RetrogeneDB ID: retro_ecab_25

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 2:60692403..60694575(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000002189
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000023845
• Aliases: None
• Description: None

Sequence

>retro_ecab_25
ATGAGGATCACACTCCTGATACACTGGCTTGCAGTGTTTCTGTCCTCCTCTGGACACATGTGGCCTGAGAACCCCCAGTA
TCACAGTCCCCCAGAAGTGGTGATTCCCTTGAAGTTACCTCGTACTGGAAGAGGCATGAAACCTCCAGGCATGCTCTCTT
ACAGCCTGCATTTTGGAGGCAAGAGACATGTTGTCCATCTGAGGGTCAAGAAGCATTTGCTGTCTAGACACCTTCCAGTG
TTCACCTACACAGACCAGGGTGCTCTCCTTGAAGAAAAGCCTTTTGTTCAGAATGATTGCTACTATCATGGTTATGTGGA
AGGGGACCTGGAATCCCTGGTTGCCCTCAGTACCTGTTCTGGTGGATTTCAAGGATTGTTACAGATAAATAGCATTGTTT
ATGAAATTGAGCCCATGGATTTTTCTCCCAAATTTGAACATCTGGTATATAAAATGGATGAGACCCAATTCCCAACCACA
AAATCTGACATTATGCAAGAGGACACTGTACACCAATTGGAGTTTCAAGAGACTGATAATTATACTCTGAAGCAAAGTTC
TTATGTGGGCTGGTGGGTCCATAAGTTCCTTGTTGAAATGGCAGTGATTGTGGACCATACTCTCTACCTTCATTATGAAA
AGAACGTCTCAAAGTTGCAGGATGATCTATATGTTATTGTAAATATAGTGGATTCCATTTATGAGGTAATGGGTATTAAG
TTGTTATTACTTGGTATGGAGGTCTGGACTGAAAAAAACTACTTTGAAGTAGGTGATATAAGCAGATCTCTGAAGCAATT
TTGTGAGTGGAAGTCCAAAAATTTTGCTCCCCGCGTGTCACATGATACTGCACATCTTTTTACATATAAGACATTAAGAG
GATTAACTGGTTTAGGCTTCGTTGCAGGGCTGTGTAAATCACACAGAAATTGTGCAGTTGTTACTTGTGTTAACAAAACC
TTGTCCATTATTGGAATTGCAATGGCTCATCATCTAGGTCATAATTTGGGGATGTTTCATGATGCTGACGAGTGTAAGTG
TGCACATCCTACATGTATAATGCGCTATGATAACCCACCAATAACTCAATTTAGCAATTGTAGTTATAATTTCTTTTGGG
AATATTCTATACGCCAGGCAAAATGTTTGATGTACACTGTGCATACAAAGGATGTGTTTACAATGAAGCGCTGTGGGAAT
GGCATTGTTGAAGAAGAAGAGGAGTGTGACTGTGGAATTTTAAGGAGTTGTTCAAAAGATCCCTGTTGTCTGTCAAACTG
CACTCTGAGTTTTGGATCTATTTGTGCTTTTGGGCTTTGTTGCAAGGACTGCGAGTTTTTACCATCAGGGAGAGTATGTA
GAAAGAAAGTCAATGAATGTGATCTTCCAGAGTGGTGCAATGGAACATCCCATATGTGTCCAGATGATGTATATGTGGAG
GACGGAATTCCTTGTAATAGCAGTGCCTACTGCTATGAAAAAAGCTGTCATAACCGTGATGAACAGTGTAGGCAGATCTT
TGGCCAAGAGGCAAAGAGTGCAAATAACAGTTGTTACAAACGAGTAAACACTAAAGGTGACCGTTTTGGTAACTGTGGTT
TCAAAGACTTTTCATATGTAAAATGTGATAGCTCAGATAGCCTGTGTGGGAGGGTTCAGTGTGAGAATGTGACAAAAATT
CCCCTTTTGAGTGATCATTCTACTGTGCATTGGACTCGCGTCAATGGTGCCATCTGCTGGGGTATAGACTACCATTTTGG
GATGACTACACCTGATATTGGTGATGTGAAAGATGGCACAGAGTGTGGCCCAGAACACGTCTGCATCCACAGGAAGTGTG
TCCATTTATCTCGCTTGGATAGTAATTGTTCACCTAAGTTTTGTAACATGAGGGGGATCTGTAACAATAAACATCACTGC
CATTGCAACTATATGTGGGACCCTCCCAATTGCCTAATAAGAGGCAGTGGAGGTAGTATCGACAGTGGCCCACCCCCTAA
GAGAGAGAAGATTAAGAAGATTTACGTGTTAGGATTTGTGCTTTTTTGGTTGATTGTTTTATTATGTTGTCTTCTTTTGC
TTTGTAAGAAGAAAAAATCTAAGAAAAAAGACCAAAAAGTTCAGGCTGAAGTTAAAAAAGCAGAAAATGTCAAGACACAA
CAACCAAAAGAA

