RetrogeneDB ID: retro_ecab_75

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 10:21525986..21527669(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000006349
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000023688
• Aliases: None
• Description: None

Sequence

>retro_ecab_75
TATGAACATAATTTATGTGCAAAGGCTTTCAGCATGGTGACAAATCTTAAGAGATGTCGCAGAATTCACATAGAAGGGAA
ACCTTATGAATGTAGTGAATGTCCAAAATCCTTCAGGTATAGGTCAAAACTCATAATACACCAGAGAACTCACACAGGGG
AAAAGCCATACAGATGTGATGAATGTCAGAAAGCTTTCAGTACCAAATGTCATCTCACTCTGCACCAGAGAACTCATACA
GGAGAGAAACCGTATGGATGTACGGAGTGTCAGAAATCTTTCAGAACAAAGTATCATCTCATTCTACACCATAGGACTCA
TACAGGAGAGAAACCCTATGAATGCAAAGAATGTGGGAAAGCTTACAGGGAGAAGACGAAGCTCAGATTACATTACAGAA
CACACACAGGAGAGAAACCTTTTGAGTGTAGTGATTGTGGGAAAGGTTTTATGCAGAAGTCAAACCTGATTATCCATCAA
AGAATTCATACGGGAGATAAACCCTATGGATGTGGAGACTGTGAAAAGGCCTTCTGTAGTAAATCTCAGCTTGTTGTTCA
CCAGCGAATTCATACAGGAGAAAAATCTTATGAATGCAGGGAATGTGGGAAAGCCTTCAATAAAAACTCGCACCTCATGA
CACATCAGAGAATTCATATAGGAGAGAAACCTTATGAATGTAGTGAATGTGGAAAAGCTTTTGTACACACATCACAGCTC
ATTGTACATCAGAGAAATCATACTGGAAGAAAACCGTATGAATGCAAGGAATGTGGGAAAGCTTTTAACAAAAAGTCACA
CTTTGTAACACATGAGAGAATTCATACTGGAGAGAAGCCATATGAATGCAGTGAATGTGGAAAAGCTTTCATAGACAACT
CACAGCTTATTGTTCATCGAAGAACTCATACAGGAGAGAAACCTTATGAATGCAAGGAATGTAGGAAAGCCTTTAATAAA
AGGTCATCTCTCATAACACATCAGAGAATTCATACAGGAGAGAAGCCTTATGAATGCAGTGAATGTGGAAAGTCTTTTAT
AGACAAGTCACATCTCATTGTCCATCAGAGAACTCATACAGGAGAGAAACCCTATGAATGCAGTGAATGTGGAAAAGCTT
TCATACGAAAGGCAATGCTCATTGTACATCAGAGGACACATACAGGAGAGAAACCCTTTGCGTGTCTTGAATGCCAGAAA
GCTTTTAGCAGTATGGCAATGCTCAGTAGACATCAGTTGATTCATACAGGAGAGAAACCCCATGGATGCAATGAATGTGG
AAAAACTTTCCGGCAAAAAAGCCATCTTATTATCCATCAACGATGCCATACTGGAGAGAAACCCTATGGATGCATTCCAT
GTGGTCAAATCTTCAACCAGAAGTCACAGCTCATTAGACATCAGAGACGTCACACAGGAGAGAAACCGTATCAGTGCACT
CAATGTGGGAAAGCCTTTTTTGAGAAATCATACCTCAATGTCCATCAGAGAAGTCATGCAGGACAGAAACCTTATGAATG
CAGTCAGTGTGGGAAAACTTTCTCTGTCAAGTTCTTTCTTACTTCACATGAGGAAATTCATAGAGCAAAGAAGTCTCAGG
AACACAGCGAGTGCTGGAAAGACTTTAGTGAGATGCCACATCTCACTGAATACAAAAGAATTCACACAAGAGAGACCCTT
TGA

Alignment

ORF - retro_ecab_75 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.82 %
• Parental protein coverage: 65.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CGKTFSKKSQLIVHQRTHTGEKPYGCGQCGKAFSQKSLLTIHQRTHSGEKPYGCGECQKAFSRKSLLVLH
          C.K.FS....L....R.H...KPY.C..C.K.F...S.L.IHQRTH.GEKPY.C.ECQKAFS.K..L.LH
Retrocopy CAKAFSMVTNLKRCRRIHIEGKPYECSECPKSFRYRSKLIIHQRTHTGEKPYRCDECQKAFSTKCHLTLH

