RetrogeneDB ID: retro_ecab_360

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 16:41618421..41618609(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SHFM1
• Ensembl ID: ENSECAG00000018179
• Aliases: None
• Description: split hand/foot malformation (ectrodactyly) type 1 [Source:HGNC Symbol;Acc:10845]

Sequence

>retro_ecab_360
ATGTCAGAGAAAACGCAGCCAGTAGACTTAGGTCTCCTGAAGGAGGACGAGTTCCCTGCGGAAGACAAGGCTGGTTTAGA
TGAAGATGCACATGTCTGGGAGGATAATTAGGATGATAACAATGTACAGGATGACTTCTCCAGTTATGAGCCGAACTAGA
GAAACATGGTTATAAGATGGAGACCTCA

Alignment

ORF - retro_ecab_360 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.83 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSEKKQPVDLGLLEEDDEFEEFPAEDWAGLDEDEDAHVWEDNWDDDNVEDDFSN-QLRAELEKHGYKMET
          MSEK.QPVDLGLL.E.....EFPAED.AGLDED..AHVWEDN.D.DN...D....QL.AELEKHGYKMET
Retrocopy MSEKTQPVDLGLLKE----DEFPAEDKAGLDED--AHVWEDN*D-DNNVQDDFS<QL*AELEKHGYKMET

Parental  S
          S
Retrocopy S

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	25.97 RPM
SRP021940_cerebellum	0.05 RPM	15.94 RPM
SRP021940_embryo	0.31 RPM	33.40 RPM
SRP021940_placental_villous	0.05 RPM	38.54 RPM
SRP021940_synovial_membrane	0.08 RPM	27.34 RPM
SRP021940_testis	0.13 RPM	29.73 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_360 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_360 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_360 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010434	1 retrocopy	retro_amel_1234,
Equus caballus	ENSECAG00000018179	1 retrocopy	retro_ecab_360 ,
Erinaceus europaeus	ENSEEUG00000002237	2 retrocopies	retro_eeur_290, retro_eeur_586,
Felis catus	ENSFCAG00000023254	2 retrocopies	retro_fcat_1138, retro_fcat_121,
Myotis lucifugus	ENSMLUG00000014208	1 retrocopy	retro_mluc_948,
Oryctolagus cuniculus	ENSOCUG00000026246	3 retrocopies	retro_ocun_1324, retro_ocun_452, retro_ocun_77,
Sus scrofa	ENSSSCG00000015337	1 retrocopy	retro_sscr_67,
Ictidomys tridecemlineatus	ENSSTOG00000011501	1 retrocopy	retro_itri_253,
Tupaia belangeri	ENSTBEG00000016474	3 retrocopies	retro_tbel_2837, retro_tbel_2998, retro_tbel_3844,