RetrogeneDB ID:

retro_ecab_692

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:28:248419..248967(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HOMER2
Ensembl ID:ENSECAG00000023619
Aliases:None
Description:homer homolog 2 (Drosophila) [Source:HGNC Symbol;Acc:17513]


Retrocopy-Parental alignment summary:






>retro_ecab_692
TCTGTGACATAGAGTGCTGCCAATGTGAAGAAATAGGAGAATAAGCTGCAGACCCTACAGGAGAGCAATGTCTGGCTGAC
CATGGCACTGCAGGAGTCAGTGGCCAGCATGGAGCAGTGAAAGAGGAAGTTCTCTATCTGCCCTGAAGAGAATGACTGGC
TGTGGAACAATCCTGAGGAGTTGGAAGAACAATGCAAAGAGATAACAAAGAGAAGGAGAAGCATACCCAGTTGAAGAAAA
GAATTGAGGAGCTGGAGTCAGAACTCTGAGAAAAGAAGATAGAGTTAAAAGACCTCCAAAAACAAAGTAAACTCAGACCT
CAGCTCATGTCAGAGTATGAATACATTTCTGAGAAGCTAGAGGCAGCAAAGAGAGATAATCAAAACCAGAGAGACAAAGT
GCTTTCTCTAAAGACAGACATTGAGGAAAGTAACTACTGACCATGCCACTTGAAGGCAGAATTGAAGAACTTCTTGAAGG
TGCTGGATGGGAAGATAAATGACCTCCACAACTTCTGTGGAGGCCTCTGCAAGCTGGGCAAGGAAAAC

ORF - retro_ecab_692 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.65 %
Parental protein coverage: 51.84 %
Number of stop codons detected: 5
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalALTQSAANVKKWEVELQTLRESNARLTAALQESAASAEQWKRQFSVCRDENDRLRHKIDELEEQCSEI-N
..T.SAANVKK.E..LQTL.ESN..LT.ALQES.AS.EQ.KR.FS.C..END.L.....ELEEQC.EI.N
RetrocopySVT*SAANVKK*ENKLQTLQESNVWLTMALQESVASMEQ*KRKFSICPEENDWLWNNPEELEEQCKEI<N
ParentalREKEKNTQLKRRIEELESELREKETELKDLRKQSEIIPQLMSECEYVSEKLEAAERDNQNLEDKVRSLKT
.EKEK.TQLK.RIEELESEL.EK..ELKDL.KQS...PQLMSE.EY.SEKLEAA.RDNQN..DKV.SLKT
RetrocopyKEKEKHTQLKKRIEELESEL*EKKIELKDLQKQSKLRPQLMSEYEYISEKLEAAKRDNQNQRDKVLSLKT
ParentalDIEESKYRQRHLKVELKNFLEVLDGKIDDLHDFRRGLSKLGTDN
DIEES.Y...HLK.ELKNFL.VLDGKI.DLH.F..GL.KLG..N
RetrocopyDIEESNY*PCHLKAELKNFLKVLDGKINDLHNFCGGLCKLGKEN

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 1 .95 RPM
SRP021940_cerebellum 0 .00 RPM 11 .74 RPM
SRP021940_embryo 0 .00 RPM 11 .97 RPM
SRP021940_placental_villous 0 .00 RPM 1 .35 RPM
SRP021940_synovial_membrane 0 .00 RPM 1 .87 RPM
SRP021940_testis 0 .00 RPM 11 .57 RPM
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_692 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_692 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_692 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 7 parental genes, and 15 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000158843 retrocopies
Cavia porcellus ENSCPOG000000146881 retrocopy
Equus caballus ENSECAG00000023619 3 retrocopies
retro_ecab_1046, retro_ecab_661, retro_ecab_692 ,
Homo sapiens ENSG000001039421 retrocopy
Macaca mulatta ENSMMUG000000082971 retrocopy
Nomascus leucogenys ENSNLEG000000109531 retrocopy
Pongo abelii ENSPPYG000000067355 retrocopies



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