Parental  QRTHTGEKPYSCRECGKAFSRKSQLKRHQRTHTVEKPYGCSDCGKAFSQKLKLISHQRMHTGEKPYKCGD
          QRTHTGEKPY.C.EC.K.F..K..L..H.RTHT.EKPY.C..CGKA...K.KL..H.R.HTGEKP..C.D
Retrocopy QRTHTGEKPYGCTECQKSFRTKYHLILHHRTHTGEKPYECKECGKAYREKTKLRLHYRTHTGEKPFECSD

Parental  CGKAFFWKSQLITHQRTHTGKKPYACSECEKAFSRNSLLIRHQRIHTGEKPYECRECGEAFIRKPQLLIR
          CGK.F..KS.LI.HQR.HTG.KPY.C..CEKAF...S.L..HQRIHTGEK.YECRECG.AF..K...L..
Retrocopy CGKGFMQKSNLIIHQRIHTGDKPYGCGDCEKAFCSKSQLVVHQRIHTGEKSYECRECGKAF-NKNSHLMT

Parental  HQKTHLGEKPYGCVECGKTFFGKSQLLTHQRTHTGEKPYECSECGKAFTQRSSLMSHQRTHTGEKPYECS
          HQ..H.GEKPY.C.ECGK.F...SQL..HQR.HTG.KPYEC.ECGKAF...S....H.R.HTGEKPYECS
Retrocopy HQRIHIGEKPYECSECGKAFVHTSQLIVHQRNHTGRKPYECKECGKAFNKKSHFVTHERIHTGEKPYECS

Parental  ECGKAFSEKSSLIHHQRTHTGEKPFECGECRKAFAWKPQLLRHQRIHTGEKPYECSECGKAFVQKVQLIK
          ECGKAF...S.LI.H.RTHTGEKP.EC.ECRKAF.....L..HQRIHTGEKPYECSECGK.F..K..LI.
Retrocopy ECGKAFIDNSQLIVHRRTHTGEKPYECKECRKAFNKRSSLITHQRIHTGEKPYECSECGKSFIDKSHLIV

Parental  HQRNHTGEKTYGCSDCAKAFFEKAQLIIHQRIHTGERPYECGECGKSFTRKSHLMRHQRIHTGDKYYGCT
          HQR.HTGEK.Y.CS.C.KAF..KA.LI.HQR.HTGE.P..C.EC.K.F.....L.RHQ.IHTG.K..GC.
Retrocopy HQRTHTGEKPYECSECGKAFIRKAMLIVHQRTHTGEKPFACLECQKAFSSMAMLSRHQLIHTGEKPHGCN

Parental  ECGTAFSRKKSRFVVHQRTRTGEKPFKCSERGKGFSQKSHLVTHHTVHTGEKLYGC-ECGKAFSRKSHLI
          ECG..F.R.KS....HQR..TGEKP..C...G..F.QKS.L..H...HTGEK.Y.C..CGKAF..KS.L.
Retrocopy ECGKTF-RQKSHLIIHQRCHTGEKPYGCIPCGQIFNQKSQLIRHQRRHTGEKPYQCTQCGKAFFEKSYLN

Parental  THKRTHTGEKPYECSDCNKVFSQTSQLIIHQRSHTGEKPYGCGECGRAFSGKSQLITHKRTHIDE
          .H.R.H.G.KPYECS.C.K.FS....L..H...H...K.....EC...FS....L...KR.H..E
Retrocopy VHQRSHAGQKPYECSQCGKTFSVKFFLTSHEEIHRAKKSQEHSECWKDFSEMPHLTEYKRIHTRE

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	1.24 RPM	3.19 RPM
SRP021940_cerebellum	0.47 RPM	7.84 RPM
SRP021940_embryo	3.73 RPM	16.03 RPM
SRP021940_placental_villous	0.24 RPM	2.21 RPM
SRP021940_synovial_membrane	0.44 RPM	4.39 RPM
SRP021940_testis	0.51 RPM	1.60 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_75 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_75 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_75 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000010608	1 retrocopy	retro_ecab_68,
Equus caballus	ENSECAG00000021667	1 retrocopy	retro_ecab_560,
Equus caballus	ENSECAG00000023688	1 retrocopy	retro_ecab_75 ,