RetrogeneDB ID: retro_ecab_1104

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:29280052..29280500(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000006602
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ARPC5
• Ensembl ID: ENSECAG00000019128
• Aliases: None
• Description: actin related protein 2/3 complex, subunit 5, 16kDa [Source:HGNC Symbol;Acc:708]

Sequence

>retro_ecab_1104
ATGTCGAAGAACACGGTGTCGTCAGCCCGGTTCCGGAAGGTGGATGTGGATGAGTATGACGAGAACAAGTTCGTGGACGA
GGAAGACGGGGGCGACGGGCAGGCCGGGCCGACGAGGGCGAGGTGGACTCCTGCCTGCGGCAAGGAAACACGATGGCTGC
CCTACAGGCAGCTCTGAAAAACCCCCCATCAACACCAAGAGTCAGGCGGTGAAGGATCGAGCAGGCAGCATTGTCTTGAA
GGTACTCATCTCTTTTAAAGCTAATGATATTGAAAAGGCAGTTCAATCCCTGGACAAGAATGGTGTGGATCACCTCATGA
AGTATATTTATAAAGGCTTTGAGAGCCCCTCTGACAATAGCAGTGCTGTGTTATTGCAGTGGCATAAAAAGGCACTTGCT
GCCGGAGGAGTAGGGTCCGTTGTTCGAGTCTTGACTGCGAGGAAAACC

Alignment

ORF - retro_ecab_1104 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.79 %
• Parental protein coverage: 99.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSKNTVSSARFRKVDVDEYDENKFVDEEDGGDGQAGP-DEGEVDSRLRQYPCPRDPRAALKN-PPINTKS
          MSKNTVSSARFRKVDVDEYDENKFVDEEDGGDGQAGP.DEGEVDS.LRQ........AALKN.PPINTKS
Retrocopy MSKNTVSSARFRKVDVDEYDENKFVDEEDGGDGQAGP<DEGEVDSCLRQGNTMAALQAALKN<PPINTKS

Parental  QAVKDRAGSIVLKVLISFKANDIEKAVQSLDKNGVDLLMKYIYKGFESPSDNSSAVLLQWHEKALAAGGV
          QAVKDRAGSIVLKVLISFKANDIEKAVQSLDKNGVD.LMKYIYKGFESPSDNSSAVLLQWH.KALAAGGV
Retrocopy QAVKDRAGSIVLKVLISFKANDIEKAVQSLDKNGVDHLMKYIYKGFESPSDNSSAVLLQWHKKALAAGGV

Parental  GSIVRVLTARKT
          GS.VRVLTARKT
Retrocopy GSVVRVLTARKT

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	0.71 RPM	9.27 RPM
SRP021940_cerebellum	1.51 RPM	17.14 RPM
SRP021940_embryo	1.69 RPM	18.77 RPM
SRP021940_placental_villous	5.05 RPM	60.09 RPM
SRP021940_synovial_membrane	4.01 RPM	47.79 RPM
SRP021940_testis	0.64 RPM	8.12 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1104 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1104 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1104 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000019128	1 retrocopy	retro_ecab_1104 ,
Echinops telfairi	ENSETEG00000014969	1 retrocopy	retro_etel_1922,
Monodelphis domestica	ENSMODG00000007194	1 retrocopy	retro_mdom_968,
Mus musculus	ENSMUSG00000008475	1 retrocopy	retro_mmus_281,