RetrogeneDB ID: retro_ecab_568

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 21:35196202..35197028(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: T
• Ensembl ID: ENSECAG00000007994
• Aliases: None
• Description: T, brachyury homolog (mouse) [Source:HGNC Symbol;Acc:11515]

Sequence

>retro_ecab_568
GTCACCCAGAAGGGCAGGAGGATGTTCCCATGTTGAAGGTGAGTGTGTCTGACCTGGACTCCAATGCCATGTATTCTTTC
CTCCTGGACTCTGTAGTGGCGGACAGACATAGTTGGAAATATGTGAACACAGAGTGGGTGCCTGGGAGTCAGTCTGAGCT
GCAGGTGCCCAGCTGAGTCTATATCCACTCTAAGTCTCTGAACTTGGAGCCCAGTTGGTGAATGCACCTGTATCCTTCAG
CAAAGTTAAACTCACCAGCAAGCACAATAGAGGGTGTCAGATCATATTGAACTCCTTACATAAATATAAACTTCAAGTCC
ACATAGTAATAGTTGAGGGTCTACAGAGGATGCTTACCAGCCATTGCATTCCCAAGACTTAATATATATCTGTGACAGCT
TATCAGAATGAGAAGATTATAGCTCTTAAAACCAAATACAATCCATTTGTAAAGGCTTGCCTTGGTGCAAAGAGAAACAG
GAATCACAAAGATAAGATGGAAGAACCCAGAGCGGAACAGCAACCCGGGTATTCTTAATGGAAGTGGCTTATCCCTGGAA
CCAGTACTTTCTGTCTGCTGCCAACCTCCATCTTCAGTTTGGAGGTGTTCTTTCATTTTCCTTCAGCCATGACTGTGAAA
GATGCCCTGTCCTGAGGAACCACAGTTTAACCCCTTCCTCAGCCAGTACACTCTTTGGAATAATTCTCCAACCTATTTTG
ACAATTCATTTGCATGTTAGCCATGCTCCAATCCTATGAGAATTGGCCCAGCCTTAGGATGTCTGTACATACCATCATGT
TACTCCTGACTCCCAACAGGACTCCA

Alignment

ORF - retro_ecab_568 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.18 %
• Parental protein coverage: 63.68 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  VTKNGRRMFP-VLKVNVSGLDPNAMYSFLLDFVAADNHRWKYVNGEWVPGGKPEPQAPSCVYIHPDSPNF
          VT..GRRMFP..LKV.VS.LD.NAMYSFLLD.V.AD.H.WKYVN.EWVPG...E.Q.PS.VYIH..S.N.
Retrocopy VTQKGRRMFP<MLKVSVSDLDSNAMYSFLLDSVVADRHSWKYVNTEWVPGSQSELQVPS*VYIHSKSLNL

Parental  -GAHWMKAPVSFSKVKLTNKLNGGGQIMLNSLHKYEPRIHIVRVGGPQRMITSHCFPETQFIAVTAYQNE
          .GA....APVSFSKVKLT.K.N.G.QI.LNSLHKY....HIV.V.G.QRM.TSHC.P.T..I.VTAYQNE
Retrocopy <GAQLVNAPVSFSKVKLTSKHNRGCQIILNSLHKYKLQVHIVIVEGLQRMLTSHCIPKT*YISVTAYQNE

Parental  EITALKIKYNPFAKAFLDAKERSDHKDMMEEPGDSQQSGYSQWGWLIPGTSTLC-PPATPHPQFGGPLSL
          .I.ALK.KYNPF.KA.L.AK....HKD.MEEP...QQ.GYS.W.WLIPGTST.C...A..H.QFGG.LS.
Retrocopy KIIALKTKYNPFVKACLGAKRNRNHKDKMEEPRAEQQPGYS*WKWLIPGTSTFC<SAANLHLQFGGVLSF

Parental  PASHGCERYPALRNH-RPSPYPSPYAHRNNSPTYSDNSSAC-LSMLQSHDNWPSLGMPAHTSMLPMSPNT
          ..SH.CER.P.LRNH....P..S.Y...NNSPTY.DNS.AC.L.MLQS..NWPSL.M..HT.ML...PN.
Retrocopy SFSHDCERCPVLRNH<QFNPFLSQYTLWNNSPTYFDNSFAC<LAMLQSYENWPSLRMSVHTIMLLLTPNR

Parental  GP
          .P
Retrocopy TP

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	0.00 RPM	0.38 RPM
SRP021940_placental_villous	0.00 RPM	0.00 RPM
SRP021940_synovial_membrane	0.00 RPM	0.00 RPM
SRP021940_testis	0.00 RPM	0.32 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_568 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_568 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_568 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
Choloepus hoffmanni	ENSCHOG00000006236	1 retrocopy	retro_chof_209,
Equus caballus	ENSECAG00000007994	1 retrocopy	retro_ecab_568 ,
Microcebus murinus	ENSMICG00000016122	1 retrocopy	retro_mmur_1130,
Nomascus leucogenys	ENSNLEG00000011552	1 retrocopy	retro_nleu_1501,