RetrogeneDB ID: retro_ecab_893

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 6:2479323..2479969(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSR3
• Ensembl ID: ENSECAG00000013501
• Aliases: None
• Description: TSR3, 20S rRNA accumulation, homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:14175]

Sequence

>retro_ecab_893
CTGCTCAGCCACCTGAGTGCTCAGAATATGTCTCCTGCAGATAGGCGGCTGGTGACACAGTCAGTGGTCCCGCCATAGAC
TGCTTGTGTGCCAGACAGGAGGAAATGCCATTTGGGAAGATGACGGAGAGCCTCTTGTGGCTGCTGACCCACTGGGTGGC
TACTAACCCTGTGAAATATGGCTGGCCCTGCAAACTGTCCACTGTAGAGGTTTTTGCTGCTACCTTCTGCATCTGGAGCA
TTTTGGACCACACAGTCATTTTGCTGCAGAAGTTTAGGTGGGGCAAGGGCTGGCTGGACCTGAACCACCAGCTTCTGGAC
AAGTGTATGACCTGCAGCAGCCTATAGTGGGTGCTTGTGGCAGAGAAGGAGCTCCTGGTAGTGCCAAGGGAGCCCCAGGA
GGAGGAAGTCAATCCCTTTGATATGAATTCAGGGCAGGAGTTTGCAAACCCCAACACACCTGTGGGACACATCGGGTTGC
CCATGGACAGTGATAACAGTGACAACCATGAGTCTGAAGACTAAAGGCCCAATACCAAGGACAGAGGACACAACAGCAGT
AGCTCAGAAGATGAGGAGAGGCAGGGAAAAAGGTAGAAGCCAGTGCACCAACAGAGGTTTGGAAAGGAATCAAGAAACAG
CAAAGA

Alignment

ORF - retro_ecab_893 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.76 %
• Parental protein coverage: 69.43 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VLSPMASQYVSPADRQLVAQSGVA-VIDCSWARLDETPFGKMRGGHLRLLPHLVAANPVNYGRPCKLSCV
          .LS....Q..SPADR.LV.QS.V...IDC..AR..E.PFGKM....L.LL.H.VA.NPV.YG.PCKLS.V
Retrocopy LLSHLSAQNMSPADRRLVTQSVVP<AIDCLCARQEEMPFGKMTESLLWLLTHWVATNPVKYGWPCKLSTV

Parental  EAFAATFCILGFSDLAVILL-RFKWGKGFLDLNRQLLDKYAACSGPEEVLQAEQEFLVHAKEHPEEEEID
          E.FAATFCI....D..VILL..F.WGKG.LDLN.QLLDK...CS....VL.AE.E.LV...E.P.EEE..
Retrocopy EVFAATFCIWSILDHTVILLQKFRWGKGWLDLNHQLLDKCMTCSSL*WVLVAEKELLVVPRE-PQEEEVN

Parental  PFDVDSGREFANPNRPVAGTRLPMDSGDSDGDSEDEPEEHGPDPEQEG-SGSCSEKE-GTPERGAEARAP
          PFD..SG.EFANPN.PV....LPMDS..SD.....E.E...P.....G...S.SE.E.G......EA.AP
Retrocopy PFDMNSGQEFANPNTPVGHIGLPMDSDNSD---NHESED*RPNTKDRGHNSSSSEDE<GEAGKKVEASAP

Parental  TEVWKGIKKRQR
          TEVWKGIKK.QR
Retrocopy TEVWKGIKKQQR

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	14.17 RPM
SRP021940_cerebellum	0.00 RPM	30.54 RPM
SRP021940_embryo	0.00 RPM	16.32 RPM
SRP021940_placental_villous	0.00 RPM	13.90 RPM
SRP021940_synovial_membrane	0.00 RPM	16.44 RPM
SRP021940_testis	0.00 RPM	17.97 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_893 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_893 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_893 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000013501	1 retrocopy	retro_ecab_893 ,
Macropus eugenii	ENSMEUG00000007498	1 retrocopy	retro_meug_117,
Myotis lucifugus	ENSMLUG00000008158	1 retrocopy	retro_mluc_744,
Tursiops truncatus	ENSTTRG00000011979	1 retrocopy	retro_ttru_630,