RetrogeneDB ID:

retro_mmus_1043

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:13:81064683..81065800(+)
Located in intron of:ENSMUSG00000097098
Retrocopy
information
Ensembl ID:ENSMUSG00000043889
Aliases:None
Status:KNOWN_PSEUDOGENE
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_1043
ATGGAAGAAGAAATTGCCGCACTCGTCATTGACAATGGCTCCGGCATGTGCAAAGCCGGCTTTGCTGGCGACGACGCCCC
CAGGGCCGTGTTCCCTTCCATCGTAGGGCGCCCCCGACACCAGGGCGTCATGGTGGGCATGGGCCAGAAAGACTCGTACG
TGGGTGACGAGGCCCAGAGCAAGAGGGGTATCCTGACCCTGAAGTACCCTATCGAACACGGCATTGTCACTAACTGGGAC
GACATGGAGAAGATCTGGCACCACACCTTCTACAATGAGCTGCGTGTGGCTCCTGAGGAGCACCCGGTGCGAGGCCCCCC
TGAACCCCAAAGCTAACAGAGAGAAGATGACGCAGATAATGTTTGAAACCTTCAATACCCCAGCCATGTACGTGGCCATT
CAGGCGGTGCTGTCCTTGTATGCATCTGGGCGCACCACTGGCATTGTCATGGACTCTGGTGACAGGGTCACACACACAGT
GCCCATCTATGAGGGCTACGCCCTTCCCCACGCCATCTTGCGTCTGGACCTGGCTGGCCGGGACCTGACAGACTACCTCA
TGAAGATCCTGACTGAACGGGGCTACAGCTTTACCACCACTGCTGAAAGGGAAATTGTTCGTGACATAAAGGAGAAGCTG
TGCTATGTTGCCCTGGATTTTGAGCAAGAAATGGCTACTGCTGCATCATCTTCCTCCTTGGAGAAGAGTTACAAGCTGCC
CGACGGGCAGGTGATCACCATTGGCAATGAGCGGTTCCGTTGTCCGGAGGCACTCTTCCAGCCTTCCTTCCTGGGCATGG
AGTCCTGTGGTATCCATGAGACCACTTTCAACTCCATCATGAAGTGTGATGTGGATATCTGCAAAGACCTGTATGCCAAT
ACAGTGCTGTCTGGTGGTACCACCATGTACCCAGGCATTGCTGACAGGATGCAGAAGGAGATCACAGCCCTAGCACCTAG
CACGATGAAGATTAAGATCATTGCTCCCCCTGAGCGCAAGTACTCAGTCTGGATCGGTGGCTCCATTCTGGCCTCACTGT
CCACCTTCCAGCAGATGTGGATCAGCAAGCAGGAGTATGATGAGTCGGGCCCCTCCATCGTCCACCGCAAATGCTTC

ORF - retro_mmus_1043 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.81 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMEEEIAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYP
MEEEIAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYP
RetrocopyMEEEIAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYP
ParentalIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPK-ANREKMTQIMFETFNTPAMYVAIQAV
IEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPV.....P..P..ANREKMTQIMFETFNTPAMYVAIQAV
RetrocopyIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPV---RGPPEPQ>ANREKMTQIMFETFNTPAMYVAIQAV
ParentalLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIV
LSLYASGRTTGIVMDSGD.VTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIV
RetrocopyLSLYASGRTTGIVMDSGDRVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIV
ParentalRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTF
RDIKEKLCYVALDFEQEMATAASSSSLEKSY.LPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTF
RetrocopyRDIKEKLCYVALDFEQEMATAASSSSLEKSYKLPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTF
ParentalNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASL
NSIMKCDVDI.KDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASL
RetrocopyNSIMKCDVDICKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASL
ParentalSTFQQMWISKQEYDESGPSIVHRKCF
STFQQMWISKQEYDESGPSIVHRKCF
RetrocopySTFQQMWISKQEYDESGPSIVHRKCF

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 .26 RPM 87 .12 RPM
SRP007412_cerebellum 0 .22 RPM 43 .55 RPM
SRP007412_heart 0 .25 RPM 49 .59 RPM
SRP007412_kidney 0 .37 RPM 94 .88 RPM
SRP007412_liver 0 .00 RPM 11 .31 RPM
SRP007412_testis 0 .37 RPM 97 .38 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_1043 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_1043 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_31239121 libraries178 libraries574 libraries182 libraries17 libraries

The graphical summary, for retro_mmus_1043 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_1043 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_1043 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
retro_acar_176, retro_acar_199, retro_acar_7,
Ailuropoda melanoleuca ENSAMEG000000160151 retrocopy
retro_amel_929,
Callithrix jacchus ENSCJAG000000028853 retrocopies
retro_cjac_139, retro_cjac_336, retro_cjac_377,
Cavia porcellus ENSCPOG000000121011 retrocopy
retro_cpor_361,
Equus caballus ENSECAG000000186001 retrocopy
retro_ecab_98,
Felis catus ENSFCAG000000264342 retrocopies
retro_fcat_257, retro_fcat_377,
Homo sapiens ENSG0000018400910 retrocopies
retro_hsap_1548, retro_hsap_1607, retro_hsap_2405, retro_hsap_2591, retro_hsap_2605, retro_hsap_3466, retro_hsap_3631, retro_hsap_409, retro_hsap_4818, retro_hsap_4935,
Gallus gallus ENSGALG000000287491 retrocopy
retro_ggal_6,
Gorilla gorilla ENSGGOG000000140436 retrocopies
retro_ggor_1495, retro_ggor_2338, retro_ggor_2449, retro_ggor_273, retro_ggor_413, retro_ggor_520,
Loxodonta africana ENSLAFG000000091671 retrocopy
retro_lafr_116,
Monodelphis domestica ENSMODG000000026473 retrocopies
retro_mdom_187, retro_mdom_59, retro_mdom_89,
Mustela putorius furoENSMPUG000000116101 retrocopy
retro_mputfur_279,
Mus musculus ENSMUSG000000252281 retrocopy
retro_mmus_2686,
Mus musculus ENSMUSG000000295807 retrocopies
retro_mmus_1613, retro_mmus_1677, retro_mmus_283, retro_mmus_2880, retro_mmus_3411, retro_mmus_3532, retro_mmus_761,
Mus musculus ENSMUSG00000062825 7 retrocopies
retro_mmus_1043 , retro_mmus_1524, retro_mmus_2383, retro_mmus_3128, retro_mmus_3265, retro_mmus_3607, retro_mmus_3705,
Nomascus leucogenys ENSNLEG000000155063 retrocopies
retro_nleu_1525, retro_nleu_1536, retro_nleu_1930,
Petromyzon marinus ENSPMAG000000041611 retrocopy
retro_pmar_4,
Pongo abelii ENSPPYG0000000873511 retrocopies
retro_pabe_1091, retro_pabe_1391, retro_pabe_1727, retro_pabe_2187, retro_pabe_2308, retro_pabe_2621, retro_pabe_2945, retro_pabe_3381, retro_pabe_3475, retro_pabe_3760, retro_pabe_600,
Pelodiscus sinensis ENSPSIG000000021022 retrocopies
retro_psin_25, retro_psin_4,
Rattus norvegicus ENSRNOG000000367011 retrocopy
retro_rnor_715,
Sus scrofa ENSSSCG000000283551 retrocopy
retro_sscr_389,
Ictidomys tridecemlineatus ENSSTOG000000068682 retrocopies
retro_itri_1675, retro_itri_531,
Xenopus tropicalis ENSXETG000000251161 retrocopy
retro_xtro_6,


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