RetrogeneDB ID:

retro_mmul_1013

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:13:118308324..118309166(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMMUG00000009165
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ESD
Ensembl ID:ENSMMUG00000004209
Aliases:None
Description:S-formylglutathione hydrolase [Source:RefSeq peptide;Acc:NP_001244408]


Retrocopy-Parental alignment summary:






>retro_mmul_1013
ATGGCACTGACACAGATTTCCAGCAACAAGTGCTTTGGGGGATTGCAGAAAGTTTTTGAACATGACAGTGTTGAACTGAA
CTGCAAAATGAAATTTGCTGTCTATTTACCACCAAAGGCAGAAACGGAAAAGTGCCCTGCACTGTATTGGCTCTCAGGTT
TAACTTGCACAGAACAAAATTTTATATCAAAATCTGGTTATCAAGCTGCTTCAGAACATGGTCTTGCTGTCATTGCTCCA
GATACCAGCCCTCGTGGCTACAATAGTAAAGGAGAAGATGAGAGCTGGGACTTTGGCACTGGTGCTGGATTTTATGTTGA
TACCACTGAAGATCCTTGGAAAACCAACTACAGAATGTACTCTTATGTCATGGAGGAACTTCCCCAACTCATAAATGCCA
GTTTTCCAGTGGATCCCCAAAGGATGTCTATTTGTGGCCACTCCATGGGAGACCATGGAGCTCTGATCTGTGCTTTGAAA
AATCCTGGAAAATACAAATCTGTGTCAGCATTTGCTCCAATTTGCAACCCTGTACTCTGTCCCTGGGGCAAAAAAGTCTT
TAGTGGATATTTGGGAACAGATCAAAGTAAATGGAAGGCTTATGAGCTACCCGTCTTCTGAAATCCTATCTAGGATCTCA
GCTGGACATACTAATTGATCAAGGAAAAGATGACCAGTTTCTTTTAGATGGACAGTTACTCCCTGATAACTTCATAGCTG
CCTGTACAGAAAAGAAAATCCCCATTGTTTTTCGATTACAAGAGGGTTATGATCATAGCTACTACTTCATTGCAACATTT
ATTACTGACCACATCAGACATCATGCTAAATACCTGGATGCA

ORF - retro_mmul_1013 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.93 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMALKQISSNKCFGGLQKVFEHDSVELNCKMKFAVYLPPKAETEKCPALYWLSGLTCTEQNFISKSGYHQA
MAL.QISSNKCFGGLQKVFEHDSVELNCKMKFAVYLPPKAETEKCPALYWLSGLTCTEQNFISKSGY.QA
RetrocopyMALTQISSNKCFGGLQKVFEHDSVELNCKMKFAVYLPPKAETEKCPALYWLSGLTCTEQNFISKSGY-QA
ParentalASEHGLVVIAPDTSPRGCNIKGEDESWDFGTGAGFYVDATEDLWKTNYRMYSYVTEELPQLINANFPVDP
ASEHGL.VIAPDTSPRG.N.KGEDESWDFGTGAGFYVD.TED.WKTNYRMYSYV.EELPQLINA.FPVDP
RetrocopyASEHGLAVIAPDTSPRGYNSKGEDESWDFGTGAGFYVDTTEDPWKTNYRMYSYVMEELPQLINASFPVDP
ParentalQRMSVFGHSMGGHGALICALKNPGKYKSVSAFAPICNPVLCPWGKKAFSGYLGTDQSKWKAYD-ATYLVK
QRMS..GHSMG.HGALICALKNPGKYKSVSAFAPICNPVLCPWGKK.FSGYLGTDQSKWKAY..AT.L.K
RetrocopyQRMSICGHSMGDHGALICALKNPGKYKSVSAFAPICNPVLCPWGKKVFSGYLGTDQSKWKAYE<ATRLLK
ParentalSYPGSQLDILIDQGKDDQFLLDGQLLPDNFIAACTEKKIPVVFRLQEGYDHSYYFIATFITDHIRHHAKY
SY.GSQLDILIDQGKDDQFLLDGQLLPDNFIAACTEKKIP.VFRLQEGYDHSYYFIATFITDHIRHHAKY
RetrocopySYLGSQLDILIDQGKDDQFLLDGQLLPDNFIAACTEKKIPIVFRLQEGYDHSYYFIATFITDHIRHHAKY
ParentalLNA
L.A
RetrocopyLDA

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 23 .87 RPM
SRP007412_brain_prefrontal_cortex 0 .00 RPM 18 .25 RPM
SRP007412_cerebellum 0 .06 RPM 15 .30 RPM
SRP007412_heart 0 .18 RPM 25 .32 RPM
SRP007412_kidney 0 .00 RPM 65 .96 RPM
SRP007412_liver 0 .08 RPM 36 .97 RPM
SRP007412_testis 0 .04 RPM 17 .30 RPM

ChIP-Seq - click to see more details

Macaca mulatta was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_mmul_1013 retrocopy.

TSS - click to see more details

Macaca mulatta was not studied using FANTOM5 data.

Lab - click to see more details

retro_mmul_1013 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_1013 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 ENSMMUG00000004209 1 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 ENSMUSG000000219969 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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