RetrogeneDB ID:

retro_ecab_899

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:6:34976979..34978083(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSECAG00000021719
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:GMCL1
Ensembl ID:ENSECAG00000016813
Aliases:None
Description:germ cell-less, spermatogenesis associated 1 [Source:HGNC Symbol;Acc:23843]


Retrocopy-Parental alignment summary:






>retro_ecab_899
GCCGGCCACGGCTTGTGTTACTGCCCGGGCAGCCGCAAGAGCAAGCGGAGCAGCGGGGCCTTCTGCTACTGTCACCCCGA
CTCCGAGACAGACGAGGATGAGGAGGAAGGGGACGAGCAGCAGCGGCTCCTCAACACCCCTCGAAGGAAAAAATTAAAGA
GTACCTCCAAATATATTTATCAAACATTATTTTTGAATGGTGAAAATAGCGACATTAAGATTTGTGCTCCAGGAGAAGAA
TGGAGTTTACACAAAATATGTTTATGTCAATCTGGCTACTTTTCTAGTATGTTCAGTGGTTCTTGGAAAGAATCCAGCAT
GAATATTATTGAACTGGAGATTCCTGATCAGAATATTGATATAGAAGCACTGCAGGTTGCATTTGGGTCACTGTATCAAG
ATGATGTCTTAATAAAGCCCAGTCGAGTTATTGCCATTTTGGCAGCAGCTTGTATGCTGCAGTTGGTTGGTTTAATACAG
CAGTGTGGTGAGACAATGAAGGAAACAATTAATGTGAAAACTGTGTGTGGCTATTACACATCAGCAGGGACCTATGGATT
AGATTCTGTAAAGAAAAAGTGCCTTGAATGGCTTCTAAACAATTTGATGACTCATCAGAATGTTGAACTTTTTAAAGAAC
TCAGTATAAATGTCATGAAGCAGCTTATTGGTTCATCTAACTTATTTGTGATGCAAGTGGAGATGGATGTATATACAGCT
CTTAAAAAGTGGATGTTTCTTCAACTTGTGCCTTCTTGGAATGGATCTTTAAAACAGCTTTTGACTGAAACAGATGTCTG
GTTTTCTAAGAGGAGAAAAGATTTTGAAGGTATGACCTTCCTTGAAACTGAGCAGGGAAAACCATTTGTGTCAGTATTCA
GACATTTAAGGTTACAGTATATTATCAGTGATTTGGCCTCTGCGAGAATTATTGAACAAGATTCTCTAGTACCTTCAGAA
TGGTTATCTTCTGTTTATAAACAGCAGTGGCTTGCTATGCTCCGGGCAGAACAAGACAGTGAGGTGGGGCCTCAAGAAAT
CAATAAAGAAGAATTAGAGGGAAATAGCATGAGGTGTGGTAGAAAGCTTGCCAAAGATGGTGAA

