RetrogeneDB ID:

retro_mmus_791

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:11:55118103..55118795(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000044751
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Atp5f1
Ensembl ID:ENSMUSG00000000563
Aliases:Atp5f1, C76477
Description:ATP synthase, H+ transporting, mitochondrial F0 complex, subunit B1 [Source:MGI Symbol;Acc:MGI:1100495]


Retrocopy-Parental alignment summary:






>retro_mmus_791
GGGGTATTACAGGCAACAAGGGCTTTTCACACAGGACAGCCTCGCCTTGCCCCTCTACCACCTCTTCCTGAATATGGAGG
AAAAGTGCGTCTTGGGCTGATTCCTGAGGAATTTTTCCAGTTCCTTTACCCTAAGACTGTGTAACAGGACCCTATGTGCT
TGGAACTGGACTTAGCTTGTATTTTCTATCCAAAGAAATATATGTGATTACCCCAGAGACCTTCTCTACCATATCAGTAG
TAGGGTTGATTGTCTATGTGATTAAGAAATATGGCGCCCCTTTTGGAGAATTTATTGACAAACTTAATGAGGAAAAAATT
GCTCAACTAGAAGAAGTAAAGCAGTCGAGCATGAAACAAATCCAGGATGCAATCGACATGGAGAAGGCACAGCAGGCACT
GGTTCAGAACCGCCATTACCTCTTCGACGTGCAGAGGAATAACATTGCCCTGGCCTTGGAGGTCACTTACCGGGAACGGC
TACATAAAGCATATAAGGAGGTAAAGAATCGCCTGGACTACCACATCTCTGTACAGAACATGATGCGTCGCAAGGAGGAA
GAACGCATGATAGACTGGGTAGAAAAGCATGTGGTGAAGAGCATTTCTGTACAGCAGGAAAAGGAGACCATTGCCAAGTG
CATTGAAGATCTAAAGCTGCTTGCAAAGAAGGCTCAAGCTCAGCCAATTATC

ORF - retro_mmus_791 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.41 %
Parental protein coverage: 90.23 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalGVLQATRAFHTGQPRLAPLPPLPEYGGKVRLGLIPEEFFQFLYPKTG-VTGPYVLGTGLSLYFLSKEIYV
GVLQATRAFHTGQPRLAPLPPLPEYGGKVRLGLIPEEFFQFLYPKT..VTGPYVLGTGLSLYFLSKEIYV
RetrocopyGVLQATRAFHTGQPRLAPLPPLPEYGGKVRLGLIPEEFFQFLYPKTV<VTGPYVLGTGLSLYFLSKEIYV
ParentalITPETFSTISVVGLIVYVIKKYGASFGEFIDKLNEEKIAQLEEVKQSSMKQIQDAIDMEKAQQALVQKRH
ITPETFSTISVVGLIVYVIKKYGA.FGEFIDKLNEEKIAQLEEVKQSSMKQIQDAIDMEKAQQALVQ.RH
RetrocopyITPETFSTISVVGLIVYVIKKYGAPFGEFIDKLNEEKIAQLEEVKQSSMKQIQDAIDMEKAQQALVQNRH
ParentalYLFDVQRNNIALALEVTYRERLHKAYKEVKNRLDYHISVQNMMRRKEEEHMIDWVEKHVVKSISVQQEKE
YLFDVQRNNIALALEVTYRERLHKAYKEVKNRLDYHISVQNMMRRKEEE.MIDWVEKHVVKSISVQQEKE
RetrocopyYLFDVQRNNIALALEVTYRERLHKAYKEVKNRLDYHISVQNMMRRKEEERMIDWVEKHVVKSISVQQEKE
ParentalTIAKCIEDLKLLAKKAQAQPIM
TIAKCIEDLKLLAKKAQAQPI.
RetrocopyTIAKCIEDLKLLAKKAQAQPII

