RetrogeneDB ID:

retro_ecab_839

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:5:60908345..60908984(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:FAM175B
Ensembl ID:ENSECAG00000023340
Aliases:None
Description:family with sequence similarity 175, member B [Source:HGNC Symbol;Acc:28975]


Retrocopy-Parental alignment summary:






>retro_ecab_839
TTTGACAAGCATAGAGTAATGAAAGACACTGAGGTAATTTACAGGTTTATAATACACTTCACCCAGGCAGTGCGTGCAGA
TGTAGAAAAGAATGAGCAAGTTGTTGAATCTTGTCAGGCAGAAGTGAACAAATTAAGAAGACAAATCAATCAGATGAAAT
GGAAAAGAACAAGAAAGACGATTGCAGCAGGCGATGCTAAGCAGACAGATGCTGTATGAAAGTTTGGAACCAGTGGTCAG
TCCTCGGATGCCCTAACTGGGTTTTTAGCTGAAGGTTGAAGTACACTGGGAGATGCAGAGGATTCTGGTCCTCCTCCTTC
TTATTCTGGTTTTTCACTCACACAGTCTGGAAAGTACTTTGAGCCTTTCTCTATGTAAAGTAGTGTCTTTGTACCTTGAC
CTCAAGCCATGGGCTCTTCCAATTATGCTTCCACCAGTGCCGGACTGAAGTATCCCAGAAGTGGAGAAGACTTTCTTCCT
TCCCAAAGAGTAGCTGGAGACAGACTTGAAGAATCAGATAAAAGTGATTACGAAAATTTGATTGATCTTACAGAGCTTTC
TAATAGGGAATACTTACATTCAAGGAATTCAGGATACGTGACATATTCCCATGGGGTCTCCAGGAACACTCAGACCTCA

ORF - retro_ecab_839 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.41 %
Parental protein coverage: 51.18 %
Number of stop codons detected: 3
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalFDKDGVMKDIRAIYQVYNALQEKVQAVCADVEKSERVVESCQAEVNKLRRQITQRK-NEKEQE-RRLQQA
FDK..VMKD...I...Y.......QAV.ADVEK.E.VVESCQAEVNKLRRQI.Q.K..EK....RRLQQA
RetrocopyFDKHRVMKDTEVI---YRFIIHFTQAVRADVEKNEQVVESCQAEVNKLRRQINQMK<MEKNKK<RRLQQA
ParentalMLSRQMAPESLEPGFSPRMP-YSGFVAEGRSPLGDAEASDPPPPYSD-FHSNNQESTLSHP-RMETSVFM
MLSRQM..ESLEP..SPRMP...GF.AEG.S.LGDAE.S.PPP.YS..FHS...ESTLS....M..SVF.
RetrocopyMLSRQMLYESLEPVVSPRMP<LTGFLAEG*STLGDAEDSGPPPSYSG>FHSHSLESTLSLS<SM*SSVFV
ParentalPRPQAVGSSSYASTSAGLKYPGSGADLPPPRRAAADSAEESDDSDYEHLIDPTEPSNSECSHSRDSRPMT
P.PQA.GSS.YASTSAGLKYP.SG.D..P..R.A.D..EESD.SDYE.LID.TE.SN.E..HSR.S...T
RetrocopyP*PQAMGSSNYASTSAGLKYPRSGEDFLPSQRVAGDRLEESDKSDYENLIDLTELSNREYLHSRNSGYVT
ParentalHPDGGSRNTQTS
...G.SRNTQTS
RetrocopyYSHGVSRNTQTS

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 7 .73 RPM
SRP021940_cerebellum 0 .00 RPM 8 .57 RPM
SRP021940_embryo 0 .00 RPM 12 .25 RPM
SRP021940_placental_villous 0 .00 RPM 5 .77 RPM
SRP021940_synovial_membrane 0 .05 RPM 7 .08 RPM
SRP021940_testis 0 .00 RPM 8 .50 RPM
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_839 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_839 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_839 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000238401 retrocopy
Choloepus hoffmanni ENSCHOG000000076353 retrocopies
Equus caballus ENSECAG00000023340 1 retrocopy
retro_ecab_839 ,



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