RetrogeneDB ID: retro_ecab_551

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 20:24191912..24192906(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C4orf27
• Ensembl ID: ENSECAG00000013735
• Aliases: None
• Description: chromosome 4 open reading frame 27 [Source:HGNC Symbol;Acc:26051]

Sequence

>retro_ecab_551
GAAGCACAGCGGTGTGAAAACACGGTTGATGGTGAAGAAGAGTAAATCCTGTGAAGCTGATATCTCCAATGACTTCAAAA
AGAGTAGGAAACCATTATAAGCTTTCTCTGCTTGAAGATTTCTATTGCTTCTCAAAGTTCTGTGAAGAACTTGACCCTGA
GAAAACAGTTGATCCACTTTCCCAAAGCCTTGGACTTCGATTAATGGGTCCTTCTGATGATATCCTTGCTGGAAAACATA
AAATGAAGAAAAAAATAGCAAGTTTGAATTTTAGCCTTAACTGGAGATATCACTAGGATACTCCTGAATTCCAGACCATT
ATTATTAGAGATAATAAAATTCATCACCACATAGCATATTTCAGGGATTTTTCTAGTGAACTTCCTGGATATGTTGGTAT
AAATAAAGCAAAGAAAAAAGGTATAATTATTGAAAATGGGGATAATGTGTTTGCTTCAGTTAAATTATTTTTGATGAAGA
AACTTAAAGAAATAACAGATAAAAAGAAAACTAGTCTCTTGAAAAACACAGACGAAAAACTCACAGAAGCAGCTAGAGAA
CTGGGATGCTCACTGGAACCGAGAACCATGAAGATGAAACAGAGAGATAAGAAAGTTGTGACGAAGACCTTTCGTGGTGC
AGGCTTGATTATCCCAGTAGATAAAAATGATGTTGGGTACAGAGAGCTCCCTGAAACAGATGCCAACCTCAAGAGAATTT
GCAAGACAACTGTTGAGGCAGCAAGTGATGAGGAGAGACTAACAGCTTTTGCTCCCATTCAGGAGGTGATGATTTTTGTG
CATTTTGCTAATGATGAATGTGATTATGGCATGGGGCTTGAGGTGGGAATGGACCTCTTTTGCTATAGTTCGCACTATTT
TCGTAAAGTTGCTGGCCAGGTTTTACCTCTTGTATGTAATGTGTTGAAGAGGAATTTCTTGCAGAAATTATTCAAGATCA
TCTGGCAAACAGAAGGAAAGAGAACGTGGACCAA

Alignment

ORF - retro_ecab_551 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.27 %
• Parental protein coverage: 95.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EGPQCEKTVD-VKKSKSCEADVSSD-LRKE-VENHYKLSLPEDFYHFWKFCEELDPEKPADSLSASLGLR
          E...CE.TVD.VKKSKSCEAD.S.D.L.KE.V.NHYKLSL.EDFY.F.KFCEELDPEK..D.LS.SLGLR
Retrocopy EAQRCENTVD>VKKSKSCEADISND<LQKE<VGNHYKLSLLEDFYCFSKFCEELDPEKTVDPLSQSLGLR

Parental  LVGPYD-LLAGKHKMKKKSASLNFNLHWRFYYDPPEFQTIIIGDDKTQFHMGYFRDSPDELPVYVGTNEA
          L.GP.D..LAGKHKMKKK.ASLNF.L.WR...D.PEFQTIII.D.K...H..YFRD...ELP.YVG.N.A
Retrocopy LMGPSDDILAGKHKMKKKIASLNFSLNWRYH*DTPEFQTIIIRDNKIHHHIAYFRDFSSELPGYVGINKA

Parental  KKNCIIVQNGDNVFAAVKLFLMKKLKEVTDKKKTSLLKNIDEKLTAAARELGYSLEQRTMKMKQRDKKVV
          KK..II..NGDNVFA.VKLFLMKKLKE.TDKKKTSLLKN.DEKLT.AARELG.SLE.RTMKMKQRDKKVV
Retrocopy KKKGIIIENGDNVFASVKLFLMKKLKEITDKKKTSLLKNTDEKLTEAARELGCSLEPRTMKMKQRDKKVV

Parental  TKTFHGAGLVVPVDKNDVGYRELPETDANLKRICKTIVEAASDEERLKAFAPIQEMMTFVQFANDECDYG
          TKTF.GAGL..PVDKNDVGYRELPETDANLKRICKT.VEAASDEERL.AFAPIQE.M.FV.FANDECDYG
Retrocopy TKTFRGAGLIIPVDKNDVGYRELPETDANLKRICKTTVEAASDEERLTAFAPIQEVMIFVHFANDECDYG

Parental  MGLELGMDLFCYGSHYFHKVAGQLLPLAYNLLKRN-LFAEIIEDHLANRSKENIDQ
          MGLE.GMDLFCY.SHYF.KVAGQ.LPL..N.LKRN...AEII.DHLANR.KEN.DQ
Retrocopy MGLEVGMDLFCYSSHYFRKVAGQVLPLVCNVLKRN<FLAEIIQDHLANRRKENVDQ

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	5.19 RPM
SRP021940_cerebellum	0.00 RPM	6.39 RPM
SRP021940_embryo	0.00 RPM	11.97 RPM
SRP021940_placental_villous	0.05 RPM	9.43 RPM
SRP021940_synovial_membrane	0.03 RPM	4.72 RPM
SRP021940_testis	0.00 RPM	3.64 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_551 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_551 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_551 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020132	1 retrocopy	retro_btau_611,
Equus caballus	ENSECAG00000013735	1 retrocopy	retro_ecab_551 ,
Gorilla gorilla	ENSGGOG00000003090	1 retrocopy	retro_ggor_2306,
Myotis lucifugus	ENSMLUG00000017052	1 retrocopy	retro_mluc_395,
Ictidomys tridecemlineatus	ENSSTOG00000001481	1 retrocopy	retro_itri_101,
Tursiops truncatus	ENSTTRG00000009751	1 retrocopy	retro_ttru_862,