RetrogeneDB ID: retro_ecab_399

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 17:48296178..48296673(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SSR1
• Ensembl ID: ENSECAG00000019520
• Aliases: None
• Description: signal sequence receptor, alpha [Source:HGNC Symbol;Acc:11323]

Sequence

>retro_ecab_399
GATGCTTCATTTCATTATCCTCAGGATCACCAGTTTTATATCCAGAATATCACAGTTCTTCATCTAAACACCATGGGGCC
ACTCAAGAGACAGGCAAATGTGAGTCCCCCTTCATTCCTGCTTGAGAGCCCATGGGTGGATGACCCTGTGATCTAGTCAT
GAATGTAAATTCAAAGATTTGAACGGCACTGTATTCCAAGATGCTATCTTCAATCAAACAGTTACAACTAATGAAAGAGA
GGATGTGTTAGATGGGGAAACAATCCTTACACATATGTTTCTTGCTGGTTTTGAGCTACTAGTTATTGTTGAACTTTACC
AACTCCTAGAATTTAGAAATCAAAAGAATTCCACATGGAAAATAGAAATGAATGCATCAGATCTGAGTGATGCTAATGTG
AATTCATTCCTCACAAAGCTCTGAATCAGATTAATAAAGCTTCACCCAGAAGTCTTCCCAGAAAACAGGCACGGAAGAGA
TGGATGGGATCTGAT

Alignment

ORF - retro_ecab_399 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.72 %
• Parental protein coverage: 63.46 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DASFRYPQDYQFYIQNFTALPLNTVVPPQRQATF-EYSFIPA-EPMGGRPFGLVINLN-YKDLNGNVFQD
          DASF.YPQD.QFYIQN.T.L.LNT..P..RQA...E..FIPA.EPMGG.P..LV.N.N..KDLNG.VFQD
Retrocopy DASFHYPQDHQFYIQNITVLHLNTMGPLKRQANV<ESPFIPA*EPMGG*PCDLVMNVN<FKDLNGTVFQD

Parental  AVFNQTVTIIEREDGLDGETIFMYMFLAGLGLLVVVGLHQLLESRKRKRPIQKVEMGTASQNDVDMS-WI
          A.FNQTVT..ERED.LDGETI...MFLAG..LLV.V.L.QLLE.R..K....K.EM......D......I
Retrocopy AIFNQTVTTNEREDVLDGETILTHMFLAGFELLVIVELYQLLEFRNQKNSTWKIEMNASDLSDANVN<FI

Parental  PQETLNQINKASPRRLPRKRAQKRSVGSD
          P...LNQINKASPR.LPRK.A.KR..GSD
Retrocopy PHKALNQINKASPRSLPRKQARKRWMGSD

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	60.56 RPM
SRP021940_cerebellum	0.00 RPM	11.74 RPM
SRP021940_embryo	0.00 RPM	39.87 RPM
SRP021940_placental_villous	0.00 RPM	47.68 RPM
SRP021940_synovial_membrane	0.00 RPM	34.26 RPM
SRP021940_testis	0.00 RPM	19.31 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_399 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_399 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_399 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000022731	1 retrocopy	retro_btau_1285,
Dasypus novemcinctus	ENSDNOG00000015772	1 retrocopy	retro_dnov_879,
Equus caballus	ENSECAG00000019520	1 retrocopy	retro_ecab_399 ,
Echinops telfairi	ENSETEG00000020111	1 retrocopy	retro_etel_1983,
Oryctolagus cuniculus	ENSOCUG00000009083	1 retrocopy	retro_ocun_1388,
Otolemur garnettii	ENSOGAG00000014234	1 retrocopy	retro_ogar_1465,
Ictidomys tridecemlineatus	ENSSTOG00000022608	1 retrocopy	retro_itri_1850,