RetrogeneDB ID:

retro_mmus_1052

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:13:98613500..98614491(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Cnn3
Ensembl ID:ENSMUSG00000053931
Aliases:Cnn3, 1600014M03Rik, C85854, Calpo3
Description:calponin 3, acidic [Source:MGI Symbol;Acc:MGI:1919244]


Retrocopy-Parental alignment summary:






>retro_mmus_1052
ATGACCCACTTCAACAAGGGCCCTTCCTACGGGCTCTCCGCCGAAGTTAAAGAACAAAATCGCATCCAAGTATGACCAGC
AGGCCGAGGAAGATCTGCCTAACTGGATAGAAGAGGTGACAGGCCTAGGCATTGGCACCAACTACCAGCTGGGGCTGAAG
GACGGCATCATCCTGTGCGAACTCATAAACAAGCTACAGTCAGGCTCTGTGAAAAAAGTCAATGAATCCTCACTAAATTG
GCCGCAGTTGGAGAATATCGGCAACTTCATTAAAGCTATCCAGGCTTACGGTATGAAGCCCCATGATATATTTGAAGCAA
ACGAACTCTTTGAGAATGGCAACATGACCCAGGTTCAGACGACACTGGTGGCTCTAGCAGGTCTGGTGAAAACAAAAGGA
TTCCATACAACCATTGACACTGGTGTTAAGTATGCAGAAAAACAAACAAGACGTTTTGATGAAGGCAAATTAAAGGCTGG
CCAGAGTGTAATTGGTTTACAGATGGGTACCAACAAATGTGCCAGCCAAGCGGGCACGACAGCCTATGGGACTCGGAGGC
ATCTTTATGATCCCAAGATGCAGACGGACAAACCCTTTGACCAGACCACGATTAGCCTGCAGATGGGCACCAACAAAGGA
GCCAGCCAGGCTGGGATGTTAACACCAGGTACCAGAAGAGACATCTATGACCAGAAGTTGACATTACAGCCAGTGGACAA
CTCGACCATTTCTCTACAGATGGGCACCAACAAAACTGCTTCCCAGAAAGGAATGAGCGTGTATTGGCTTGGGCGGCAAG
TGTATGACCCCAAGTACTGTGCCGCACCCACAGAACCTGTCATTCACAACGGAAGCCAGGGCACGGGCACCAATGGGTCG
GAAATCAGTGATAGCGATTATCAGGCAGAATACCCCGATAAATAGCATGGCGAGCACCCAGATGACTACCCTCGAGAGTA
CCAGTATGGCGATGACCAGGGCATTGATTAT

ORF - retro_mmus_1052 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.77 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMTHFNKGPSYGLSAEVK-NKIASKYDQQAEEDLRNWIEEVTGLGIGTNFQLGLKDGIILCELINKLQPGS
MTHFNKGPSYGLSAEVK.NKIASKYDQQAEEDL.NWIEEVTGLGIGTN.QLGLKDGIILCELINKLQ.GS
RetrocopyMTHFNKGPSYGLSAEVK>NKIASKYDQQAEEDLPNWIEEVTGLGIGTNYQLGLKDGIILCELINKLQSGS
ParentalVKKVNESSLNWPQLENIGNFIKAIQAYGMKPHDIFEANDLFENGNMTQVQTTLVALAGLAKTKGFHTTID
VKKVNESSLNWPQLENIGNFIKAIQAYGMKPHDIFEAN.LFENGNMTQVQTTLVALAGL.KTKGFHTTID
RetrocopyVKKVNESSLNWPQLENIGNFIKAIQAYGMKPHDIFEANELFENGNMTQVQTTLVALAGLVKTKGFHTTID
ParentalIGVKYAEKQTRRFDEGKLKAGQSVIGLQMGTNKCASQAGMTAYGTRRHLYDPKMQTDKPFDQTTISLQMG
.GVKYAEKQTRRFDEGKLKAGQSVIGLQMGTNKCASQAG.TAYGTRRHLYDPKMQTDKPFDQTTISLQMG
RetrocopyTGVKYAEKQTRRFDEGKLKAGQSVIGLQMGTNKCASQAGTTAYGTRRHLYDPKMQTDKPFDQTTISLQMG
ParentalTNKGASQAGMLAPGTRRDIYDQKLTLQPVDNSTISLQMGTNKVASQKGMSVYGLGRQVYDPKYCAAPTEP
TNKGASQAGML.PGTRRDIYDQKLTLQPVDNSTISLQMGTNK.ASQKGMSVY.LGRQVYDPKYCAAPTEP
RetrocopyTNKGASQAGMLTPGTRRDIYDQKLTLQPVDNSTISLQMGTNKTASQKGMSVYWLGRQVYDPKYCAAPTEP
ParentalVIHNGSQGTGTNGSEISDSDYQAEYPDEYHGEYPDDYPREYQYGDDQGIDY
VIHNGSQGTGTNGSEISDSDYQAEYPD..HGE.PDDYPREYQYGDDQGIDY
RetrocopyVIHNGSQGTGTNGSEISDSDYQAEYPDK*HGEHPDDYPREYQYGDDQGIDY

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(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 .05 RPM 46 .98 RPM
SRP007412_cerebellum 0 .00 RPM 53 .36 RPM
SRP007412_heart 0 .03 RPM 34 .71 RPM
SRP007412_kidney 0 .15 RPM 122 .12 RPM
SRP007412_liver 0 .08 RPM 111 .83 RPM
SRP007412_testis 0 .00 RPM 5 .58 RPM
RNA Polymerase II actvity near the 5' end of retro_mmus_1052 was not detected
No EST(s) were mapped for retro_mmus_1052 retrocopy.


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_31958479 libraries419 libraries170 libraries4 libraries0 libraries
TSS #2 TSS_31959834 libraries69 libraries89 libraries70 libraries10 libraries

The graphical summary, for retro_mmus_1052 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)

retro_mmus_1052 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_1052 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 13 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000167071 retrocopy
Bos taurus ENSBTAG000000203451 retrocopy
Callithrix jacchus ENSCJAG000000181283 retrocopies
Echinops telfairi ENSETEG000000100951 retrocopy
Homo sapiens ENSG000001175191 retrocopy
Gorilla gorilla ENSGGOG000000138701 retrocopy
Macropus eugenii ENSMEUG000000029212 retrocopies
Macaca mulatta ENSMMUG000000016901 retrocopy
Monodelphis domestica ENSMODG000000043261 retrocopy
Mus musculus ENSMUSG000000046652 retrocopies
Mus musculus ENSMUSG00000053931 2 retrocopies
retro_mmus_1052 , retro_mmus_2544,
Sarcophilus harrisii ENSSHAG000000026701 retrocopy
Vicugna pacos ENSVPAG000000048892 retrocopies



Copyright © RetrogeneDB 2014-2017