RetrogeneDB ID:

retro_ecab_510

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:2:13006808..13007382(-)
Located in intron of:ENSECAG00000017621
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GM2A
Ensembl ID:ENSECAG00000020587
Aliases:None
Description:ganglioside GM2 activator [Source:RefSeq peptide;Acc:NP_001075381]


Retrocopy-Parental alignment summary:






>retro_ecab_510
AGACCCTCGATGCAGGCTCCATTCCTGATCGCCGTGGGCTTGCTTCTTGCTGGCCCTGCGGCTCCTGTAAGCATCCTCCT
AGACAGCTCAGTAGATTTTCCTGGGTAACTGTGATGAGGGGAAGGATCCTGTGGTGATCAAAACCCTGACTGTGGAACCT
GACCCCATTGCTGTTCCTGGAAACGTGACTGTCAGTGCCGAGGTAAAGACCACTGTCCCCTTCATTGCTCCTCAGAAGGT
GGAAATAACTCTGGATAAGGAAGTGGCCAGTGTATGGGTCAAAATCCCGTGTATGGAACAAATCGGTAGCTGTACATTTG
ACAATGCCTATGATATGCTTGACACTTAAGACTCCCCCTGGGCAATCCTGCCCAGAGCCCCTGCACACCTATGGGCTTCC
TTGTCGCTGTCCCTTCAAAGAAGCCACCTACTCATTGCCCAAGAGTACTTTCCCCTCCCCAACCTGGAGCTGCCCAGCTG
GCTCAACAACAGGAACTACCGCATCCAGAGCGTCCTGAGCGGCAGTGGGACTCGTCTGGGCTGTATCAAGATCTCCACCT
CTCTAAAGGGCAAA

ORF - retro_ecab_510 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.04 %
Parental protein coverage: 99.48 %
Number of stop codons detected: 0
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalRPSMQAPFLIALGLLLAGPAAPVSVLSE-RLRSFSW-DNCDEGKDPMVLKSLTLEPDPIAVPGNVTVSAE
RPSMQAPFLIA.GLLLAGPAAPVS.L....L..FSW..NCDEGKDP.V.K.LT.EPDPIAVPGNVTVSAE
RetrocopyRPSMQAPFLIAVGLLLAGPAAPVSILLD<QLSRFSW<GNCDEGKDPVVIKTLTVEPDPIAVPGNVTVSAE
ParentalVKTTVALSAPQKVELTVEKEVAGVWVKIPCVDQIGSCTFDNACDILDA-LTPPGQPCPEPLHTFGLPCHC
VKTTV...APQKVE.T..KEVA.VWVKIPC..QIGSCTFDNA.D.LD...TPPGQ.CPEPLHT.GLPC.C
RetrocopyVKTTVPFIAPQKVEITLDKEVASVWVKIPCMEQIGSCTFDNAYDMLDT>KTPPGQSCPEPLHTYGLPCRC
ParentalPFKEGTYSLPKST-FPLPDLELPSWLSNGNYRVQSILSSGGKRLGCVKITASLKAK
PFKE.TYSLPKST.FPLP.LELPSWL.N.NYR.QS.LS..G.RLGC.KI..SLK.K
RetrocopyPFKEATYSLPKST<FPLPNLELPSWLNNRNYRIQSVLSGSGTRLGCIKISTSLKGK

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(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 .00 RPM 11 .16 RPM
SRP021940_cerebellum 0 .05 RPM 23 .47 RPM
SRP021940_embryo 0 .03 RPM 11 .15 RPM
SRP021940_placental_villous 0 .34 RPM 3507 .01 RPM
SRP021940_synovial_membrane 0 .03 RPM 27 .89 RPM
SRP021940_testis 0 .00 RPM 48 .21 RPM
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_510 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_510 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_510 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 14 parental genes, and 17 retrocopies.

Species Parental gene accession Retrocopies number
Equus caballus ENSECAG00000020587 1 retrocopy
retro_ecab_510 ,
Homo sapiens ENSG000001967432 retrocopies
Gorilla gorilla ENSGGOG000000153022 retrocopies
Macropus eugenii ENSMEUG000000104211 retrocopy
Microcebus murinus ENSMICG000000006901 retrocopy
Myotis lucifugus ENSMLUG000000032151 retrocopy
Macaca mulatta ENSMMUG000000228691 retrocopy
Nomascus leucogenys ENSNLEG000000109661 retrocopy
Oryctolagus cuniculus ENSOCUG000000158371 retrocopy
Ochotona princeps ENSOPRG000000061711 retrocopy
Pongo abelii ENSPPYG000000159621 retrocopy
Pan troglodytes ENSPTRG000000174312 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000285001 retrocopy
Tursiops truncatus ENSTTRG000000005031 retrocopy



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