RetrogeneDB ID: retro_ecab_657

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 26:20345688..20346518(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DONSON
• Ensembl ID: ENSECAG00000007826
• Aliases: None
• Description: downstream neighbor of SON [Source:HGNC Symbol;Acc:2993]

Sequence

>retro_ecab_657
ACTCCAGATGTATCATTCTCGGATCTGATATTCCATCCTCAGAAAGTACGGGGTTACCCGTGGACTGCAGTATTAAAACC
TGACTCCTTTCACCTCTTCTCAACTTTATCTGAGAGATCATTTGAAAGCAAAGGGAAAGGCTCAAGGTATTGTCCAGCAT
TGTAGGACAATAGAAGTTATTTTGCCTCAAAGTACACAGGATCCGAAACTCTTCCCTGAGCTCCGTTGTACATTCCAGCA
CTGTCTTATCTATTGGCTCCACCCTGCCTTGCCTTGGCTACCACTGTTCCCCGATGTTGGAACTGATAGAAAATAGCGGA
AAAGACAAGTCCTTGGGCAAATGATGAAACTGTGCAACGTATTTTAATGAATAACTCGTCTGTGAGCTTTAATTCTCTGT
ATAATCTGCTGAAGACAAAACTTTATCCCAAGTTCTACATTTATATCTATGAGCTTACTATCCTGTTCCATGCAGCAGGA
TTAGCAGGAAATGATATCCTCATGGCTGTCATATCTCCTACAATTAGAGGTGTAAGACAAGGCATGGAAAAATGAAAGTA
CTACGTTTTCTCTACCTTTAATAAAAGAAAATGGTCATAAATAGAAGAAAGCCTCTGGACAAAGGGACAGGAGGAACGAG
CAATCAGTGATGAAGATGATGAAGATGGAGAAGAAAGTTTTTCCTGGCTTAAAGAGATAGGTGTGCAAGACAAAATTTTA
AAAAAAGCAGACATACTCTCTGTCAAGCTATGTAAAGAGAAACATGAATACAAAAGGATCACAGACCTGGGTCTGTTGTA
TTGGCGAATGGAATCCACGTCTTTGCTGTA

Alignment

ORF - retro_ecab_657 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.05 %
• Parental protein coverage: 63.89 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  TPHVSSSE-SDILSSGSTELPVDWSIKTRLL-FTSSQPFTWADHLKAQEEAQGVVQHCRATEVTLPPSIQ
          TP.VS.S..SDI.SS.ST.LPVD.SIKT.LL.FTSSQ.....DHLKA...AQG.VQHCR..EV.LP.S.Q
Retrocopy TPDVSFSD<SDIPSSESTGLPVDCSIKT*LL<FTSSQLYL-RDHLKAKGKAQGIVQHCRTIEVILPQSTQ

Parental  DPKLCTELRRAFQQSLVYWLHPAFPWLPLFPRIGADRK-MAGKASPWSADEALQDILMSDWSVSFTSLYN
          DPKL..ELR..FQ..L.YWLHPA.PWLPLFP..G.DRK..A.K.SPW..DE..Q.ILM...SVSF.SLYN
Retrocopy DPKLFPELRCTFQHCLIYWLHPALPWLPLFPDVGTDRK<IAEKTSPWANDETVQRILMNNSSVSFNSLYN

Parental  LLKTKLCPYFYVCTYQFTILFRAAGLAGNDVITALISPTTRGLREAM-KNEGIEFSLPLIKENGQE-KKA
          LLKTKL.P.FY...Y..TILF.AAGLAGND...A.ISPT.RG.R..M.KNE...FSLPLIKENG...KKA
Retrocopy LLKTKLYPKFYIYIYELTILFHAAGLAGNDILMAVISPTIRGVRQGM>KNESTTFSLPLIKENGHK*KKA

Parental  S-RTSLGHEEEQAMSDEDEEESFSWL-EEMGVQDKI-KKPDILSIRLRKEKHE-VQMDHRPESVVLVKGM
          S.......E.........E...F..L..E.GVQDKI.KK.DILS..L.KEKHE..Q.DHRP.SVVL..G.
Retrocopy SGQRDRRNEQSXXXXXXXEKKVFPGL<KEIGVQDKILKKADILSVKLCKEKHE<IQKDHRPGSVVLANGI

Parental  NTFTL
          ..F..
Retrocopy HVFAV

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	2.30 RPM
SRP021940_cerebellum	0.00 RPM	9.24 RPM
SRP021940_embryo	0.00 RPM	30.20 RPM
SRP021940_placental_villous	0.00 RPM	6.59 RPM
SRP021940_synovial_membrane	0.00 RPM	7.30 RPM
SRP021940_testis	0.00 RPM	92.85 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_657 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_657 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_657 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	ENSECAG00000007826	1 retrocopy	retro_ecab_657 ,
Echinops telfairi	ENSETEG00000019380	1 retrocopy	retro_etel_2077,
Macaca mulatta	ENSMMUG00000003701	1 retrocopy	retro_mmul_711,