RetrogeneDB ID:

retro_ecab_288

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:13:19674539..19675297(-)
Located in intron of:ENSECAG00000014460
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CAB39
Ensembl ID:ENSECAG00000015288
Aliases:None
Description:calcium binding protein 39 [Source:HGNC Symbol;Acc:20292]


Retrocopy-Parental alignment summary:






>retro_ecab_288
TTGAAGGAAATTCCGTATGGTACAAATGAAAAAGAACCACAGACAGAAGCGGCGGCCAACTCGCTCAAGAACTCTGTAAC
AGTGGGCTCCTTAGCACCCTGGTAGCTGACTTACAGCTCATTGACTTTGAGGGCAAAAAAAGATGTGGCTCAAATTTTCA
ACAATATTCTCAGAAGACAAATTGGTACAAGAACTCCCACTGTTGAATACATCTGCACCCAACAGAATATTTTGTTCGTG
TTATTGAAAGGGTATGAATCTCCAGAAATAGCTCTAAATTGTGGAATAATGTTGAGAGAATGCATCAGACACGAACCACT
TGCAAAAATCATTTTTGGTCAGAACAATTTTATGATTTCTTCAGATGTGTCGAAATGTCAATATTTGACGTAGCTTCAGA
TGCATTCGCCACATTCAAGGATTTACTTACAAGACATAAATTGCTCAGTGCAGAATTTTTGGAACAGCATTATGATAGAT
TCTTCAGTGAACATGAGAAGTTACTTCATTCAGAAAATTAGGTGACAAAAAGACAGTCACCCAAGCTTCTCGGTGAGTTA
CTATTAGACAGACACAACTTCACGATTATGACAAAATCCATCAGTAAACCTGAGAACCTCAAATTAATGATGAACCTTCT
GCGAGACAAAAGTTGTAACATCCAATTTGAGGCCTTTCACATTTTTAAGGTGTTTGTAGCCAATCCTAACAAGACACAGC
CCATCCTCAACATCCTCCTCTAGAACCAGACCAAACTC

ORF - retro_ecab_288 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.19 %
Parental protein coverage: 74.19 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMKEILYGTNEKEPQTEAVA-QLAQELYNSGLLSTLVADLQLIDFEGKK-DVAQIFNNILRRQIGTRTPTV
.KEI.YGTNEKEPQTEA.A.QLAQEL.NSGLLSTLVADLQLIDFEGKK.DVAQIFNNILRRQIGTRTPTV
RetrocopyLKEIPYGTNEKEPQTEAAA<QLAQELCNSGLLSTLVADLQLIDFEGKK>DVAQIFNNILRRQIGTRTPTV
ParentalEYICTQQNILFMLLKGYESPEIALNCGIMLRECIRHEPLAKIIL-WSEQFYDFFRYVEMSTFDIASDAFA
EYICTQQNILF.LLKGYESPEIALNCGIMLRECIRHEPLAKII..WSEQFYDFFR.VEMS.FD.ASDAFA
RetrocopyEYICTQQNILFVLLKGYESPEIALNCGIMLRECIRHEPLAKIIF<WSEQFYDFFRCVEMSIFDVASDAFA
ParentalTFKDLLTRHKLLSAEFLEQHYDRFFSEYEKLLHSENYVTKRQSLKLLGELLLDRHNFTIMTKYISKPENL
TFKDLLTRHKLLSAEFLEQHYDRFFSE.EKLLHSEN.VTKRQS.KLLGELLLDRHNFTIMTK.ISKPENL
RetrocopyTFKDLLTRHKLLSAEFLEQHYDRFFSEHEKLLHSEN*VTKRQSPKLLGELLLDRHNFTIMTKSISKPENL
ParentalKLMMNLLRDKSRNIQFEAFHVFKVFVANPNKTQPILDILLKNQTKL
KLMMNLLRDKS.NIQFEAFH.FKVFVANPNKTQPIL.ILL.NQTKL
RetrocopyKLMMNLLRDKSCNIQFEAFHIFKVFVANPNKTQPILNILL*NQTKL

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 13 .40 RPM
SRP021940_cerebellum 0 .00 RPM 18 .44 RPM
SRP021940_embryo 0 .00 RPM 14 .19 RPM
SRP021940_placental_villous 0 .10 RPM 25 .93 RPM
SRP021940_synovial_membrane 0 .08 RPM 11 .31 RPM
SRP021940_testis 0 .06 RPM 27 .24 RPM
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_288 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_288 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_288 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000133491 retrocopy
Equus caballus ENSECAG00000015288 1 retrocopy
retro_ecab_288 ,
Otolemur garnettii ENSOGAG000000020001 retrocopy



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