RetrogeneDB ID: retro_ecab_1

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 12:12386414..12387311(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000006775
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000008180
• Aliases: None
• Description: None

Sequence

>retro_ecab_1
ATGGCCAGTACAAATAACGTGACTGAGTTAATATTCACTGGCCTTTTCCGGGATCCAGATGTGCAGAGAGTGTGTTTTGT
GGCATTTCTCATTGTGTACTTGGCCACAGTGGTGGGCAATGGCCTCATCGTTCTGACGGTTAGCATCAGCAAAAGTCTCA
ATTCCCCCATGTACTTCTTCCTAAGCCAGCTGTCTCTGGTGGAGATCAGTTACTCCTCTACGGTTGTCCCTAAATTCATC
ACAGACTTACTTGCCAAGATTAAAACCATCTCCCTGGAGGGCTGTCTGGCTCAGATATTCTTCTTCCACTTCTTTGGAGT
CACTGAGATCCTCCTGCTTGTGGTGATGGCCTATGACCGCTATGTGGCCATCTGCAAGCCTCTTCATTATATGAACATTA
TGAGCCACCAAGTGTGTCAAGTACTGGTGGCTGGTTCCTGGCTGGGAGGCTTTGTTCACTCCATAATTCAGATTCTCATC
ACCATCCAATTGCCCTTCTGTGGTCCCAATGTGATTGACCACTACTTCTGTGATCTCCAGCCATTGTTCAAGCTTACCTG
CACTGACACCTTTGTGGAGGGGGTTATTGTGTTGGCCAATAGTGGCTTAATTGCTTTGTGCTCCTTCCTCATCTTGGTGA
CATCCTATATTGTCATCCTGGTCAACGTTAGGAACCATTCTGCAGAGGGAAAGCGCAAAGCCCTCTCTACCTGTGCCTCT
CACATCACAGTGGTCATCTTGTTCTTCGGACCTGCCATCTTCTTCTACATGCGACCCTCCTCCACCTTCACTGAGGACAA
ACTAGTGGCTGTGTTCTATACTGTCATCACCCCAATGCTGAACCCCATCATCTACACACTCAGAAATGCTGAGGTGAAAA
TGGCCATGAGGAGGTTG

Alignment

ORF - retro_ecab_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.15 %
• Parental protein coverage: 96.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NMTELIFTGIFQDPEVQRVCFEVFILVYLATVVGNGLIILMVSISNSLHSPMYFFLSHLSLAEINCNYSS
          N.TELIFTG.F.DP.VQRVCF..F..VYLATVVGNGLI.L.VSIS.SL.SPMYFFLS.LSL.EI...YSS
Retrocopy NVTELIFTGLFRDPDVQRVCFVAFLIVYLATVVGNGLIVLTVSISKSLNSPMYFFLSQLSLVEIS--YSS

Parental  TVVPKFITDLLAKIKTISLEGCLAQIFFFHFFGVTEIFLLVVMAYDRYVAICKPLHYMNIMSNLLCYVMV
          TVVPKFITDLLAKIKTISLEGCLAQIFFFHFFGVTEI.LLVVMAYDRYVAICKPLHYMNIMS...C.V.V
Retrocopy TVVPKFITDLLAKIKTISLEGCLAQIFFFHFFGVTEILLLVVMAYDRYVAICKPLHYMNIMSHQVCQVLV

Parental  AGSWLGGFFHSIIQILITIQLPFCGPNVIDHYFCDLHPLFKLACSDTFVEGVIVLVNSGLISVFSFLLLV
          AGSWLGGF.HSIIQILITIQLPFCGPNVIDHYFCDL.PLFKL.C.DTFVEGVIVL.NSGLI...SFL.LV
Retrocopy AGSWLGGFVHSIIQILITIQLPFCGPNVIDHYFCDLQPLFKLTCTDTFVEGVIVLANSGLIALCSFLILV

Parental  SSYIIIMYNLRNHSAEGRRKALSTCASHITVVILFFGPAIFLYMRPSSTFTEDKLVAVFYTVITPMLNPI
          .SYI.I..N.RNHSAEG.RKALSTCASHITVVILFFGPAIF.YMRPSSTFTEDKLVAVFYTVITPMLNPI
Retrocopy TSYIVILVNVRNHSAEGKRKALSTCASHITVVILFFGPAIFFYMRPSSTFTEDKLVAVFYTVITPMLNPI

Parental  IYTLRNAEMKIAMRRL
          IYTLRNAE.K.AMRRL
Retrocopy IYTLRNAEVKMAMRRL

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	0.10 RPM	0.00 RPM
SRP021940_embryo	0.26 RPM	0.00 RPM
SRP021940_placental_villous	0.00 RPM	0.00 RPM
SRP021940_synovial_membrane	0.03 RPM	0.00 RPM
SRP021940_testis	0.13 RPM	0.00 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000008180	1 retrocopy	retro_ecab_1 ,