RetrogeneDB ID: retro_ecab_946

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 7:6197476..6198190(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RFC5
• Ensembl ID: ENSECAG00000015326
• Aliases: None
• Description: replication factor C (activator 1) 5, 36.5kDa [Source:HGNC Symbol;Acc:9973]

Sequence

>retro_ecab_946
AAGCTGCTGCACCTGCTTCTCTATGATCCTCCAGGGACAGGAAAGACATCCACCATCGTAGCCTGTGCTAAACAGCTGTA
CAAAGATAAAGAATTCAGCTCCATGGTCTTAGAGCTGAATGTTTCAGATGACCAAGGAATAGATATCATTTGGGGACTGA
TCCTGAGCTTTGCTAGCACAGGGACACTATTTAAGAAAGGCTTTCAAATAGTGATCTTGGATGAAGCTGATGCCATGAGT
CAAGATGCCCAGAATGCCTTGAGGAGAGTGATTGAGAAATTTACTGAGAACACCAGATTTTGCCTCATTTGTAACTGTCT
GTCAAAGATCATCCCGACCTTGCAGTCCCGATACACAAGGTTCTGATTTGCTCCCCTCACTCCTAAACTCATGGTTCCCT
GCCTGGAACATGCTGTGGAAGCAGAGAAAGTTGGTCTAAGCGTAGACAGGATGAAAGCACTTGTAACTCTCTCCAGTGGA
GACATGCGAAGGGCCCTGAACATTTTGCAGAGCACCAATATGGCCTTTGGAAAGGTGACAGAGGAGACTGTCTACACCAG
CACAGGGCACTCACTCAAGTCAGACGTCACCAACATTCCAGACTGGGTGTTGAATCAAGACTTCACCACAGCCTACAGGA
ATGTTAGGGAGCTGAACACTCTGAGGGGCTTGGCGTTACGTGATATCCTGACAAAGATATACTTGCTTGTGCAC

Alignment

ORF - retro_ecab_946 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.93 %
• Parental protein coverage: 74.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RLPHLLLYGPPGTGKTSTILACAKQLYKDKEFGSMVLELNASDDRGIDIVRGPILSFASTRTIFKKGFKL
          .L.HLLLY.PPGTGKTSTI.ACAKQLYKDKEF.SMVLELN.SDD.GIDI..G.ILSFAST.T.FKKGF..
Retrocopy KLLHLLLYDPPGTGKTSTIVACAKQLYKDKEFSSMVLELNVSDDQGIDIIWGLILSFASTGTLFKKGFQI

Parental  VILDEADAMTQDAQNALRRVIEKFTENTRFCLICNYLSKIIPALQSRCTRFRFGPLTPELMVPRLQHVVE
          VILDEADAM.QDAQNALRRVIEKFTENTRFCLICN.LSKIIP.LQSR.TRF.F.PLTP.LMVP.L.H.VE
Retrocopy VILDEADAMSQDAQNALRRVIEKFTENTRFCLICNCLSKIIPTLQSRYTRF*FAPLTPKLMVPCLEHAVE

Parental  EEKVAISEDGMKALVTLSSGDMRRALNILQSTNMAFGKVTEETVYTCTGHPLKSDIANILDWMLNQDFTT
          .EKV..S.D.MKALVTLSSGDMRRALNILQSTNMAFGKVTEETVYT.TGH.LKSD..NI.DW.LNQDFTT
Retrocopy AEKVGLSVDRMKALVTLSSGDMRRALNILQSTNMAFGKVTEETVYTSTGHSLKSDVTNIPDWVLNQDFTT

Parental  AYRNITELKTLKGLALHDILTEIHLFVH
          AYRN..EL.TL.GLAL.DILT.I.L.VH
Retrocopy AYRNVRELNTLRGLALRDILTKIYLLVH

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	6.85 RPM
SRP021940_cerebellum	0.00 RPM	9.71 RPM
SRP021940_embryo	0.00 RPM	21.92 RPM
SRP021940_placental_villous	0.00 RPM	6.11 RPM
SRP021940_synovial_membrane	0.00 RPM	7.36 RPM
SRP021940_testis	0.00 RPM	40.92 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_946 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_946 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_946 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000015326	2 retrocopies	retro_ecab_613, retro_ecab_946 ,
Mus musculus	ENSMUSG00000029363	1 retrocopy	retro_mmus_2495,
Oryctolagus cuniculus	ENSOCUG00000010377	1 retrocopy	retro_ocun_1316,
Rattus norvegicus	ENSRNOG00000001134	1 retrocopy	retro_rnor_1139,