RetrogeneDB ID: retro_ecab_673

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 27:13541684..13542034(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GABARAPL3
• Ensembl ID: ENSECAG00000014832
• Aliases: None
• Description: GABA(A) receptors associated protein like 3, pseudogene [Source:HGNC Symbol;Acc:4069]

Sequence

>retro_ecab_673
ATGAAGTTCCAGTAGAAGAAGGACCATCCCTTTAAATATTGGAAAAGAAAGGAGAAAAGATCTGGAAGAAATATCCAGAC
AGAGTCCCTGTGATCGTGGAGAAATCTACTAAAGTCAGAGTGCCTGATCTGGACGAGAGGAAGTACCTAGCGCCCTCTGA
CCTCACTGTTGGCCAGTTCTACTTCTTAATCTGGAAGAGGATCCACCTGAGACCTGAGGACGCCTTATTCCTCTTTGTCA
ACAACACTATCCGTCCCACCAGCGCTGTAATGGGCCAGCTGTATGAGGACAACCATGAGGGAGACTATTTTCTGTATGTG
GCCTGCAGTGATGAGAGTGTCTATGGGAAG

Alignment

ORF - retro_ecab_673 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.75 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKFQYKEDHPFEYRK-KEGEKIRKKYPDRVPVIVEKAPKARVPDLDKRKYLVPSDLTVGQFYFLIRKRIH
          MKFQ.K.DHPF.Y.K.K.GEKI.KKYPDRVPVIVEK..K.RVPDLD.RKYL.PSDLTVGQFYFLI.KRIH
Retrocopy MKFQ*KKDHPFKYWK<KKGEKIWKKYPDRVPVIVEKSTKVRVPDLDERKYLAPSDLTVGQFYFLIWKRIH

Parental  LRPEDALFFFVNNTIPPTSATMGQLYEDNHEEDYFLYVAYSDESVYGK
          LRPEDALF.FVNNTI.PTSA.MGQLYEDNHE.DYFLYVA.SDESVYGK
Retrocopy LRPEDALFLFVNNTIRPTSAVMGQLYEDNHEGDYFLYVACSDESVYGK

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	16.35 RPM
SRP021940_cerebellum	0.26 RPM	294.98 RPM
SRP021940_embryo	0.00 RPM	32.99 RPM
SRP021940_placental_villous	0.05 RPM	113.01 RPM
SRP021940_synovial_membrane	0.03 RPM	38.57 RPM
SRP021940_testis	0.00 RPM	67.52 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_673 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_673 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_673 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000014832	1 retrocopy	retro_ecab_673 ,
Homo sapiens	ENSG00000139112	1 retrocopy	retro_hsap_60,
Gorilla gorilla	ENSGGOG00000022360	1 retrocopy	retro_ggor_1219,
Macropus eugenii	ENSMEUG00000002873	3 retrocopies	retro_meug_1584, retro_meug_1840, retro_meug_905,
Sarcophilus harrisii	ENSSHAG00000007434	1 retrocopy	retro_shar_82,
Ictidomys tridecemlineatus	ENSSTOG00000002246	1 retrocopy	retro_itri_391,