RetrogeneDB ID: retro_ecab_990

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 8:37009018..37009830(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000012757
• Aliases: None
• Description: None

Sequence

>retro_ecab_990
AATGAAACAGAAATAAGTGACCTACCTGACAAAGAGTTCAAACAAAAACTCCTAAGGATGCTCACAGATATTGGGAGAAG
ACTGGATGAACACAGTGAGCTCATCAACAAGGAACTGGAAAATATAAAAAAAAAAAACCAATCAGAAATGAAGACTACAA
TACTGGAAATGAAAAATTCACTAGAGGGACTCAATAGCTGAGTAGAGGATGCAGAAGAATGGATCAGCGAGCTAGATGAA
AGACTAGAGGAAATCACCCAAGCTGAACAGAAAAAAGAAAAAAGAATTACAGTGAGAACAATCTAAGGGAACTCTGGAAC
AATATCAAGCACATTAACATTCAGAGTATAGGTGTCCCAGAAGGAGAAGACAGAGACAAAGGGGCAGAAAATTTATTTGA
AGAAATAATAGATGAAAATTTTCCTAAGCTAAGGAAGGAAACAGACATCCAAGTACAGGAAGCACAGAGAGCTCCAAACA
AGATAAGCCCAAAGAGGCCCACACCAAGACACATTATAAATAAAAGGTCCAAAATTAAAGATAAAGAGGAATCCTAAAAG
TGGCAAGAGAAAGGCAACAATTGACATACAAAGGAAAGCCCATAAGGCTATCAGTGTACTTCTCAGTTGAAACCGTACAG
GTGAGAAGAGAATGGCATGACATATTTAAAGTGCTAAAAGGAAAAAAACCTACAGCCAAGAATACTCTATCCATCAAGGG
TGTCATTCAGAATGGAAGGAGAAATAAAGAGCTTCCCAGACAAACAAAAATTAAAAGAGTTTACCACCAAGAAACCAGTT
CTACAAGAAATG

Alignment

ORF - retro_ecab_990 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.36 %
• Parental protein coverage: 98.18 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NEKEINNVTDEEYKLTVIRVLTNLGRRMDELSENFKKELENKKRTNQK--KTTILEIKNSLEGLNGRVDD
          NE.EI....D.E.K....R.LT..GRR.DE.SE...KELEN.....Q...KTTILE.KNSLEGLN..V.D
Retrocopy NETEISDLPDKEFKQKLLRMLTDIGRRLDEHSELINKELENXXXXXQSEMKTTILEMKNSLEGLNS*VED

Parental  TEEWISELDERLEEITQASQIKETRIIKNT-NMVKELWDNIKHNNIRLVGVPEGAERDKGAENLFEEVIA
          .EEWISELDERLEEITQA.Q.....I...T.N...ELW.NIKH.NI...GVPEG..RDKGAENLFEE.I.
Retrocopy AEEWISELDERLEEITQAEQXXXXXITVRT<NL-RELWNNIKHINIQSIGVPEGEDRDKGAENLFEEIID

Parental  ENFPNLRKETDWKTKKANRSPNFTNVKRPTPRHIVVKLAKVNDKEK-ILRAARQ-NKITYKGTSIRLSEN
          ENFP.LRKETD.....A.R.PN....KRPTPRHI..K..K..DKE..IL..AR.....TYKG..IRLS..
Retrocopy ENFPKLRKETDIQVQEAQRAPNKISPKRPTPRHIINKRSKIKDKEE<ILKVARERQQLTYKGKPIRLSVY

Parental  FSADTLQARREWNDIFRTL-KDKNLQPRILYAVKISFKYDGEIKTFQDKQKLREFIATRPPLQEM
          FS..T.Q.RREW.DIF..L.K.KNLQPRILY....SF...GEIK.F.DKQKL.EF....P.LQEM
Retrocopy FSVETVQVRREWHDIFKVL>KEKNLQPRILYPSRVSFRMEGEIKSFPDKQKLKEFTTKKPVLQEM

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	0.00 RPM
SRP021940_cerebellum	0.00 RPM	0.00 RPM
SRP021940_embryo	0.05 RPM	0.10 RPM
SRP021940_placental_villous	0.00 RPM	0.00 RPM
SRP021940_synovial_membrane	0.05 RPM	0.00 RPM
SRP021940_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_990 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_990 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_990 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000012757	4 retrocopies	retro_ecab_1053, retro_ecab_387, retro_ecab_602, retro_ecab_990 ,