RetrogeneDB ID: retro_ecab_6

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 2:71046665..71048546(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000002749
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TKTL1
• Ensembl ID: ENSECAG00000021992
• Aliases: None
• Description: transketolase-like 1 [Source:HGNC Symbol;Acc:11835]

Sequence

>retro_ecab_6
ACCATAGCCGACAACGCCAAGCCCCGTGCGAATACGTTGCAGGTGCTGCGGGACATGGCCAACCGCCTGCGGATCCATTC
CATCAGGGCCACGTGTGCCTCCCGCTCCGGCCACCCCACGTCGTGCTGCAGCGCAGCTGAGATCATGTCCGTGCTGTTCT
TCCACACGATGCGGTATAAACAGACAGAGCCGGAACACCCTGACAACGACCGATTCATCCTCTCCAAGGGCCATGCTGCT
CCCATCCTCTATGCGGCTTGGGCAGAGCTGGGCATCATCAGTGAATCCGACTTGCTGAACTTGAGGAAAATTAACTGTGA
CTTAGAGGGACATCCCACCCCAAGACTGTCGTTCGTTGATGTGGCAACCGGATCGCTTGGGCAAGGATTGGGTGCCGCCT
GCGGAATGGCTTATACTGGCAAGTACTTTGACAAGGCCAGCTACCGAGTGTTCTGCCTTATGGGAGATGGTGAATCCTCG
GAAGGTTCAGTCTGGGAGGCTCTGGACTTCGCTTCCCACTACAATTTGGACAATCTCGTGGCAGTCTTTGACGTGAACCG
TTTGGGACAAAGTGGTGTCACGCCCCTTGAGCACTGCACAGACGTCTATCAGAATCGCTGTGAAGCCTTTGGGTGGAATA
CTTACTTAGTGGATGGCCATGATGTGGAGGGGTTGTGCCATGCGTTCTGGCAAGCAACTCAAGTGAAGAACAAGCCCACT
GCCATAGTAGCCAAGACCTTCAAGGGCCGGGGTATTCCAGACATTGAGGATGCAGAAAATTGGCATGGAAAGCCAATGCC
AAAAGAAAGAGCAGATGCAATCATCAAATTAATTGAGAGTCAGATACAGACCAATAGAAATTTCATAGTGAAACCCCCTC
TTGAAGACTCACCGCAAGTCAGCATCAGGAATATAAAAATGACCTGTCTGCCTGATTATGAAGTTGGTGACAAGATAGCT
ACTCAGAAAGCATATGGTTTGGCTCTGGTTAAACTGGGACGTGCAAATGACAGACTTATTGTGCTGGATGGTGACGCAAA
GAACTCCACCTTTTCTGAGATATTCAAGAAAGAATACCCTGAGCGTTTCATTGAGTGTGTTATGGCTGAGCAAAACATGG
TAAGTGTGGCACTGGGCTGCGCCACACGTGATCGAACTGTTGCTTTTATTAGTACCCTTGCTGCCTGTTTGACCCGAGCA
TTTGATCAGATCCGGATGGGAGCCATATCTCAAACCAATATCAATCTTATTGGTTCCCACTGCGGGGTATCTATGGGTGA
AGAAGGATCCTCCCAGATGGCTCTGGAGGATCTCGCCATGTTCCGAAGCATTCCCAATTGCACCGTTTTCTATCCAAGTG
ATGCCATCTCGGCAGAGCATGCTGTTTATCTGGCTGCCAGTACCAAAGGAATGTGCTTCATTCGGACCAGCCGACAAGAA
ACTGCCGTTATTTATACCCCACAAGAAAATTTTGTGATTGGACAGGCCAGGGTCATCCGCCACAGTGTCAATGACAAAGT
TACAGTTATTGGAGCAGGAGTTACTCTCCATGAAGCCTTAGCAGCTGCTGCTGATCTTTCTCAACAAGGCATTTCTATCC
GTGTCATTGACCCGTTTACCATTAAACCCCTGGATGCTGCCACCATCATCTCCAGTGCAAAAGCTACAGGTGGTCGGGTT
ATCACAGTAGAGGATCACTACCGAGAAGGTGGCCTTGGAGAAGCTGTGTGTACAGCTGTCTCTGGGGAGCCTGACATCCT
TGTTCATCAGCTGGCAGTGTCAGGAGTGCCCCAAAGTGGGAAACCTGGTGAATTGCTGGATATGTTTGGAATCAGTGCCA
GACACATCATAGCTGCTGTGAAATACACTTTAATGAACTAA

Alignment

ORF - retro_ecab_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.03 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAEETKPDAKTVQVLQDMANRLRIQSIRAACASSSGHPTSCSSAAEIMAVLFFHTMRYKQADPDDPDNDR
          .A...KP.A.T.QVL.DMANRLRI.SIRA.CAS.SGHPTSC.SAAEIM.VLFFHTMRYKQ..P..PDNDR
Retrocopy IADNAKPRANTLQVLRDMANRLRIHSIRATCASRSGHPTSCCSAAEIMSVLFFHTMRYKQTEPEHPDNDR

