RetrogeneDB ID:

retro_mmus_3265

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:9:39074101..39074899(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Actg1
Ensembl ID:ENSMUSG00000062825
Aliases:Actg1, AL023024, Actg, Actl, E51
Description:actin, gamma, cytoplasmic 1 [Source:MGI Symbol;Acc:MGI:87906]


Retrocopy-Parental alignment summary:






>retro_mmus_3265
ATGGAAGAAGAAATCGCCACACTCGTCATTGTCAATGGCTCCAGCATGTGCAAAGCTGGCTTTGCTGGAGACGACGCCCC
CAGGGCCGTGTTCCCTTCCATCGTAGGGTGCCCCCGACACCAGGACGTCATGGTGGGCATGGGCCAGAAAGACTCGTATG
TGGGTGACAAGGCCCAGAGCAAGAGGGGTATCCTGACCCTGAAGTACCCTATCGAACACGGCATTGTCACCAACTGGGAT
GACATGGAGAAGATCTGGCACCACACCTTCTACAATGAGCTGCGTGTGGCCCCTGAGGAGCACCCGGTGCTTCTGACCGA
GGCCCCCCTGAACCCCAAAGCTAACAGAGAGAAGATGACGCAGATAATGTTTGAAACCTTCAATACCCCAGCCATGTACG
TGGCCATTCAGGCGGTGCTGTCCTTGTATGCATCTGGGTGCACCACTGGCATTGTCATGGACTCTGGTGACAGGGTCACA
CACACAGTGCCCATCTATGAGGGCTACGCCCTTCCCCATGCCGTCTTGCGTCTGGACCTGGCTGGTCGGGTCCTGACAGA
CTACCTCATGAAGATCCTGACTGAACGGGGCTACAGCTTTACCACCACTGCTAAGAGGGAAATTGTTCGAGACATAAAGG
AGAAGCTGTGCTATGTTGCCCTGTATTTTGAGCAAGAAATGGCTACTGCTACATCATCTTCCTCCTTGGAGAAGAGTTAC
GAGCTGCCCGATGGGCAAGTTATCACCATCGGCAATGAGCGGTTCCGGTGTCCAGAGGCACTCTTCCAGACTTCCTTC

ORF - retro_mmus_3265 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.74 %
Parental protein coverage: 70.93 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMEEEIAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYP
MEEEIA.LVI.NGS.MCKAGFAGDDAPRAVFPSIVG.PRHQ.VMVGMGQKDSYVGD.AQSKRGILTLKYP
RetrocopyMEEEIATLVIVNGSSMCKAGFAGDDAPRAVFPSIVGCPRHQDVMVGMGQKDSYVGDKAQSKRGILTLKYP
ParentalIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVL
IEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVL
RetrocopyIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVL
ParentalSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVR
SLYASG.TTGIVMDSGD.VTHTVPIYEGYALPHA.LRLDLAGR.LTDYLMKILTERGYSFTTTA.REIVR
RetrocopySLYASGCTTGIVMDSGDRVTHTVPIYEGYALPHAVLRLDLAGRVLTDYLMKILTERGYSFTTTAKREIVR
ParentalDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSF
DIKEKLCYVAL.FEQEMATA.SSSSLEKSYELPDGQVITIGNERFRCPEALFQ.SF
RetrocopyDIKEKLCYVALYFEQEMATATSSSSLEKSYELPDGQVITIGNERFRCPEALFQTSF

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 .07 RPM 87 .12 RPM
SRP007412_cerebellum 0 .04 RPM 43 .55 RPM
SRP007412_heart 0 .50 RPM 49 .59 RPM
SRP007412_kidney 0 .17 RPM 94 .88 RPM
SRP007412_liver 0 .03 RPM 11 .31 RPM
SRP007412_testis 0 .14 RPM 97 .38 RPM
RNA Polymerase II actvity near the 5' end of retro_mmus_3265 was not detected
No EST(s) were mapped for retro_mmus_3265 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_149635176 libraries380 libraries450 libraries59 libraries7 libraries

The graphical summary, for retro_mmus_3265 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_3265 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_3265 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 23 parental genes, and 70 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000152383 retrocopies
Ailuropoda melanoleuca ENSAMEG000000160151 retrocopy
Callithrix jacchus ENSCJAG000000028853 retrocopies
Cavia porcellus ENSCPOG000000121011 retrocopy
Equus caballus ENSECAG000000186001 retrocopy
Felis catus ENSFCAG000000264342 retrocopies
Homo sapiens ENSG0000018400910 retrocopies
Gallus gallus ENSGALG000000287491 retrocopy
Gorilla gorilla ENSGGOG000000140436 retrocopies
Loxodonta africana ENSLAFG000000091671 retrocopy
Monodelphis domestica ENSMODG000000026473 retrocopies
Mustela putorius furoENSMPUG000000116101 retrocopy
Mus musculus ENSMUSG000000252281 retrocopy
Mus musculus ENSMUSG000000295807 retrocopies
Mus musculus ENSMUSG00000062825 7 retrocopies
Nomascus leucogenys ENSNLEG000000155063 retrocopies
Petromyzon marinus ENSPMAG000000041611 retrocopy
Pongo abelii ENSPPYG0000000873511 retrocopies
Pelodiscus sinensis ENSPSIG000000021022 retrocopies
Rattus norvegicus ENSRNOG000000367011 retrocopy
Sus scrofa ENSSSCG000000283551 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000068682 retrocopies
Xenopus tropicalis ENSXETG000000251161 retrocopy



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