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 symbol: CHTOP
• Ensembl ID: ENSECAG00000020889
• Aliases: None
• Description: chromatin target of PRMT1 [Source:HGNC Symbol;Acc:24511]

Sequence

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

Alignment

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:

Parental  MAAQSAPKVVLKSTTKMSLNERFTNMLKNKQPMPVNIRASMQQQQQLASARNRRLAQQMENRPSVQAALK
          MAAQSAPKVVLKSTTKMSLNERFTNMLKNKQPMPVNIRASMQQQQQLASARNRRLAQQMENRPSVQAALK
Retrocopy MAAQSAPKVVLKSTTKMSLNERFTNMLKNKQPMPVNIRASMQQQQQLASARNRRLAQQMENRPSVQAALK

Parental  LKQSLKQRLGKSNIQARLGRPIGALARGAIGGRGLPIIQRGLPRGGLRGGRATRTLLRGGMSLRGQNLLR
          LKQSLKQRLGKSNIQARLGRP.GALARGAIGGRGLPIIQRGLPRGGLRGGRATRTLLRGGMSLRGQNLLR
Retrocopy LKQSLKQRLGKSNIQARLGRPTGALARGAIGGRGLPIIQRGLPRGGLRGGRATRTLLRGGMSLRGQNLLR

Parental  GGR-AVAPRMGLRRGGVRGRGGPGRGGLGRGAMGRGGIGGRGRGMIGRGRGGFGGRGRGRGRGRGALARP
          GG..AVAPRMGLRRGGVRGRGGPGRGGLGRGAMGRGGIGGRGRGMIGRGRGGFGGRGRGRGRGRGALARP
Retrocopy GGQ<AVAPRMGLRRGGVRGRGGPGRGGLGRGAMGRGGIGGRGRGMIGRGRGGFGGRGRGRGRGRGALARP

Parental  VLTKEQLDNQLDAYMSKTKGHLDAELDAYMAQTDPETND
          VLTKEQLDNQLDAYMSKTKGHLDAELDAY.AQTDPETND
Retrocopy VLTKEQLDNQLDAYMSKTKGHLDAELDAYVAQTDPETND

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

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

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_729 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_729 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_729 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013518	1 retrocopy	retro_chof_6,
Dasypus novemcinctus	ENSDNOG00000004834	1 retrocopy	retro_dnov_1054,
Equus caballus	ENSECAG00000020889	1 retrocopy	retro_ecab_729 ,
Loxodonta africana	ENSLAFG00000002658	3 retrocopies	retro_lafr_131, retro_lafr_282, retro_lafr_656,
Myotis lucifugus	ENSMLUG00000016098	2 retrocopies	retro_mluc_201, retro_mluc_247,
Rattus norvegicus	ENSRNOG00000012760	1 retrocopy	retro_rnor_1095,
Vicugna pacos	ENSVPAG00000010259	1 retrocopy	retro_vpac_353,