RetrogeneDB ID: retro_ecab_1053

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:19204783..19205595(+)
• 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_1053
AACAAAACAGAGATAAATGATCTACCTGGCAAAGAGTACAAAGTAATAGTCATAAGGATGCTCACTGATCTTGGGACAAG
AATGGATGAACTCAGTGAGAACTTCAACAAAGAATTGGAAAATATAAAAAAGACCCAATCAGAAATGAAGAATACTGGAA
ATGAAAAATTTACTAGAGCTACTCAATAGCAGAGTAGATGATACAGAAGAACAGATCAGTGAGCTGGATGAAAGACTAGA
GGGAGTCTTCCAAGCTGAACAGATAAAGGAAAAAAAGAATTAAAAAGAACGATGACAGTCTAAGGGACCTCTGGTACAAC
ATCAAGCACACTAACATCCATATTATAGGTGTCCCAGAAGGAGAAGAGAGAGACAAAGGAGCAGAGAATCTATTTGAAGA
AATAATAGCTGAAAATTTTCCTAACCTGAAGAAGGAAACAGACATCCAGGTACAGGAAGTACAGAGAGCACCAAACAAGA
TGAACCCAAAGAGGCCCACTCCAAGACACATTATAAGTAAAATGTCAAGAATTAAAGGGAGAGAATCCTACAAACTGCAA
GAGAAAGGCAGCAAGTGACATGGAAAGGAACCTCTATAAGGCTATCAGCTGACTTTTCAGCAGAAACTTTACATGCTAGA
AGCGAGTGGCACAATATATTTAAAGTGCTAAAAGGAAAAAACCTGCAGCCAAGAATACTCTACCCAGCAAGGTTATCATT
CAGAATTGAAGGAGAGATAAAGAGTTTCCCAGACAAGCAAAAACTAAAGGAGTTTATCACCAAGAAAACTAGTTTTAAAA
GAAATGCTAAAG

Alignment

ORF - retro_ecab_1053 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.82 %
• Parental protein coverage: 98.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  NEKEINNVTDEEYKLTVIRVLTNLGRRMDELSENFKKELENKKRT-NQKKTTILEIKNSLEGLNGRVDDT
          N..EIN.....EYK..VIR.LT.LG.RMDELSENF.KELEN.K.T.NQ.K..ILE.KN.LE.LN.RVDDT
Retrocopy NKTEINDLPGKEYKVIVIRMLTDLGTRMDELSENFNKELENIKKT>NQ-K*RILEMKNLLELLNSRVDDT

Parental  EEWISELDERLEEITQASQIKE-TRIIKNTNMVKELWDNIKHNNIRLVGVPEGAERDKGAENLFEEVIAE
          EE.ISELDERLE...QA.QIKE..RI.KN......LW.NIKH.NI...GVPEG.ERDKGAENLFEE.IAE
Retrocopy EEQISELDERLEGVFQAEQIKE>KRIKKNDDSLRDLWYNIKHTNIHIIGVPEGEERDKGAENLFEEIIAE

Parental  NFPNLRKETDWKTKKANRSPNFTNVKRPTPRHIVVKLAKVNDKEK-ILRAARQNKITYKGTSIRLSENFS
          NFPNL.KETD.......R.PN..N.KRPTPRHI..K.......E.....A......T.KGTSIRLS..FS
Retrocopy NFPNLKKETDIQVQEVQRAPNKMNPKRPTPRHIISKMSRIKGRES<LQTARERQQVTWKGTSIRLSADFS

Parental  ADTLQARREWNDIFRTLKDKNLQPRILYAVKISFKYDGEIKTFQDKQKLREFIATRPP-LQEMLR
          A.TL.AR.EW..IF..LK.KNLQPRILY....SF...GEIK.F.DKQKL.EFI......L.EML.
Retrocopy AETLHARSEWHNIFKVLKGKNLQPRILYPARLSFRIEGEIKSFPDKQKLKEFITKKTS>LKEMLK

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	0.00 RPM	0.10 RPM
SRP021940_placental_villous	0.00 RPM	0.00 RPM
SRP021940_synovial_membrane	0.00 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_1053 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1053 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1053 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,