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 .47 RPM 127 .98 RPM
SRP007412_cerebellum 0 .22 RPM 109 .77 RPM
SRP007412_heart 1 .68 RPM 436 .91 RPM
SRP007412_kidney 0 .94 RPM 295 .85 RPM
SRP007412_liver 0 .41 RPM 166 .47 RPM
SRP007412_testis 0 .32 RPM 55 .62 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_791 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_791 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_1390278 libraries192 libraries664 libraries118 libraries20 libraries

The graphical summary, for retro_mmus_791 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_791 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_791 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 26 parental genes, and 77 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000054331 retrocopy
retro_amel_1118,
Bos taurus ENSBTAG000000064411 retrocopy
retro_btau_745,
Callithrix jacchus ENSCJAG000000133539 retrocopies
retro_cjac_1943, retro_cjac_2270, retro_cjac_2482, retro_cjac_2747, retro_cjac_2815, retro_cjac_2854, retro_cjac_3067, retro_cjac_528, retro_cjac_833,
Cavia porcellus ENSCPOG000000140703 retrocopies
retro_cpor_1120, retro_cpor_448, retro_cpor_563,
Equus caballus ENSECAG000000185991 retrocopy
retro_ecab_494,
Echinops telfairi ENSETEG000000107133 retrocopies
retro_etel_105, retro_etel_1784, retro_etel_408,
Felis catus ENSFCAG000000283211 retrocopy
retro_fcat_1012,
Homo sapiens ENSG000001164596 retrocopies
retro_hsap_1705, retro_hsap_1951, retro_hsap_3673, retro_hsap_3762, retro_hsap_3812, retro_hsap_828,
Gorilla gorilla ENSGGOG000000052156 retrocopies
retro_ggor_1279, retro_ggor_1721, retro_ggor_2482, retro_ggor_2530, retro_ggor_2564, retro_ggor_678,
Loxodonta africana ENSLAFG000000048091 retrocopy
retro_lafr_602,
Microcebus murinus ENSMICG000000119921 retrocopy
retro_mmur_846,
Myotis lucifugus ENSMLUG000000124171 retrocopy
retro_mluc_2184,
Macaca mulatta ENSMMUG000000033133 retrocopies
retro_mmul_1086, retro_mmul_1659, retro_mmul_1791,
Mus musculus ENSMUSG00000000563 2 retrocopies
retro_mmus_2215, retro_mmus_791 ,
Nomascus leucogenys ENSNLEG000000039718 retrocopies
retro_nleu_172, retro_nleu_2090, retro_nleu_2153, retro_nleu_2154, retro_nleu_2546, retro_nleu_260, retro_nleu_524, retro_nleu_975,
Oryctolagus cuniculus ENSOCUG000000078091 retrocopy
retro_ocun_25,
Otolemur garnettii ENSOGAG000000114863 retrocopies
retro_ogar_2102, retro_ogar_2295, retro_ogar_2887,
Pongo abelii ENSPPYG000000010323 retrocopies
retro_pabe_2056, retro_pabe_3012, retro_pabe_3111,
Pan troglodytes ENSPTRG000000010995 retrocopies
retro_ptro_1154, retro_ptro_1305, retro_ptro_2553, retro_ptro_2586, retro_ptro_578,
Pteropus vampyrus ENSPVAG000000106043 retrocopies
retro_pvam_1061, retro_pvam_1110, retro_pvam_283,
Sorex araneus ENSSARG000000021073 retrocopies
retro_sara_424, retro_sara_428, retro_sara_610,
Sarcophilus harrisii ENSSHAG000000131851 retrocopy
retro_shar_700,
Ictidomys tridecemlineatus ENSSTOG000000076303 retrocopies
retro_itri_1146, retro_itri_1219, retro_itri_503,
Tarsius syrichta ENSTSYG000000004205 retrocopies
retro_tsyr_1226, retro_tsyr_1553, retro_tsyr_1852, retro_tsyr_502, retro_tsyr_511,
Tursiops truncatus ENSTTRG000000015461 retrocopy
retro_ttru_1654,
Vicugna pacos ENSVPAG000000002062 retrocopies
retro_vpac_154, retro_vpac_319,




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