RetrogeneDB ID: retro_ecab_156

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:13144009..13144264(-)
• Located in intron of: ENSECAG00000023764

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: FCER1G
• Ensembl ID: ENSECAG00000009535
• Aliases: None
• Description: Fc fragment of IgE, high affinity I, receptor for; gamma polypeptide [Source:HGNC Symbol;Acc:3611]

Sequence

>retro_ecab_156
ATGCCAGCAGTGGTCTTGCTCTCACTCCTTTTGGTTGAACAAGCAGCGGCCCTGGAAGAGCATCAGCTCTGCTGTATCCT
GGATGCTATCCTGTTTTTGTGTGGTTTTGTCCTCATCCTGCTCTACTGTCGACTCAAGAGCCAGGTGCTGAAGGCAGCCA
TAGCCCCCGATGAGAAATCAGATGACATTTACACGGGCTTGAGTACCCTGAACCAGGAGACTTATGGGACCCTGCAGCAT
GAGAAACCGCCACAG

Alignment

ORF - retro_ecab_156 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.82 %
• Parental protein coverage: 98.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IPAVVLLLLLLVEQAAALGEPQLCYILDAILFLYGIVLTLLYCRLKIQVRKAAIASYEKSDAVYTGLSTR
          .PAVVLL.LLLVEQAAAL.E.QLC.ILDAILFL.G.VL.LLYCRLK.QV.KAAIA..EKSD..YTGLST.
Retrocopy MPAVVLLSLLLVEQAAALEEHQLCCILDAILFLCGFVLILLYCRLKSQVLKAAIAPDEKSDDIYTGLSTL

Parental  TQETYETLKHEKPPQ
          .QETY.TL.HEKPPQ
Retrocopy NQETYGTLQHEKPPQ

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	0.41 RPM	2.77 RPM
SRP021940_cerebellum	0.10 RPM	11.43 RPM
SRP021940_embryo	0.03 RPM	5.11 RPM
SRP021940_placental_villous	0.14 RPM	31.51 RPM
SRP021940_synovial_membrane	0.08 RPM	112.99 RPM
SRP021940_testis	0.00 RPM	3.01 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_156 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_156 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_156 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000009535	1 retrocopy	retro_ecab_156 ,