RetrogeneDB ID: retro_ecab_479

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 19:56737353..56737850(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000023307
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: C2orf68
• Ensembl ID: ENSECAG00000014919
• Aliases: None
• Description: chromosome 2 open reading frame 68 [Source:HGNC Symbol;Acc:34353]

Sequence

>retro_ecab_479
GAAGCGGCGCGGGATCCCAGGCCGGGGCTCTGCTGCAAGCCTGGCGGGCGGCTGGACATGAGTCAGGGCTTCGTGCACCA
TATCCGAAGGAACCAGCTCGCCCGGGACGACTACGACAAGAAGGTGAAGCAGGCTGCCCAAGGAGAAGGCAAGGAGGCGG
CGCACGCCCCGCGCCGACGCGGCCCCGCAAGCCCGACCTGCAGGTGTACCTGCCGCGACGCCGAGGTGTCTCTACCCACC
CAAGCAACCCAGACTGTGAGGAGTCCGGTGAAAGCAGCAGTAGTGGTGGTTCCGAGCCAGAACCTTCTGGCCATCAGCTC
TTCTGCGTAGAATATGAGGCAGACAGCGGAGAGGTCACCTCAGTTATCGTGTATCAGGACGATGATCCAGAAAGGGTGAG
TGAGGAGGTGTCAACACACATGCCTCTGGATCCACCCATGCGAGAGGCCCTCAAGTTGCGCATCCAGGAAGAGATTGCAA
AGCGCCAGAGCCGATAC

Alignment

ORF - retro_ecab_479 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.01 %
• Parental protein coverage: 99.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EAAPEPRPGLCCKPGGRLDMSHGFVHHIRRNQLARDDYDKKVKQAA-KEKARRRHTP-APTRPRKPDLQV
          EAA..PRPGLCCKPGGRLDMS.GFVHHIRRNQLARDDYDKKVKQAA.KEKARRR.TP.APTRPRKPDLQV
Retrocopy EAARDPRPGLCCKPGGRLDMSQGFVHHIRRNQLARDDYDKKVKQAA>KEKARRRRTP>APTRPRKPDLQV

Parental  YLPRRRDVSTHPSNPDCEESGESSSSGGSEPEPSGHQLFCLEYEADSGEVTSVIVYQDDDPERVSEEVST
          YLPRRR.VSTHPSNPDCEESGESSSSGGSEPEPSGHQLFC.EYEADSGEVTSVIVYQDDDPERVSEEVST
Retrocopy YLPRRRGVSTHPSNPDCEESGESSSSGGSEPEPSGHQLFCVEYEADSGEVTSVIVYQDDDPERVSEEVST

Parental  HTPLDPPMREALKLRIQEEIAKRQSRH
          H.PLDPPMREALKLRIQEEIAKRQSR.
Retrocopy HMPLDPPMREALKLRIQEEIAKRQSRY

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	0.00 RPM	5.96 RPM
SRP021940_cerebellum	0.00 RPM	1.51 RPM
SRP021940_embryo	0.03 RPM	11.84 RPM
SRP021940_placental_villous	0.00 RPM	2.65 RPM
SRP021940_synovial_membrane	0.14 RPM	6.51 RPM
SRP021940_testis	0.32 RPM	21.04 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_479 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_479 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_479 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019632	4 retrocopies	retro_cjac_2584, retro_cjac_2787, retro_cjac_453, retro_cjac_952,
Equus caballus	ENSECAG00000014919	1 retrocopy	retro_ecab_479 ,
Otolemur garnettii	ENSOGAG00000033817	1 retrocopy	retro_ogar_1736,