ORF - retro_ecab_899 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.83 %
Parental protein coverage: 75.31 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalAGHGFCYCPGSRKRKRSSG-FCYCHPD-ETDEDEEEGDEQQRLLNTPRRKKLKSTSKYIYQTLFLNGENS
AGHG.CYCPGSRK.KRSSG.FCYCHPD.ETDEDEEEGDEQQRLLNTPRRKKLKSTSKYIYQTLFLNGENS
RetrocopyAGHGLCYCPGSRKSKRSSGAFCYCHPDSETDEDEEEGDEQQRLLNTPRRKKLKSTSKYIYQTLFLNGENS
ParentalDIKICALGEEWSLHKIYLCQSGYFSSMFSGSWKESSMNIIELEIPDQNIDIEALQVAFGSLYRDDVLIKP
DIKICA.GEEWSLHKI.LCQSGYFSSMFSGSWKESSMNIIELEIPDQNIDIEALQVAFGSLY.DDVLIKP
RetrocopyDIKICAPGEEWSLHKICLCQSGYFSSMFSGSWKESSMNIIELEIPDQNIDIEALQVAFGSLYQDDVLIKP
ParentalSRVIAILAAACMLQLDGLIQQCGETMKETINVKTVCGYYTSAGTYGLDSVKKKCLEWLLNNLMTHQNVEL
SRVIAILAAACMLQL.GLIQQCGETMKETINVKTVCGYYTSAGTYGLDSVKKKCLEWLLNNLMTHQNVEL
RetrocopySRVIAILAAACMLQLVGLIQQCGETMKETINVKTVCGYYTSAGTYGLDSVKKKCLEWLLNNLMTHQNVEL
ParentalFKELSINVMKQLIGSSNLFVMQVEMDVYTALKKWMFLQLVPSWNGSLKQLLTETDVWFSKRRKDFEGMTF
FKELSINVMKQLIGSSNLFVMQVEMDVYTALKKWMFLQLVPSWNGSLKQLLTETDVWFSKRRKDFEGMTF
RetrocopyFKELSINVMKQLIGSSNLFVMQVEMDVYTALKKWMFLQLVPSWNGSLKQLLTETDVWFSKRRKDFEGMTF
ParentalLETEQGKPFVSVFRHLRLQYIISDLASARIIEQDSLVPSEWLSSVYKQQWLAMLRAEQDSEVGPQEINKE
LETEQGKPFVSVFRHLRLQYIISDLASARIIEQDSLVPSEWLSSVYKQQWLAMLRAEQDSEVGPQEINKE
RetrocopyLETEQGKPFVSVFRHLRLQYIISDLASARIIEQDSLVPSEWLSSVYKQQWLAMLRAEQDSEVGPQEINKE
ParentalELEGNSMRCGRKLAKDGE
ELEGNSMRCGRKLAKDGE
RetrocopyELEGNSMRCGRKLAKDGE

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
SRP021940_articular_cartilage 0 .53 RPM 1 .48 RPM
SRP021940_cerebellum 0 .05 RPM 1 .30 RPM
SRP021940_embryo 0 .64 RPM 3 .17 RPM
SRP021940_placental_villous 0 .05 RPM 1 .64 RPM
SRP021940_synovial_membrane 0 .03 RPM 1 .04 RPM
SRP021940_testis 11 .00 RPM 76 .92 RPM

ChIP-Seq - click to see more details

Equus caballus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ecab_899 retrocopy.

TSS - click to see more details

Equus caballus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ecab_899 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_899 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 19 parental genes, and 29 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000161161 retrocopy
retro_amel_1915,
Choloepus hoffmanni ENSCHOG000000123062 retrocopies
retro_chof_1562, retro_chof_802,
Equus caballus ENSECAG00000016813 2 retrocopies
retro_ecab_1109, retro_ecab_899 ,
Homo sapiens ENSG000000873381 retrocopy
retro_hsap_3407,
Loxodonta africana ENSLAFG000000025653 retrocopies
retro_lafr_220, retro_lafr_592, retro_lafr_98,
Myotis lucifugus ENSMLUG000000091832 retrocopies
retro_mluc_1521, retro_mluc_31,
Macaca mulatta ENSMMUG000000008581 retrocopy
retro_mmul_98,
Mus musculus ENSMUSG000000011571 retrocopy
retro_mmus_3665,
Nomascus leucogenys ENSNLEG000000101321 retrocopy
retro_nleu_2993,
Oryctolagus cuniculus ENSOCUG000000158082 retrocopies
retro_ocun_112, retro_ocun_160,
Otolemur garnettii ENSOGAG000000084081 retrocopy
retro_ogar_151,
Pongo abelii ENSPPYG000000123341 retrocopy
retro_pabe_209,
Pan troglodytes ENSPTRG000000120211 retrocopy
retro_ptro_2314,
Pteropus vampyrus ENSPVAG000000012423 retrocopies
retro_pvam_1259, retro_pvam_370, retro_pvam_816,
Sorex araneus ENSSARG000000046511 retrocopy
retro_sara_425,
Sus scrofa ENSSSCG000000083351 retrocopy
retro_sscr_62,
Ictidomys tridecemlineatus ENSSTOG000000007141 retrocopy
retro_itri_59,
Tursiops truncatus ENSTTRG000000074933 retrocopies
retro_ttru_1039, retro_ttru_1647, retro_ttru_1648,
Vicugna pacos ENSVPAG000000017561 retrocopy
retro_vpac_617,


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