RetrogeneDB ID:

retro_mmus_1237

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:14:3210973..3211832(-)
Located in intron of:ENSMUSG00000091849
Retrocopy
information
Ensembl ID:ENSMUSG00000095512
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Esd
Ensembl ID:ENSMUSG00000021996
Aliases:Esd, Es-10, Es10, FGH, sid478
Description:esterase D/formylglutathione hydrolase [Source:MGI Symbol;Acc:MGI:95421]


Retrocopy-Parental alignment summary:






>retro_mmus_1237
CCGAGGAGGAGAATGGCACTCAAACAGATTTCCAGCAACAGGTACTTTGGCGGGCTCCAGTAAGTTTTTGAACATAGCAG
TGTTGAGCTGAAATGTAAAATGAAATTTGCTGTCTACCTACCACCCCAGGCCGAGAGTGGAAAATGTCCAGCGCTTTACT
GGCTGTCTGGTTTAACTTGCACAGAACAAAATTTCATATCAAAGTCTGGCTATCAGCAAGCTGCCTCAGAGCCCGGCCTT
GTGGTCATTGCCCCTGATACCAGCCCTCGTGGCTGCAATATTAAAGGAGAAGATGACAGCTGGGACTTCGGCACTGGTGC
TGGGTTTTATGTGAATGCCACTGAAGATCCTTGGAAAGCTAACTACAGAATGTACTCTTATGTCACAGAGGAGCTTCCAC
AACTCATAAATGCCAATTTCCCAGTGGACCCACAGAGGATGGTCTATTTTTGATCACTCCATGAGAGGCCACGGAGCTCT
GATTTGTGCTTTGAAAAATCCTGGAAAATACAGATCTCTGTCAGCATTTGCTCCAATTTGCAACCCTGTGCTCTGTCCTT
GGGGCAAAAAAGCTTTTAGTGGATATTTGGGACCAGATGAAAGCAAATGGAAGGCATATGATGCAACCTGTCTCGTGAAG
TCCTATTCGGGTTCCCAGATTGACATCCTAATTGATCAAGGAAAAGATGACGAGATTCTTTCAAATGGGCAGTTACTCCC
TGATAACTTCATAGCTGCCTGCACAGAGAAGAAAATCCCTGTTGTTTTTAGGCTACAAGAGGGTTATGATCATAGCTACT
GCTTCATTGCAACCTTAATCGCTGACCACATCAGACACCATGCTAAGTACCTGAATGCA

ORF - retro_mmus_1237 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.47 %
Parental protein coverage: 96.95 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalPRRRMALKQISSNRCFGGLQKVFEHSSVELKCKMRFAVYLPPQAESGKCPALYWLSGLTCTEQNFISKSG
PRRRMALKQISSNR.FGGLQ.VFEHSSVELKCKM.FAVYLPPQAESGKCPALYWLSGLTCTEQNFISKSG
RetrocopyPRRRMALKQISSNRYFGGLQ*VFEHSSVELKCKMKFAVYLPPQAESGKCPALYWLSGLTCTEQNFISKSG
ParentalYQQAASEHGLVVIAPDTSPRGCNIKGEDDSWDFGTGAGFYVNATEDPWKANYRMYSYVTEELPQLINANF
YQQAASE.GLVVIAPDTSPRGCNIKGEDDSWDFGTGAGFYVNATEDPWKANYRMYSYVTEELPQLINANF
RetrocopyYQQAASEPGLVVIAPDTSPRGCNIKGEDDSWDFGTGAGFYVNATEDPWKANYRMYSYVTEELPQLINANF
ParentalPVDPQRM-SIFGHSMGGHGALICALKNPGKYRSVSAFAPICNPVLCSWGKKAFSGYLGPDESKWKAYDAT
PVDPQRM.SIF.HSM.GHGALICALKNPGKYRS.SAFAPICNPVLC.WGKKAFSGYLGPDESKWKAYDAT
RetrocopyPVDPQRM>SIFDHSMRGHGALICALKNPGKYRSLSAFAPICNPVLCPWGKKAFSGYLGPDESKWKAYDAT
ParentalCLVKAYSGSQIDILIDQGKDDEFLSNGQLLPDNFIAACTEKKIPVVFRLQEGYDHSYYFIATFIADHIRH
CLVK.YSGSQIDILIDQGKDDE.LSNGQLLPDNFIAACTEKKIPVVFRLQEGYDHSY.FIAT.IADHIRH
RetrocopyCLVKSYSGSQIDILIDQGKDDEILSNGQLLPDNFIAACTEKKIPVVFRLQEGYDHSYCFIATLIADHIRH
ParentalHAKYLNA
HAKYLNA
RetrocopyHAKYLNA

