RetrogeneDB ID:

retro_mmus_80

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:8:92901484..92902228(+)
Located in intron of:ENSMUSG00000033192
Retrocopy
information
Ensembl ID:ENSMUSG00000078144
Aliases:Capns2, 2310005G05Rik, 30K-2
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Capns1
Ensembl ID:ENSMUSG00000001794
Aliases:Capns1, Capa-4, Capa4, Capn4, D7Ertd146e
Description:calpain, small subunit 1 [Source:MGI Symbol;Acc:MGI:88266]


Retrocopy-Parental alignment summary:






>retro_mmus_80
ATGTTTCTCGCAAAGGCGATCCTGGAAGGTGCAGATCGGGGGCTTGGAGGGGCTCTTGGAGGCCTTCTTGGAGGAGGTGG
TCAGGCAAGAGCAGGCGGGGGCAACATCGGGGGAATCCTTGGAGGAATTGTCAATTTTATCAGCGAGGCTGCCGCAGCTC
AGTACACCCCAGAGCCGCCTCCCCAACAGCAGCATTTTACCGTCGTGGAGGCCTCAGAAAGTGAGGAAGTCAGACGTTTT
CGGCAGCAATTTACACAGCTGGCTGGACCCGACATGGAGGTGGGTGCTACTGACCTGATGAATATTCTCAACAAAGTCCT
TTCTAAGCATAAAGAGCTGAAGACAGAGGGCTTCAGCCTTGATACCTGTAGGAGCATTGTGTCTGTCATGGACAGTGACA
CCACAGGGAAACTGGGATTTGAGGAATTTAAGTACCTGTGGAACAACATCAAGAAATGGCAGTGTGTTTTCAAGCAGTAC
GACAGTGACCATTCTGGCTCCCTCGGAAGCTCCCAGCTGCACGGGGCCATGCAGGCAGCGGGCTTCCAGCTCAATGAGCA
ACTTTACCTAATGATTGTCCGTCGGTATGCTGACGAAGATGGCGGGATGGATTTTAACAACTTTATCAGCTGCCTGGTTC
GCCTGGATGCTATGTTTCGAGCTTTCAAGGCTCTGGACCGAGATAGGGATGGCCTGATTCAGGTGTCCATCCGAGAATGG
CTGCAGCTGACCATGTATTCCTGA

ORF - retro_mmus_80 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.77 %
Parental protein coverage: 88.81 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalLISGAAGGGGGGGGGMGLGGGG---GGGGTAMRILGGVISAISEAAA-QYNPEPPPPRSHYSNIEANESE
...GA..G.GG..GG..LGGGG....GGG....ILGG....ISEAAA.QY.PEPPP...H....EA.ESE
RetrocopyILEGADRGLGGALGGL-LGGGGQARAGGGNIGGILGGIVNFISEAAAAQYTPEPPPQQQHFTVVEASESE
ParentalEVRQFRKLFVQLAGDDMEVSATELMNILNKVVTRHPDLKTDGFGIDTCRSMVAVMDSDTTGKLGFEEFKY
EVR.FR..F.QLAG.DMEV.AT.LMNILNKV...H..LKT.GF..DTCRS.V.VMDSDTTGKLGFEEFKY
RetrocopyEVRRFRQQFTQLAGPDMEVGATDLMNILNKVLSKHKELKTEGFSLDTCRSIVSVMDSDTTGKLGFEEFKY
ParentalLWNNIKKWQAIYKRFDTDRSGTIGSHELPGAFEAAGFHLNEHLYSMIIRRYADESGNMDFDNFISCLVRL
LWNNIKKWQ...K..D.D.SG..GS..L.GA..AAGF.LNE.LY.MI.RRYADE.G.MDF.NFISCLVRL
RetrocopyLWNNIKKWQCVFKQYDSDHSGSLGSSQLHGAMQAAGFQLNEQLYLMIVRRYADEDGGMDFNNFISCLVRL
ParentalDAMFRAFKSLDKNGTGQIQVNIQEWLQLTMYS
DAMFRAFK.LD....G.IQV.I.EWLQLTMYS
RetrocopyDAMFRAFKALDRDRDGLIQVSIREWLQLTMYS