Parental  FVLSKRGWPLRALRCRWTQQATISRSDLLGSRKIGFDLEGHPTPRLSFVDVATGWLGQGLGAACGMAYTG
          F.LSK.G.....L...W.....IS.SDLL..RKI..DLEGHPTPRLSFVDVATG.LGQGLGAACGMAYTG
Retrocopy FILSK-GHAAPILYAAWAELGIISESDLLNLRKINCDLEGHPTPRLSFVDVATGSLGQGLGAACGMAYTG

Parental  KYFDKASYRVFCLLGDGEFSEGSVWEALAFASHYSLDNLVAVFDVNRLGHSGTLPLENCIDVYQKRCEAF
          KYFDKASYRVFCL.GDGE.SEGSVWEAL.FASHY.LDNLVAVFDVNRLG.SG..PLE.C.DVYQ.RCEAF
Retrocopy KYFDKASYRVFCLMGDGESSEGSVWEALDFASHYNLDNLVAVFDVNRLGQSGVTPLEHCTDVYQNRCEAF

Parental  GWNTYVVDGRDVEALCQVFWQAAQVKNKPTAVVAKTFKGRGIPNVEDAENWHGKPMPKERADAIIKLIES
          GWNTY.VDG.DVE.LC..FWQA.QVKNKPTA.VAKTFKGRGIP..EDAENWHGKPMPKERADAIIKLIES
Retrocopy GWNTYLVDGHDVEGLCHAFWQATQVKNKPTAIVAKTFKGRGIPDIEDAENWHGKPMPKERADAIIKLIES

Parental  QIETNQNLEPKPPIEDSPQITITDIEMTSPPAYKDGDKIATRKACGLALAKLGHANNRVIVLDGDTKNST
          QI.TN.N...KPP.EDSPQ..I..I.MT..P.Y..GDKIAT.KA.GLAL.KLG.AN.R.IVLDGD.KNST
Retrocopy QIQTNRNFIVKPPLEDSPQVSIRNIKMTCLPDYEVGDKIATQKAYGLALVKLGRANDRLIVLDGDAKNST

Parental  FSEIFKKEHPERFIECFIAEQNMVSVALGCAIRDRTIAFVSTFAAFLTRAFDQIRVGAISQSNINLIGSH
          FSEIFKKE.PERFIEC..AEQNMVSVALGCA.RDRT.AF.ST.AA.LTRAFDQIR.GAISQ.NINLIGSH
Retrocopy FSEIFKKEYPERFIECVMAEQNMVSVALGCATRDRTVAFISTLAACLTRAFDQIRMGAISQTNINLIGSH

Parental  CGVSVGEDGPSQMALEDLAMFRAVPNCTIFYPSDAISTEHAVFLAANTKGMCYIRTSRPETSVIYTAQER
          CGVS.GE.G.SQMALEDLAMFR..PNCT.FYPSDAIS.EHAV.LAA.TKGMC.IRTSR.ET.VIYT.QE.
Retrocopy CGVSMGEEGSSQMALEDLAMFRSIPNCTVFYPSDAISAEHAVYLAASTKGMCFIRTSRQETAVIYTPQEN

Parental  FEIGQAKVVRHSVNDKVTVIGAGVTLHEALAAADDLSKQDISVRVIDLFTIKPLDAATIISNAKATGGRI
          F.IGQA.V.RHSVNDKVTVIGAGVTLHEALAAA.DLS.Q.IS.RVID.FTIKPLDAATIIS.AKATGGR.
Retrocopy FVIGQARVIRHSVNDKVTVIGAGVTLHEALAAAADLSQQGISIRVIDPFTIKPLDAATIISSAKATGGRV

Parental  ITVEDHYPEGGIGEAVCAAVSMEPDILVHQLAAPGVPQSGKPSELLDMFGVSARHIIVAVKCMLMN
          ITVEDHY.EGG.GEAVC.AVS.EPDILVHQLA..GVPQSGKP.ELLDMFG.SARHII.AVK..LMN
Retrocopy ITVEDHYREGGLGEAVCTAVSGEPDILVHQLAVSGVPQSGKPGELLDMFGISARHIIAAVKYTLMN

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	0.05 RPM	0.68 RPM
SRP021940_embryo	0.00 RPM	0.03 RPM
SRP021940_placental_villous	0.05 RPM	0.19 RPM
SRP021940_synovial_membrane	0.00 RPM	0.00 RPM
SRP021940_testis	129.55 RPM	206.60 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_6 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_6 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_6 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_47
Pan troglodytes	retro_ptro_126
Macaca mulatta	retro_mmul_74
Mus musculus	retro_mmus_220
Oryctolagus cuniculus	retro_ocun_62
Bos taurus	retro_btau_176

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018441	1 retrocopy	retro_amel_119,
Equus caballus	ENSECAG00000021992	1 retrocopy	retro_ecab_6 ,
Felis catus	ENSFCAG00000011392	1 retrocopy	retro_fcat_84,
Loxodonta africana	ENSLAFG00000005145	1 retrocopy	retro_lafr_6,
Pongo abelii	ENSPPYG00000020870	1 retrocopy	retro_pabe_205,
Ictidomys tridecemlineatus	ENSSTOG00000005014	1 retrocopy	retro_itri_30,