nleu_2442,
Oryctolagus cuniculus ENSOCUG000000143151 retrocopy
retro_ocun_212,
Pongo abelii ENSPPYG000000206872 retrocopies
retro_pabe_1786, retro_pabe_1833,
Pan troglodytes ENSPTRG000000222411 retrocopy
retro_ptro_1396,
Pteropus vampyrus ENSPVAG000000132493 retrocopies
retro_pvam_1323, retro_pvam_645, retro_pvam_867,
Rattus norvegicus ENSRNOG000000025632 retrocopies
retro_rnor_1841, retro_rnor_957,
Ictidomys tridecemlineatus ENSSTOG000000114962 retrocopies
retro_itri_1136, retro_itri_1468,
Tupaia belangeri ENSTBEG000000106662 retrocopies
retro_tbel_1485, retro_tbel_4265,
Tarsius syrichta ENSTSYG000000014401 retrocopy
retro_tsyr_55,
Tursiops truncatus ENSTTRG000000072081 retrocopy
retro_ttru_1587,
Vicugna pacos ENSVPAG000000018011 retrocopy
retro_vpac_138,




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