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 .40 RPM 111 .60 RPM
SRP007412_cerebellum 0 .04 RPM 161 .31 RPM
SRP007412_heart 0 .00 RPM 265 .70 RPM
SRP007412_kidney 0 .06 RPM 196 .98 RPM
SRP007412_liver 0 .03 RPM 77 .75 RPM
SRP007412_testis 0 .91 RPM 188 .17 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_mmus_80 was not detected

EST - click to see more details

1 EST(s) were mapped to retro_mmus_80 retrocopy
EST ID Start End Identity Match Mis-match Score
EH109772 92901645 92901921 100 276 0 276

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_1453331022 libraries 39 libraries 8 libraries 2 libraries 1 library
TSS #2 TSS_145334959 libraries 43 libraries 43 libraries 7 libraries 20 libraries
TSS #3 TSS_145335996 libraries 43 libraries 20 libraries 5 libraries 8 libraries
TSS #4 TSS_1453361033 libraries 25 libraries 14 libraries 0 libraries 0 libraries
TSS #5 TSS_145337984 libraries 26 libraries 37 libraries 8 libraries 17 libraries

The graphical summary, for retro_mmus_80 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_80 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_80 has 10 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_98
Pan troglodytes retro_ptro_1112
Gorilla gorilla retro_ggor_1241
Pongo abelii retro_pabe_1359
Macaca mulatta retro_mmul_1567
Rattus norvegicus retro_rnor_1447
Bos taurus retro_btau_692
Sus scrofa retro_sscr_73
Canis familiaris retro_cfam_942
Equus caballus retro_ecab_707
Parental genes homology:
Parental genes homology involve 26 parental genes, and 36 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000005111 retrocopy
retro_acar_205,
Ailuropoda melanoleuca ENSAMEG000000010241 retrocopy
retro_amel_136,
Bos taurus ENSBTAG000000148722 retrocopies
retro_btau_1126, retro_btau_692,
Canis familiaris ENSCAFG000000313141 retrocopy
retro_cfam_942,
Callithrix jacchus ENSCJAG000000095941 retrocopy
retro_cjac_2940,
Cavia porcellus ENSCPOG000000001151 retrocopy
retro_cpor_1131,
Equus caballus ENSECAG000000122101 retrocopy
retro_ecab_707,
Felis catus ENSFCAG000000141491 retrocopy
retro_fcat_1691,
Homo sapiens ENSG000001262471 retrocopy
retro_hsap_98,
Gorilla gorilla ENSGGOG000000036992 retrocopies
retro_ggor_1241, retro_ggor_263,
Myotis lucifugus ENSMLUG000000249441 retrocopy
retro_mluc_2336,
Macaca mulatta ENSMMUG000000002492 retrocopies
retro_mmul_1334, retro_mmul_1567,
Monodelphis domestica ENSMODG000000141791 retrocopy
retro_mdom_410,
Mustela putorius furoENSMPUG000000056171 retrocopy
retro_mputfur_444,
Mus musculus ENSMUSG00000001794 1 retrocopy
retro_mmus_80 ,
Nomascus leucogenys ENSNLEG000000117122 retrocopies
retro_nleu_1328, retro_nleu_992,
Ornithorhynchus anatinus ENSOANG000000027361 retrocopy
retro_oana_113,
Pongo abelii ENSPPYG000000098982 retrocopies
retro_pabe_1359, retro_pabe_448,
Pelodiscus sinensis ENSPSIG000000127931 retrocopy
retro_psin_45,
Pan troglodytes ENSPTRG000000108872 retrocopies
retro_ptro_1112, retro_ptro_168,
Pteropus vampyrus ENSPVAG000000128853 retrocopies
retro_pvam_1375, retro_pvam_639, retro_pvam_737,
Rattus norvegicus ENSRNOG000000457472 retrocopies
retro_rnor_1447, retro_rnor_2145,
Sorex araneus ENSSARG000000042661 retrocopy
retro_sara_215,
Sus scrofa ENSSSCG000000301492 retrocopies
retro_sscr_495, retro_sscr_73,
Ictidomys tridecemlineatus ENSSTOG000000262351 retrocopy
retro_itri_342,
Vicugna pacos ENSVPAG000000080741 retrocopy
retro_vpac_64,


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