RetrogeneDB ID:

retro_ecab_638

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:24:26494474..26494931(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL9
Ensembl ID:ENSECAG00000016489
Aliases:None
Description:ribosomal protein L9 [Source:HGNC Symbol;Acc:10369]


Retrocopy-Parental alignment summary:






>retro_ecab_638
GACTTGAAAGACATCAATGTAGAATTCAGTCTCCTTGGAAAGAAAAAGAGCCTCTGGGTTGACAAATAGTAAAGAAACAG
GAACTGGCTACAGTTGGCACTCTGTAGTCACGTACGGAACACGATCAAAGGCATTACATTAGACACCCATTACTGGACGA
GGTCTGCGTATGCTCACCGCCCCATCAACATTGTCATTCAGGAGAATGGGTCTCTTGTTGAAATCCAAAATTTCTTGAGT
AAAAAAGGCATCCATAAAATTCAGATGAGGCCAGGTGCTGCTTGTTCACTATCTCAAGCCCAGAAAGATGAGTTAATTCT
TGAAGTAAACGACATTGAACTCGCACCAAATTTGTTGCGTTGATTCAGCAAGCCACAGCAGTTAAAACAAGGATATCAGA
AAATTTTTAGATAGTATCTATGTCTCTAAAAAAGGAACAGTTCAGCAGGTTGATGAA

ORF - retro_ecab_638 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.35 %
Parental protein coverage: 81.25 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalDFNHINVELSLLGKKKKRLRVDKWWGNRKELATVRTICSHVQNMIKGVTLGFRYKMRSVYAHFPINVVIQ
D...INVE.SLLGKKK..L.VDK...NR..L......CSHV.N.IKG.TL...Y..RS.YAH.PIN.VIQ
RetrocopyDLKDINVEFSLLGKKKS-LWVDK**RNRNWLQLA--LCSHVRNTIKGITLDTHYWTRSAYAHRPINIVIQ
ParentalENGSLVEIRNFLGEKYIRRVRMRPGVACSVSQAQKDELILEGNDIELVSN-SAALIQQATTVK-NKDIRK
ENGSLVEI.NFL..K.I....MRPG.ACS.SQAQKDELILE.NDIEL..N...ALIQQAT.VK.NKDIRK
RetrocopyENGSLVEIQNFLSKKGIHKIQMRPGAACSLSQAQKDELILEVNDIELAPN<FVALIQQATAVK<NKDIRK
ParentalFLDGIYVSEKGTVQQADE
FLD.IYVS.KGTVQQ.DE
RetrocopyFLDSIYVSKKGTVQQVDE

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 957 .88 RPM
SRP021940_cerebellum 0 .05 RPM 227 .52 RPM
SRP021940_embryo 0 .08 RPM 519 .56 RPM
SRP021940_placental_villous 0 .00 RPM 418 .61 RPM
SRP021940_synovial_membrane 0 .08 RPM 422 .90 RPM
SRP021940_testis 0 .00 RPM 173 .99 RPM
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_638 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_638 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_638 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 26 parental genes, and 471 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000073171 retrocopy
Ailuropoda melanoleuca ENSAMEG0000000318731 retrocopies
Bos taurus ENSBTAG000000145183 retrocopies
Canis familiaris ENSCAFG0000001600828 retrocopies
Callithrix jacchus ENSCJAG0000000072329 retrocopies
Danio rerio ENSDARG000000373501 retrocopy
Dasypus novemcinctus ENSDNOG0000000741118 retrocopies
Equus caballus ENSECAG00000016489 7 retrocopies
Erinaceus europaeus ENSEEUG0000000439439 retrocopies
Felis catus ENSFCAG0000001228434 retrocopies
Homo sapiens ENSG0000016368228 retrocopies
Gorilla gorilla ENSGGOG0000002279926 retrocopies
Gadus morhua ENSGMOG000000010021 retrocopy
Loxodonta africana ENSLAFG0000001202138 retrocopies
Macropus eugenii ENSMEUG000000167228 retrocopies
Microcebus murinus ENSMICG0000001677818 retrocopies
Myotis lucifugus ENSMLUG0000000459734 retrocopies
Macaca mulatta ENSMMUG0000000855322 retrocopies
Monodelphis domestica ENSMODG000000205537 retrocopies
Nomascus leucogenys ENSNLEG0000001710026 retrocopies
Otolemur garnettii ENSOGAG0000000493520 retrocopies
Pongo abelii ENSPPYG0000001467510 retrocopies
Sarcophilus harrisii ENSSHAG000000049188 retrocopies
Sus scrofa ENSSSCG0000002519215 retrocopies
Tupaia belangeri ENSTBEG0000000604218 retrocopies
Vicugna pacos ENSVPAG000000020231 retrocopy



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