RetrogeneDB ID: retro_ecab_689

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 28:32063978..32064702(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000006639
• Aliases: None
• Description: None

Sequence

>retro_ecab_689
AAGGTAAAAGAGAGTGTAGAGAAACAATTCAACGAGTTCAGCAGCTACTGCACAAAAGAGATTGAAACTATAAAGAAGAA
TCAATTAGAAATATTAGAGATGAAAGATGCAAGGGAAGAAATAAAACAAAATATGGATTCCCTAAATGCTTGAGTGGACA
CCATAGAGGAGCATCAGCATAATTGAAGATAGACATGTTGAAATACTCCAGATAGAGGAGGAGAGAGAACTAAGACTAAA
AAGAAATGAAGAAAGTCTCCGAGAAATATCTGACTCAATTAGGAAATGCAACATAAGAATTATAGGTATTCAAGGAGAAG
AGAAGAAGAATAGAGTAGAAAGCTTGTTCAAAGAAATAATAGCAGAGAATTTCCCAAACCTAGGGAAGGAAATCCACATG
GAAGAGACTGTCAGATCCCCTAAATATGTCAATGTAAAAAGACCTACTGCAAGGCATATAGTAGTGAAATTGGCAAAAGT
GAATGACAAAGAAAGAATACAGAAGAAAATAACCTACAAAGGAACCCCCGTCAGGCTTTCAGTGGATTTCCCTGCGGAAA
GCTTACAGGCTAGGAGAGAGTGGAATGACATATTCAAATCTTTGAAGGACAAAAGCTTTCATCCAAGAATACTCTGTCCA
GTGAAAATATCCTTCAGATATGATGGAGAAATAAAAACATTTTCAGACAAACATAAGCTAAGGGAGTTCATAGCTATGAG
ACCT

Alignment

ORF - retro_ecab_689 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.6 %
• Parental protein coverage: 95.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RILTDLGRRMGELSENINKEVGNIKKNQS---EMKNTILERKISLEGLNSRVDDTEEW-MSKLDKRQEEI
          ...........E.S....KE...IKKNQ....EMK....E.K.....LN..V.DT.E...S....R..EI
Retrocopy KVKESVEKQFNEFSSYCTKEIETIKKNQLEILEMKDAREEIKQNMDSLNA*V-DTIEE>ISIIEDRHVEI

Parental  TQAEQIKEKKIQKEGENFQETTDSMRKCNIRIIRIPEGDEKENGTESVLKGIIAENFPDLENETETRVEE
          .Q.E...E.......E...E..DS.RKCNIRII.I..G.EK.N..ES..K.IIAENFP.L..E.....EE
Retrocopy LQIEEERELRLKRNEESLREISDSIRKCNIRIIGI-QGEEKKNRVESLFKEIIAENFPNLGKEIH--MEE

Parental  AFRSPRYVNVKRTTARHIVVKLAKLNDERILRAARQKKITYKGTPLRLSVDFSVETLQAWRDWNDILKTL
          ..RSP.YVNVKR.TARHIVVKLAK.ND........QKKITYKGTP.RLSVDF..E.LQA.R.WNDI.K.L
Retrocopy TVRSPKYVNVKRPTARHIVVKLAKVNDKERI----QKKITYKGTPVRLSVDFPAESLQARREWNDIFKSL

Parental  KDNNLQPRILYPAKISFRYEGE-KSFLDKQKLRDFTAMRP
          KD....PRIL.P.KISFRY.GE.K.F.DK.KLR.F.AMRP
Retrocopy KDKSFHPRILCPVKISFRYDGEIKTFSDKHKLREFIAMRP

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	0.03 RPM
SRP021940_placental_villous	0.00 RPM	0.00 RPM
SRP021940_synovial_membrane	0.00 RPM	0.05 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_689 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_689 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_689 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000005242	2 retrocopies	retro_ecab_192, retro_ecab_934,
Equus caballus	ENSECAG00000006639	4 retrocopies	retro_ecab_274, retro_ecab_484, retro_ecab_671, retro_ecab_689 ,