RetrogeneDB ID:

retro_ecab_509

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:2:172359..172797(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS2
Ensembl ID:ENSECAG00000009065
Aliases:None
Description:ribosomal protein S2 [Source:HGNC Symbol;Acc:10404]


Retrocopy-Parental alignment summary:






>retro_ecab_509
AAGGGACATGGTCTGGGCAGGGCTTGACATCAAAGAGCTCTCTGAGGCAAAGCCAAGGACAAGAGGTGGCTCCTCATAAC
TAAGCTGGGCCTCATGGTCAGGACATGAAGATAAAGTCCTTGCAGGAGGTCTATCTCTTCTCCCCATCAAAGAGTCTGAG
GTCACCAACCTTGTTCTGGAGACAGCCCTCAAAGACAAGGTTTGGAAGATTAGGCCCCTACAAAAGCAAACCTGCACTGG
CCAGCAGACCAAGTTCAAGCATTTGTCACCATCAGGGACTACAGTGGCCACGTTGGTCTGGGTGGTAAGTGCTCCAGGGA
GGTAGCCGTTGCCACGCACTGGGCCACCGTCCTGGTCCACAACTCCATAGACGCAGGGTGGCGAGGCCACAAGTGGATCA
AGTTTGGCAAGCCCCACACCATCCCTTGCAAGGTGACA

ORF - retro_ecab_509 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 56.95 %
Parental protein coverage: 50.51 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalRGRGRGRGRGRGARGGKAEDKEWIPVTKLGRLVK-DMKIKSLEEIYLFSLPIK-ESEIIDFFLGASLKDE
.G.G.GR.....A..GKA.DK.W...TKLG..V..DMKIKSL.E.YLFS.P.K.ESE.....L...LKD.
RetrocopyKGHGLGRA*HQRAL*GKAKDKRWLLITKLGLMVR<DMKIKSLQEVYLFS-PSK<ESEVTNLVLETALKDK
ParentalVLKIMPVQKQTRAGQRTRFK-AFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKI
V.KI.P.QKQT..GQ.T.FK.AFV.I.DY.GHVGLG.KCS.EVA.A...A..L...SI....RG....K.
RetrocopyVWKIRPLQKQTCTGQQTKFK<AFVTIRDYSGHVGLGGKCSREVAVATHWATVLVHNSIDAGWRGHKWIKF
ParentalGKPHTVPCKVT
GKPHT.PCKVT
RetrocopyGKPHTIPCKVT

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 1345 .23 RPM
SRP021940_cerebellum 0 .00 RPM 357 .55 RPM
SRP021940_embryo 0 .05 RPM 851 .49 RPM
SRP021940_placental_villous 0 .00 RPM 688 .28 RPM
SRP021940_synovial_membrane 0 .00 RPM 1087 .71 RPM
SRP021940_testis 0 .00 RPM 354 .05 RPM
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_509 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_509 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_509 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 9 parental genes, and 65 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000025491 retrocopy
Canis familiaris ENSCAFG0000001947219 retrocopies
Cavia porcellus ENSCPOG0000001165111 retrocopies
Equus caballus ENSECAG00000009065 7 retrocopies
Monodelphis domestica ENSMODG000000160771 retrocopy
Mus musculus ENSMUSG000000445331 retrocopy
Pteropus vampyrus ENSPVAG000000167048 retrocopies
Rattus norvegicus ENSRNOG0000001417912 retrocopies
Sarcophilus harrisii ENSSHAG000000152135 retrocopies



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