RetrogeneDB ID: retro_ecab_596

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 22:34818278..34818509(-)
• Located in intron of: ENSECAG00000021884

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM18
• Ensembl ID: ENSECAG00000008640
• Aliases: None
• Description: transmembrane protein 18 [Source:HGNC Symbol;Acc:25257]

Sequence

>retro_ecab_596
ATGCTGTCCGCCTTCTCAGTCAGCTCTTTCCCCACCAGCATTCCTGCTGTGATCATGCAGACAGACCGGACCGAGCTGCG
GCTCATAGGGCTGCCTGGCTTCCATGTGGTCTGGCTGCTGCTCACGTGTTTCTCCTTCCAGAGGTATAAACTGTAGGTGG
GGCATTTCCTGTGCCTAATTTTAGTCTGTTGTGCTGAATATATCAATGAAGTGGCAGCAATGAATTGGAGG

Alignment

ORF - retro_ecab_596 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.36 %
• Parental protein coverage: 55.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPSPFSVSSFPVSIPAVIAQTDWTEPWLLGLGGFHLLCLLLTWFSSKRYRLQVGHFLCLIALVCCAESIN
          M.S.FSVSSFP.SIPAVI.QTD.TE..L.GL.GFH...LLLT.FS..RY.L.VGHFLCLI.LVCCAE.IN
Retrocopy MLSAFSVSSFPTSIPAVIMQTDRTELRLIGLPGFHVVWLLLTCFSFQRYKL*VGHFLCLI-LVCCAEYIN

Parental  EVAALNWR
          EVAA.NWR
Retrocopy EVAAMNWR

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	0.30 RPM	6.91 RPM
SRP021940_cerebellum	0.05 RPM	12.93 RPM
SRP021940_embryo	0.03 RPM	12.27 RPM
SRP021940_placental_villous	0.00 RPM	9.24 RPM
SRP021940_synovial_membrane	0.05 RPM	9.44 RPM
SRP021940_testis	0.13 RPM	48.66 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_596 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_596 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_596 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000543	1 retrocopy	retro_chof_31,
Cavia porcellus	ENSCPOG00000012522	1 retrocopy	retro_cpor_1298,
Dipodomys ordii	ENSDORG00000001854	1 retrocopy	retro_dord_416,
Equus caballus	ENSECAG00000008640	1 retrocopy	retro_ecab_596 ,
Monodelphis domestica	ENSMODG00000014284	1 retrocopy	retro_mdom_790,