RetrogeneDB ID:

retro_mmus_1659

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:17:68371451..68371872(-)
Located in intron of:ENSMUSG00000041565
Retrocopy
information
Ensembl ID:ENSMUSG00000090224
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Prdx1
Ensembl ID:ENSMUSG00000028691
Aliases:None
Description:peroxiredoxin 1 [Source:MGI Symbol;Acc:MGI:99523]


Retrocopy-Parental alignment summary:






>retro_mmus_1659
ATGTCTGCAGGAAATGTAAAAATTTGGACATCTGGCTCCCAACTTCAAAGTTACGGCTGTTTATGCCAGATGGACAATTC
AAAGATATCGGCCTAAGTGAATACAGAGGAAAATATGTTGTGTTCTTCTTTTACCCTCTTGACTTTACTTTTGTGTGTCC
CACAGAAATCATTGCTTTCAGTGATAGAGCAGATTTTAAGAAACTCAACTGCCAAGTGATTGGAACTTCTGTGGATTCTT
ACTTCTGTCATCTGTCATGGAACAACACACCCAAGAAACAAGGAGGATGGGACCCATGAACATTCCCTTAATATCAATTT
CCAAGTGGACCATTGCTCAGGATTATGGAGTCTTAAAGGCTGATGAAGGTATCTCTCTCAGGGGCCTCTTTATTATTGAT
GATAAAGGTATTCTTTGACAA

ORF - retro_mmus_1659 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.42 %
Parental protein coverage: 80.11 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMSSGNAKI-GYPAPNFKATAV-MPDGQFKDISLSEYKGKYVVFFFYPLDFTFVCPTEIIAFSDRADEFKK
MS.GN.KI.G..APNFK.TAV.MPDGQFKDI.LSEY.GKYVVFFFYPLDFTFVCPTEIIAFSDRAD.FKK
RetrocopyMSAGNVKI>GHLAPNFKVTAV>MPDGQFKDIGLSEYRGKYVVFFFYPLDFTFVCPTEIIAFSDRAD-FKK
ParentalLNCQVIGASVDSHFCHLAWINTPKKQGG-LGPMNIPLISDPKRTIAQDYGVLKADEGISFRGLFIIDDKG
LNCQVIG.SVDS.FCHL.W.NTPKKQGG..GPMNIPLIS..K.TIAQDYGVLKADEGIS.RGLFIIDDKG
RetrocopyLNCQVIGTSVDSYFCHLSWNNTPKKQGG<MGPMNIPLISISKWTIAQDYGVLKADEGISLRGLFIIDDKG
ParentalILRQ
IL.Q
RetrocopyIL*Q

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 .02 RPM 62 .31 RPM
SRP007412_cerebellum 0 .00 RPM 37 .21 RPM
SRP007412_heart 0 .00 RPM 97 .38 RPM
SRP007412_kidney 0 .04 RPM 222 .20 RPM
SRP007412_liver 0 .03 RPM 363 .61 RPM
SRP007412_testis 0 .14 RPM 28 .86 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_1659 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_1659 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_1659 retrocopy 5' end.

Lab - click to see more details

retro_mmus_1659 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_1659 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 32 parental genes, and 87 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000136322 retrocopies
retro_amel_1116, retro_amel_539,
Bos taurus ENSBTAG000000036422 retrocopies
retro_btau_1299, retro_btau_1446,
Canis familiaris ENSCAFG000000045675 retrocopies
retro_cfam_1313, retro_cfam_270, retro_cfam_577, retro_cfam_834, retro_cfam_988,
Choloepus hoffmanni ENSCHOG000000033585 retrocopies
retro_chof_1140, retro_chof_134, retro_chof_1714, retro_chof_2035, retro_chof_2450,
Ciona intestinalis ENSCING000000030021 retrocopy
retro_cint_8,
Callithrix jacchus ENSCJAG000000048072 retrocopies
retro_cjac_1201, retro_cjac_2884,
Cavia porcellus ENSCPOG000000141373 retrocopies
retro_cpor_1079, retro_cpor_290, retro_cpor_398,
Dasypus novemcinctus ENSDNOG000000184881 retrocopy
retro_dnov_2071,
Dipodomys ordii ENSDORG000000089751 retrocopy
retro_dord_727,
Equus caballus ENSECAG000000086781 retrocopy
retro_ecab_81,
Echinops telfairi ENSETEG0000000792211 retrocopies
retro_etel_112, retro_etel_1157, retro_etel_1245, retro_etel_1442, retro_etel_1838, retro_etel_2121, retro_etel_2122, retro_etel_308, retro_etel_367, retro_etel_460, retro_etel_556,
Felis catus ENSFCAG000000284841 retrocopy
retro_fcat_1714,
Homo sapiens ENSG000001174501 retrocopy
retro_hsap_4230,
Macropus eugenii ENSMEUG000000068204 retrocopies
retro_meug_1694, retro_meug_1711, retro_meug_2059, retro_meug_662,
Macaca mulatta ENSMMUG000000062211 retrocopy
retro_mmul_762,
Monodelphis domestica ENSMODG000000023822 retrocopies
retro_mdom_1787, retro_mdom_555,
Mus musculus ENSMUSG000000051612 retrocopies
retro_mmus_2403, retro_mmus_472,
Mus musculus ENSMUSG000000249971 retrocopy
retro_mmus_2443,
Mus musculus ENSMUSG00000028691 5 retrocopies
retro_mmus_1466, retro_mmus_1659 , retro_mmus_1786, retro_mmus_3129, retro_mmus_3167,
Nomascus leucogenys ENSNLEG000000145242 retrocopies
retro_nleu_1040, retro_nleu_1627,
Oryctolagus cuniculus ENSOCUG000000059512 retrocopies
retro_ocun_1064, retro_ocun_1124,
Otolemur garnettii ENSOGAG000000023034 retrocopies
retro_ogar_1219, retro_ogar_1333, retro_ogar_1588, retro_ogar_486,
Pongo abelii ENSPPYG000000014111 retrocopy
retro_pabe_3409,
Pan troglodytes ENSPTRG000000006751 retrocopy
retro_ptro_2874,
Pteropus vampyrus ENSPVAG000000150011 retrocopy
retro_pvam_179,
Rattus norvegicus ENSRNOG000000171948 retrocopies
retro_rnor_1401, retro_rnor_1488, retro_rnor_1574, retro_rnor_1656, retro_rnor_1736, retro_rnor_2063, retro_rnor_2292, retro_rnor_2401,
Sorex araneus ENSSARG000000047035 retrocopies
retro_sara_153, retro_sara_370, retro_sara_399, retro_sara_633, retro_sara_95,
Sus scrofa ENSSSCG000000039141 retrocopy
retro_sscr_719,
Ictidomys tridecemlineatus ENSSTOG000000234132 retrocopies
retro_itri_631, retro_itri_817,
Tupaia belangeri ENSTBEG000000159974 retrocopies
retro_tbel_3922, retro_tbel_4017, retro_tbel_4024, retro_tbel_4669,
Tarsius syrichta ENSTSYG000000110311 retrocopy
retro_tsyr_1781,
Tursiops truncatus ENSTTRG000000088584 retrocopies
retro_ttru_1350, retro_ttru_1878, retro_ttru_234, retro_ttru_36,


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