RetrogeneDB ID: retro_ecab_232

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 10:16587153..16587756(-)
• Located in intron of: ENSECAG00000026972

Retrocopy information

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

Parental gene information

• Parental gene symbol: EBAG9
• Ensembl ID: ENSECAG00000009719
• Aliases: None
• Description: estrogen receptor binding site associated, antigen, 9 [Source:HGNC Symbol;Acc:3123]

Sequence

>retro_ecab_232
CAGTTTCAGCTACTTGAAGTCTGTGTGTGCCCAGCAACAGTATTGTCACTCCTAAAGGGATTAATATGCAGATCTAACAG
AGGATGGAAATTAAGTCGAGATCAAATAACTTTGCCAACTACAGTTGATTGTTCAAAGTTCCTGGGCAGATGGGCGTTGA
AGATGGACCTCCTGGGAGGAAGATGCACCCACACGTGTAAAGACGGAAGGAGGGACTGGGAAAGTGGCCACACTATGAAA
AACAGCGGGAAACACAAAGGAACCCGACAATTTTAAGGACATGATAACAACTAGAAGGAAAACTGAGAAAATCAGTATCG
AGAAGAGCGAACTATTAAATTTTCACCAGTCAGTTGGGAGCACAGTTTTCTCTAGTAAATTAGCAACTACACAGGATGTT
CCTTTTATGCATCTATCTCCAGAATTAGGTGACAGAGAGGCCTGGCAAGAAAATACCAGTGCACGGGAAGAAGGTATGGC
CTGGCGAGCAGAAGCTCTGTAGCAGCAGAAAACAGCAGACGGAGAACAAAGAACCGCAGAAAACAAAGGAAGAAAATGGA
AAAGGAAGCACGGGGAGGACAGAAGAAGGAACAATGGAAACTG

Alignment

ORF - retro_ecab_232 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.46 %
• Parental protein coverage: 95.77 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QFRLFKVCTCLATVFSFLKRLICRSGRGRKLSGDQITLPTTVDYSS-VPKQTDVEE-WTSWDEDAPTSVK
          QF.L..VC.C.ATV.S.LK.LICRS.RG.KLS.DQITLPTTVD.S..VP.Q..VE..WTSW.EDAPT.VK
Retrocopy QFQLLEVCVCPATVLSLLKGLICRSNRGWKLSRDQITLPTTVDCSK<VPGQMGVED<WTSWEEDAPTRVK

Parental  IEGGNGNVATQ-QNALEQLEPDYFKDMTPTIRKTQKIIIKKREPLNFGIPDGSTGFSSRLAATQDMPFIH
          .EGG.G.VAT....A....EPD.FKDM..T.RKT.KI.I.K.E.LNF....GST.FSS.LA.TQD.PF.H
Retrocopy TEGGTGKVATL*KTAGNTKEPDNFKDMITTRRKTEKISIEKSELLNFHQSVGSTVFSSKLATTQDVPFMH

Parental  QSPELGDLDTWQENTNAWEEEEDAAWQAEEVLRQQKIADREKRAAE-QQRKKMEKEAQRLMKKEQNKI
          .SPELGD...WQENT.A...EE..AW.A.E.L.QQK.AD.E.R.AE..QRKKMEKEA....KKEQ.K.
Retrocopy LSPELGDREAWQENTSA--REEGMAWRA-EAL*QQKTADGEQRTAE<KQRKKMEKEARGGQKKEQWKL

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	24.03 RPM
SRP021940_cerebellum	0.31 RPM	18.54 RPM
SRP021940_embryo	0.13 RPM	15.83 RPM
SRP021940_placental_villous	0.00 RPM	16.31 RPM
SRP021940_synovial_membrane	0.00 RPM	8.48 RPM
SRP021940_testis	0.00 RPM	25.90 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_232 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_232 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_232 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006190	1 retrocopy	retro_amel_1656,
Choloepus hoffmanni	ENSCHOG00000007848	5 retrocopies	retro_chof_1116, retro_chof_1455, retro_chof_1805, retro_chof_2245, retro_chof_751,
Cavia porcellus	ENSCPOG00000001059	1 retrocopy	retro_cpor_1185,
Dipodomys ordii	ENSDORG00000010177	2 retrocopies	retro_dord_418, retro_dord_91,
Equus caballus	ENSECAG00000009719	2 retrocopies	retro_ecab_211, retro_ecab_232 ,
Felis catus	ENSFCAG00000025490	1 retrocopy	retro_fcat_777,
Macropus eugenii	ENSMEUG00000014115	3 retrocopies	retro_meug_1871, retro_meug_2058, retro_meug_597,
Monodelphis domestica	ENSMODG00000004795	2 retrocopies	retro_mdom_261, retro_mdom_665,
Mus musculus	ENSMUSG00000022339	1 retrocopy	retro_mmus_3501,
Rattus norvegicus	ENSRNOG00000004220	2 retrocopies	retro_rnor_2914, retro_rnor_2980,
Sus scrofa	ENSSSCG00000006024	1 retrocopy	retro_sscr_569,
Ictidomys tridecemlineatus	ENSSTOG00000015326	1 retrocopy	retro_itri_1119,
Tursiops truncatus	ENSTTRG00000001745	2 retrocopies	retro_ttru_496, retro_ttru_672,