RetrogeneDB ID:

retro_ecab_714

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:3:39219756..39220578(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSECAG00000022782
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSECAG00000023806
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ecab_714
AGGAGACAAAGGAATATGTTCCAAATAAGGGAACAGGACAGTTCCTCAGAAAAAGAGCTAAACAAAACAGAGATAAACAA
TCTACTTGATAAAGAGTACAAACTAATACTCATAAGGATGCTTACTGATCTGGGGAGAAGAATAGATGAACACAGTGAGA
ACTTCAACAAAGAACTAGAAAATATGAAAAAGAACCAATCAGAGCTGAAGAATACAATAATGGAAATGAAAATTTCACTT
GAGGGAATCAACAGCAGAGTAGATGACACAGAAGAACTGATCAGCCATCTGGATGACAGAGTAGAGGAAATAGCCTAAGC
TGAACAGAAAAAAAGAAAAAAGAATTAAAAAAAATGAGGACAGTCTAAGGGACCTCTGGGACAACATCAAATGTATTAAC
ACCTGCATTATAAATGTCCCAGAAGGAAAAGAGAAAGACAAGGGGCACAGAACTTATTTGAAGAAATAATACCTGAAAAC
TTCCGTAACCTGAGAAAGGAAACAGATATCCAGGTACTGGAAACACCGAAAGCACCACACAAGATGAATCCAAAGAGGCC
CACACCAAGACACATTATAATAAAAATGTCAAGAATTAAAGATAAGGAGAGAATCCTAAAAGCTGCAAGAGACAAGCAAT
AAGTTACATACAAAACCCCCCATAAATCTATAAGCTGACTTTTCAGCAGAAACTTTACAGGCTAGAAGGGAGTGGCACTA
TATACTCAAAGTGATGAAAGAAAAAACCTACCATCAAGAATACTGTACCTGGCAAGGTTATCATTCAGAATTGAAGGAGA
GATAAAGAGATTTACAGATGAG

ORF - retro_ecab_714 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 58.78 %
Parental protein coverage: 97.86 %
Number of stop codons detected: 2
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalRRQRNMFHARVQDKTPEKELNETQRDNLPDKEFKQKGIRMLIDLGRRMDKHSENVNKELENIKKSQSEMK
RRQRNMF..R.QD...EKELN.T...NL.DKE.K...IRML.DLGRR.D.HSEN.NKELEN.KK.QSE.K
RetrocopyRRQRNMFQIREQDSSSEKELNKTEINNLLDKEYKLILIRMLTDLGRRIDEHSENFNKELENMKKNQSELK
ParentalSTILKMKNSLEGLNSRVDDTEEWIKKLDEKLEEIS-QVNQVKEKTILKNDSKIKELWDNIKHANIRIISV
.TI..MK.SLEG.NSRVDDTEE.I..LD...EEI....N................LWDNIK..N..II.V
RetrocopyNTIMEMKISLEGINSRVDDTEELISHLDDRVEEIA>KLNXXXXXXXXXXEDSLRDLWDNIKCINTCIINV
ParentalPGGEERHKGE-ENLFEEIIDENFPNLRKETDIQVQEEQRAPNKSSPKRPTPIHIII-KMSKIKDKERILK
P.G.E..KG...NLFEEII.ENF.NLRKETDIQV.E...AP.K..PKRPTP.HIII.K....K......K
RetrocopyPEGKEKDKGH<QNLFEEIIPENFRNLRKETDIQVLETPKAPHKMNPKRPTPRHIII>KCQELKIRRES*K
ParentalAARERPEVTYKGKPIRLSADFSAETLQATREWHDIFKVLKGK-NLQPRIFYPSRSSFRMEGEIKRFPDK
...E.........PI.L.ADFSAETLQA.REWH.I.KV.K.K.NL..RI.Y..R.SFR.EGEIKRF.D.
RetrocopyL-QETSNKLHTKPPINL*ADFSAETLQARREWHYILKVMKEK<NLPSRILYLARLSFRIEGEIKRFTDE

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 0 .12 RPM
SRP021940_cerebellum 0 .00 RPM 0 .00 RPM
SRP021940_embryo 0 .00 RPM 0 .28 RPM
SRP021940_placental_villous 0 .00 RPM 0 .00 RPM
SRP021940_synovial_membrane 0 .00 RPM 0 .08 RPM
SRP021940_testis 0 .00 RPM 0 .00 RPM
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_714 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_714 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_714 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 5 parental genes, and 54 retrocopies.

Species Parental gene accession Retrocopies number
Equus caballus ENSECAG0000001003021 retrocopies
Equus caballus ENSECAG000000165275 retrocopies
Equus caballus ENSECAG000000203329 retrocopies
Equus caballus ENSECAG000000220344 retrocopies
Equus caballus ENSECAG00000023806 15 retrocopies



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