RetrogeneDB ID: retro_ecab_1093

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:121567569..121568229(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000014684
• Aliases: None
• Description: None

Sequence

>retro_ecab_1093
GAAGAAAGAGCTGTAGCTGAGGCCGAGGCTCCAGGTGACGAAGGAGCTGCAGGTGTGGCAAGAGCCATCAACGAGGCAGC
AGCCCGGAGCCAGCACTGGCGGCAGACGTTGCAGCCTCTGCTCGATGCTATGGCCTACCGGGTACTGAGAAGGTTTTCTG
GGGTGGAAGAGCCGGGCTGTGGAGAAGAGTCTTTTGAGAGCGGGCTGCACCATGCCAACAACACGCTGTACCTGTGGCGC
CACATGTCAGAGAGGGAGAGGAGGAGGAGACTGGTGGAGAGCTTGGGTGGCCCCGTGCTGGATCTCATGTGTGGCCTCCT
GGAGGAAAATCCCGACACCCCTGCACAGGACTGCCTGGCCGCGCTGGTGCAGGTGTTCGGGAACAAGGATGCCCAGATGA
CCGCACGGCTGAAGTTCCTGACTTGTGCGCAGAGGCCCCAGGAGGCTCTCTTTGCCTACGTGATGCGCCTGGAAGGCCTG
CTGCAGGCGGCCTTGGAGAAGGGGGCCATCCGGCCCGCCATCGCAGAGCAGCTGCGCGCCAGGCAGGTGCTGATGCAGGC
CCGGCCCAACGAGACGCTCGAGAACAAGCTGAGGAGGATGCGTCTGGAGAGGAGGCCGCCTGGCTTCCTGGGGATGCTGC
AGCTCATTCGGGAGACGGAG

Alignment

ORF - retro_ecab_1093 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.89 %
• Parental protein coverage: 66.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QRQAVAGRAEAPGEEGAAGPGVPAASEEEAAAARSQHWRQTLQSLLDAMAYRALRRFSGVEEPGCGEESF
          ...AVA..AEAPG.EGAA..GV..A..E..AAARSQHWRQTLQ.LLDAMAYR.LRRFSGVEEPGCGEESF
Retrocopy EERAVA-EAEAPGDEGAA--GVARAINE--AAARSQHWRQTLQPLLDAMAYRVLRRFSGVEEPGCGEESF

Parental  ESWLHHANDTLYLWRHMSERERRSRLVESLGGPALDLICGLLEENPDTPVQDCLAALVQVFGSKDAQMTA
          ES.LHHAN.TLYLWRHMSERERR.RLVESLGGP.LDL.CGLLEENPDTP.QDCLAALVQVFG.KDAQMTA
Retrocopy ESGLHHANNTLYLWRHMSERERRRRLVESLGGPVLDLMCGLLEENPDTPAQDCLAALVQVFGNKDAQMTA

Parental  RLKFLTCAQRPQEALFAYVMRLEGLLQAALEKGAIRPAIADQLRARQVLMGARPNETLENKLRRMRLERR
          RLKFLTCAQRPQEALFAYVMRLEGLLQAALEKGAIRPAIA.QLRARQVLM.ARPNETLENKLRRMRLERR
Retrocopy RLKFLTCAQRPQEALFAYVMRLEGLLQAALEKGAIRPAIAEQLRARQVLMQARPNETLENKLRRMRLERR

Parental  PPGFLGMLQLIRETE
          PPGFLGMLQLIRETE
Retrocopy PPGFLGMLQLIRETE

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	0.78 RPM
SRP021940_embryo	0.00 RPM	0.15 RPM
SRP021940_placental_villous	0.00 RPM	0.05 RPM
SRP021940_synovial_membrane	0.00 RPM	0.00 RPM
SRP021940_testis	0.06 RPM	6.01 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1093 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1093 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1093 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	ENSECAG00000014684	1 retrocopy	retro_ecab_1093 ,