RetrogeneDB ID: retro_ecab_1008

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 9:37973888..37974490(+)
• Located in intron of: ENSECAG00000026869

Retrocopy information

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

Parental gene information

• Parental gene symbol: MOB2
• Ensembl ID: ENSECAG00000020591
• Aliases: None
• Description: MOB kinase activator 2 [Source:HGNC Symbol;Acc:24904]

Sequence

>retro_ecab_1008
GAAGGCCAAGCGAAGCCCAACGGGGAGAAGCCGGCCGCGGAGAAGATGTACCTAGGAGCTGGAGTACACCAAGTCCGGAA
TCACCGACTTCCAGGTCAAGGGACTGCTGGTGCTGCCCGGGGAGAATGACCTCCACGTGCGGCTGGCCAGCACATCACGA
CATTTTTCTGCAGGTCAACCTGCAGCATAGCACTGCCTCAGAATTCTGCACAGGAGAGGCGTGCCAGACGATGGCCGTGT
GTGACACACGGTACTACTGGTGAGAGCTGGGGAAGAAGGTCAAGTGCACACGCCCCAGTATGTCGACTTTGTCTTGAGCT
CAGCGCAGAACCGGGTGATCAACGAGGGCGTGTTCCACATGAAATAGGCAGTGAATTCTCCAGCTCCTTCGAGTCAATGG
TGAAGAAGATCTGCAAATACCTGTTCCCGATGCTAGGGTACGTCTGCTCGTCCCACTTCCAGGAAACCCTGGCCTTGGAG
CTGCACGCGCGCTTGAATACACTCTATGGCCAGTTCCTCTTCTCCACGAAGTTCAACCTGCTTGGTTCCAAAGAGACCCT
GGTCATGACCATTGCATCGAGGTGCTGTGCAGCGGCAGGGGT

Alignment

ORF - retro_ecab_1008 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.51 %
• Parental protein coverage: 89.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  KSKAKPNGKKPAAEEKKMYL-EPEYTKSRITDFEFKELVVLPREIDLNEWLASNT-TTFFHH-VNLQYST
          ...AKPNG.KPAAE..KMYL.E.EYTKS.ITDF..K.L.VLP.E.DL...LAS...TTFF...VNLQ.ST
Retrocopy EGQAKPNGEKPAAE--KMYL>ELEYTKSGITDFQVKGLLVLPGENDLHVRLASTS<TTFFCR<VNLQHST

Parental  ISEFCTGEACQTMAVCNTQYYWHDERGKKVKCT-APQYVDFVMSSVQKLVTDEDVF-PTKYGREFPSSFE
          .SEFCTGEACQTMAVC.T.YYW..E.GKKVKCT..PQYVDFV.SS.Q..V..E.VF.P...G.EF.SSFE
Retrocopy ASEFCTGEACQTMAVCDTRYYW*-ELGKKVKCT<TPQYVDFVLSSAQNRVINEGVF<PHEIGSEFSSSFE

Parental  SLVKKICKYLFHVLAHIYSSHFKETLALELHGHLNTLYVHFILFAREFNLLDPKETAVM-DDLTEVLCSS
          S.VKKICKYLF..L....SSHF.ETLALELH..LNTLY..F.LF...FNLL..KET.VM.D...EVLCS.
Retrocopy SMVKKICKYLFPMLGYVCSSHFQETLALELHARLNTLYGQF-LFSTKFNLLGSKETLVM<DHCIEVLCSG

Parental  GG
          .G
Retrocopy RG

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	8.21 RPM
SRP021940_cerebellum	0.00 RPM	12.00 RPM
SRP021940_embryo	0.08 RPM	9.16 RPM
SRP021940_placental_villous	0.10 RPM	19.77 RPM
SRP021940_synovial_membrane	0.03 RPM	15.15 RPM
SRP021940_testis	0.26 RPM	26.09 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1008 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1008 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1008 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000020591	1 retrocopy	retro_ecab_1008 ,
Myotis lucifugus	ENSMLUG00000006539	1 retrocopy	retro_mluc_1044,