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 .00 RPM 34 .41 RPM
SRP007412_cerebellum 0 .00 RPM 20 .84 RPM
SRP007412_heart 0 .03 RPM 37 .70 RPM
SRP007412_kidney 0 .00 RPM 126 .60 RPM
SRP007412_liver 0 .00 RPM 101 .26 RPM
SRP007412_testis 0 .00 RPM 3 .70 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_1237 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_1237 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_1237 retrocopy 5' end.

Lab - click to see more details

retro_mmus_1237 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_1237 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 22 parental genes, and 52 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000133772 retrocopies
retro_amel_1085, retro_amel_1803,
Bos taurus ENSBTAG000000034151 retrocopy
retro_btau_908,
Canis familiaris ENSCAFG000000044732 retrocopies
retro_cfam_1381, retro_cfam_1762,
Callithrix jacchus ENSCJAG000000093802 retrocopies
retro_cjac_24, retro_cjac_257,
Cavia porcellus ENSCPOG000000110893 retrocopies
retro_cpor_1253, retro_cpor_1396, retro_cpor_568,
Dasypus novemcinctus ENSDNOG000000175532 retrocopies
retro_dnov_2502, retro_dnov_96,
Equus caballus ENSECAG000000243501 retrocopy
retro_ecab_808,
Felis catus ENSFCAG000000268262 retrocopies
retro_fcat_1641, retro_fcat_812,
Loxodonta africana ENSLAFG000000069011 retrocopy
retro_lafr_843,
Macaca mulatta ENSMMUG000000042091 retrocopy
retro_mmul_1013,
Monodelphis domestica ENSMODG000000112902 retrocopies
retro_mdom_1607, retro_mdom_1608,
Mustela putorius furoENSMPUG000000014942 retrocopies
retro_mputfur_1339, retro_mputfur_543,
Mus musculus ENSMUSG00000021996 9 retrocopies
retro_mmus_1159, retro_mmus_1160, retro_mmus_1161, retro_mmus_1162, retro_mmus_1163, retro_mmus_1166, retro_mmus_1168, retro_mmus_1236, retro_mmus_1237 ,
Oryctolagus cuniculus ENSOCUG000000099681 retrocopy
retro_ocun_709,
Otolemur garnettii ENSOGAG000000100481 retrocopy
retro_ogar_162,
Ochotona princeps ENSOPRG000000114612 retrocopies
retro_opri_230, retro_opri_845,
Procavia capensis ENSPCAG000000044021 retrocopy
retro_pcap_354,
Pteropus vampyrus ENSPVAG000000099103 retrocopies
retro_pvam_1309, retro_pvam_299, retro_pvam_87,
Rattus norvegicus ENSRNOG000000095122 retrocopies
retro_rnor_1053, retro_rnor_1593,
Sarcophilus harrisii ENSSHAG000000095813 retrocopies
retro_shar_307, retro_shar_337, retro_shar_570,
Ictidomys tridecemlineatus ENSSTOG000000028542 retrocopies
retro_itri_182, retro_itri_639,
Tupaia belangeri ENSTBEG000000051207 retrocopies
retro_tbel_1621, retro_tbel_1776, retro_tbel_2, retro_tbel_296, retro_tbel_3059, retro_tbel_3072, retro_tbel_3698,




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