RetrogeneDB ID:

retro_ecab_729

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:3:81135273..81136016(+)
Located in intron of:ENSECAG00000005039
Retrocopy
information
Ensembl ID:ENSECAG00000012204
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CHTOP
Ensembl ID:ENSECAG00000020889
Aliases:None
Description:chromatin target of PRMT1 [Source:HGNC Symbol;Acc:24511]


Retrocopy-Parental alignment summary:






>retro_ecab_729
ATGGCTGCACAGTCAGCGCCGAAAGTTGTGCTAAAAAGCACCACCAAGATGTCTCTAAATGAGCGCTTTACTAATATGCT
GAAGAACAAACAGCCGATGCCAGTGAATATTCGAGCTTCGATGCAGCAACAACAGCAGCTAGCCAGTGCCAGAAACAGAA
GACTGGCCCAGCAGATGGAGAATAGACCCTCTGTCCAGGCAGCATTAAAACTTAAGCAGAGCTTAAAGCAGCGCCTAGGT
AAAAGTAACATCCAGGCACGGTTAGGCCGACCCACAGGGGCCCTGGCCAGGGGAGCAATCGGAGGACGAGGCCTGCCCAT
AATCCAGAGAGGCTTGCCCAGAGGCGGACTACGTGGGGGACGTGCCACAAGAACCCTACTTAGGGGCGGGATGTCGCTCC
GAGGTCAAAACCTGCTCCGAGGTGGACAGCCGTAGCTCCCCGAATGGGCTTAAGAAGAGGTGGTGTTCGAGGTCGTGGAG
GTCCTGGGAGAGGGGGCCTAGGGCGCGGAGCTATGGGTCGTGGCGGAATCGGTGGTAGAGGTCGGGGTATGATAGGTCGG
GGAAGAGGGGGCTTTGGAGGCAGAGGCAGAGGCCGTGGACGAGGGAGAGGTGCCCTTGCTCGCCCTGTACTGACCAAGGA
GCAGCTGGACAACCAGTTGGATGCATACATGTCGAAAACGAAAGGACACCTGGATGCTGAGTTGGATGCCTACGTGGCAC
AGACAGATCCTGAAACCAATGAT

ORF - retro_ecab_729 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 98.39 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMAAQSAPKVVLKSTTKMSLNERFTNMLKNKQPMPVNIRASMQQQQQLASARNRRLAQQMENRPSVQAALK
MAAQSAPKVVLKSTTKMSLNERFTNMLKNKQPMPVNIRASMQQQQQLASARNRRLAQQMENRPSVQAALK
RetrocopyMAAQSAPKVVLKSTTKMSLNERFTNMLKNKQPMPVNIRASMQQQQQLASARNRRLAQQMENRPSVQAALK
ParentalLKQSLKQRLGKSNIQARLGRPIGALARGAIGGRGLPIIQRGLPRGGLRGGRATRTLLRGGMSLRGQNLLR
LKQSLKQRLGKSNIQARLGRP.GALARGAIGGRGLPIIQRGLPRGGLRGGRATRTLLRGGMSLRGQNLLR
RetrocopyLKQSLKQRLGKSNIQARLGRPTGALARGAIGGRGLPIIQRGLPRGGLRGGRATRTLLRGGMSLRGQNLLR
ParentalGGR-AVAPRMGLRRGGVRGRGGPGRGGLGRGAMGRGGIGGRGRGMIGRGRGGFGGRGRGRGRGRGALARP
GG..AVAPRMGLRRGGVRGRGGPGRGGLGRGAMGRGGIGGRGRGMIGRGRGGFGGRGRGRGRGRGALARP
RetrocopyGGQ<AVAPRMGLRRGGVRGRGGPGRGGLGRGAMGRGGIGGRGRGMIGRGRGGFGGRGRGRGRGRGALARP
ParentalVLTKEQLDNQLDAYMSKTKGHLDAELDAYMAQTDPETND
VLTKEQLDNQLDAYMSKTKGHLDAELDAY.AQTDPETND
RetrocopyVLTKEQLDNQLDAYMSKTKGHLDAELDAYVAQTDPETND

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 .18 RPM 24 .20 RPM
SRP021940_cerebellum 0 .10 RPM 48 .30 RPM
SRP021940_embryo 0 .41 RPM 53 .55 RPM
SRP021940_placental_villous 0 .34 RPM 33 .82 RPM
SRP021940_synovial_membrane 0 .49 RPM 32 .61 RPM
SRP021940_testis 1 .60 RPM 92 .40 RPM
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_729 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_729 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_729 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000135181 retrocopy
Dasypus novemcinctus ENSDNOG000000048341 retrocopy
Equus caballus ENSECAG00000020889 1 retrocopy
retro_ecab_729 ,
Loxodonta africana ENSLAFG000000026583 retrocopies
Myotis lucifugus ENSMLUG000000160982 retrocopies
Rattus norvegicus ENSRNOG000000127601 retrocopy
Vicugna pacos ENSVPAG000000102591 retrocopy



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