Alignment

ORF - retro_ecab_25 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.82 %
• Parental protein coverage: 99.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VRLILLLLWLRVFLFLSALSQVGLSSHHGPPEVVIPLRFARSAAGSPVFRWLSYRMNFGGQRHIVHMKVN
          .R..LL..WL.VFL..S..........H.PPEVVIPL...R...G......LSY...FGG.RH.VH..V.
Retrocopy MRITLLIHWLAVFLSSSGHMWPENPQYHSPPEVVIPLKLPRTGRGMKPPGMLSYSLHFGGKRHVVHLRVK

Parental  KHFLYRHLSVFTYTDQGTLLEDQPFVQNDCYYHGYVE-DSESLVSLNTCVGGFQGIIQTMDTIYEITPKR
          KH.L.RHL.VFTYTDQG.LLE..PFVQNDCYYHGYVE.D.ESLV.L.TC.GGFQG..Q.....YEI.P..
Retrocopy KHLLSRHLPVFTYTDQGALLEEKPFVQNDCYYHGYVEGDLESLVALSTCSGGFQGLLQINSIVYEIEPMD

Parental  LTI-FEHLVHRIDSEETQSPPMRCGLTDEEIARQLKLQGSDTFTLMRTPYEGWWLHKRYLEIAVVVDNNR
          ....FEHLV...D..ETQ.P........E....QL..Q..D..TL....Y.GWW.HK...E.AV.VD...
Retrocopy FSPKFEHLVYKMD--ETQFPTTKSDIMQEDTVHQLEFQETDNYTLKQSSYVGWWVHKFLVEMAVIVDHTL

Parental  FIHRDSNVSDVQKEAYEVIHHTNNFFKTVDIEVTLMGIEIWTEGNLILLDDIYRGLRRFCDWKRQGFNDR
          ..H...NVS..Q...Y..............I...L.G.E.WTE.N.....DI.R.L..FC.WK...F..R
Retrocopy YLHYEKNVSKLQDDLYVIVNIVDSIYEVMGIKLLLLGMEVWTEKNYFEVGDISRSLKQFCEWKSKNFAPR

Parental  LPHDAAHIFSGKGFGIVGGLAYVGTVCNSRHNCGIESFQTEDLVSFANTVTHEVGHTVGMKHDDGTCTCG
          ..HD.AH.F..K......GL..V...C.S..NC.........L........H..GH..GM.HD...C.C.
Retrocopy VSHDTAHLFTYKTLRGLTGLGFVAGLCKSHRNCAVVTCVNKTLSIIGIAMAHHLGHNLGMFHDADECKCA

Parental  RSRCIMNAGKGDTHRFSNCSYTWYSELMLR-TKCMYIPPSPERIFTMTRCGNSVVEEGEECDCGSL-TCI
          ...CIM.........FSNCSY....E...R..KC..........FTM.RCGN..VEE.EECDCG.L..C.
Retrocopy HPTCIMRYDNPPITQFSNCSYNFFWEYSIRQAKCLMYTVHTKDVFTMKRCGNGIVEEEEECDCGILRSCS

Parental  EDHCCQSNCTLIPEADCAFGLCCQDCKFMPSGTMCRKKENECDLPEWCNGTSHQCPEDVYMQDGFLCKSG
          .D.CC.SNCTL.....CAFGLCC.DC.F.PSG..CRKK.NECDLPEWCNGTSH.CP.DVY..DG..C.S.
Retrocopy KDPCCLSNCTLSFGSICAFGLCCKDCEFLPSGRVCRKKVNECDLPEWCNGTSHMCPDDVYVEDGIPCNSS

Parental  DYCYEKRCNNRDEQCRKIFGKEAKSANQSCYMRINTRGDRFGHCGLKNTAFVRCNTSDSLCGRVQCENVT
          .YCYEK.C.NRDEQCR.IFG.EAKSAN.SCY.R.NT.GDRFG.CG.K....V.C..SDSLCGRVQCENVT
Retrocopy AYCYEKSCHNRDEQCRQIFGQEAKSANNSCYKRVNTKGDRFGNCGFKDFSYVKCDSSDSLCGRVQCENVT

Parental  KIPFLEEHSTVHWTHFNDVTCWGTDYHYGMTIPDIGEVKDGTECGVDHICIQKKCMPMSHLDRDCSPETC
          KIP.L..HSTVHWT..N...CWG.DYH.GMT.PDIG.VKDGTECG..H.CI..KC...S.LD..CSP..C
Retrocopy KIPLLSDHSTVHWTRVNGAICWGIDYHFGMTTPDIGDVKDGTECGPEHVCIHRKCVHLSRLDSNCSPKFC

Parental  NMKGVCNNRHH-HCNYPWDPPDCLKNGTGGSIDSGPP
          NM.G.CNN.HH.HCNY.WDPP.CL..G.GGSIDSGPP
Retrocopy NMRGICNNKHHCHCNYMWDPPNCLIRGSGGSIDSGPP

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	0.03 RPM	0.00 RPM
SRP021940_placental_villous	0.05 RPM	0.00 RPM
SRP021940_synovial_membrane	0.00 RPM	0.00 RPM
SRP021940_testis	64.52 RPM	39.33 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_25 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_25 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_25 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	ENSECAG00000023845	1 retrocopy	retro_ecab_25 ,