RetrogeneDB ID: retro_ecab_1118

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:68937646..68938227(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NT5C3A
• Ensembl ID: ENSECAG00000011777
• Aliases: NT5C3A, NT5C3
• Description: 5'-nucleotidase, cytosolic IIIA [Source:HGNC Symbol;Acc:17820]

Sequence

>retro_ecab_1118
CAAAGTTTAGTTCTCACCAAGAACCCTACAAGACTAGAAGAAAATCTCTGTGGTCTTATCAAAGGAGGAGCTGCCAAATT
TCAGATACTAACAGACTTTTATATGATACTATGTAGATTTTCCTTAGGAAAAAGATGCTCAACATGACACAATATCATTG
ACAACTGTAAGCTGGTTACAAATGAATGTCAAAAAATGTTACTGAAGCTAAATAAAAAAACATTATGCTATTAAAATTGA
TCTTAATCTAACTTTAGAAGGGAAGTACCCTTGTATGATAGAAGGGTATACTAAATCACATGATTTTCTTTTTGAAAAGA
CTTTACCAAAATCTAAGCTTAAAGAAATGACAGCAGAATCTGACATTATGCTCAAAGAAAGATGTGAAATTTTCTTTGAT
AAGTTCTAAGAAAACAGTATCCCTATATTTATATTTTCAGCTGGTATTGGTGATATGTTATAGATGGTATCCATCAAGGT
GGTATTTATCATCCAGATGTCAAAGTAGCCTCAACTTCATGGATTTTTATGAAAATGGGATTCTCAAAGGATTTAAAGAA
CTATTTCATATAATTAACAAA

Alignment

ORF - retro_ecab_1118 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.83 %
• Parental protein coverage: 58.33 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KSSVRIKNPTRVEEIICGLIKGGAAKLQIITDFDMTLSRFSYEGKRCPTCHNIIDNCKLVTDECRKKLLQ
          .S.V..KNPTR.EE..CGLIKGGAAK.QI.TDF.M.L.RFS..GKRC.T.HNIIDNCKLVT.EC.K.LL.
Retrocopy QSLVLTKNPTRLEENLCGLIKGGAAKFQILTDFYMILCRFSL-GKRCST*HNIIDNCKLVTNECQKMLLK

Parental  LKEK-YYAIEVDPVLTVEEKYPYMVEWYTKSHGLLVEQALPKAKLKEIVAESDVMLKEGYENFFDKLQQH
          L..K..YAI..D..LT.E.KYP.M.E.YTKSH..L.E..LPK.KLKE..AESD.MLKE..E.FFDK....
Retrocopy LNKK>HYAIKIDLNLTLEGKYPCMIEGYTKSHDFLFEKTLPKSKLKEMTAESDIMLKERCEIFFDKF*EN

Parental  SIPVFIFSAGIGDVLEEV-IRQAGVYHPNVKVVS-NFMDFDDKGLLKGFKGELIHVFNK
          SIP.FIFSAGIGD.L..V.I.Q.G.YHP.VKV.S.NFMDF...G.LKGFK.EL.H..NK
Retrocopy SIPIFIFSAGIGDML*MV<IHQGGIYHPDVKVAS<NFMDFYENGILKGFK-ELFHIINK

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	3.54 RPM
SRP021940_cerebellum	0.00 RPM	7.37 RPM
SRP021940_embryo	0.00 RPM	5.27 RPM
SRP021940_placental_villous	0.00 RPM	8.13 RPM
SRP021940_synovial_membrane	0.00 RPM	3.40 RPM
SRP021940_testis	0.00 RPM	3.96 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1118 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1118 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1118 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006624	1 retrocopy	retro_amel_875,
Bos taurus	ENSBTAG00000016709	1 retrocopy	retro_btau_1465,
Canis familiaris	ENSCAFG00000003154	1 retrocopy	retro_cfam_1295,
Equus caballus	ENSECAG00000011777	1 retrocopy	retro_ecab_1118 ,
Homo sapiens	ENSG00000122643	1 retrocopy	retro_hsap_3084,
Gorilla gorilla	ENSGGOG00000028164	1 retrocopy	retro_ggor_2119,
Mustela putorius furo	ENSMPUG00000005546	2 retrocopies	retro_mputfur_1175, retro_mputfur_577,
Pteropus vampyrus	ENSPVAG00000013182	2 retrocopies	retro_pvam_148, retro_pvam_706,
Rattus norvegicus	ENSRNOG00000005981	1 retrocopy	retro_rnor_632,
Sus scrofa	ENSSSCG00000022912	1 retrocopy	retro_sscr_540,
Ictidomys tridecemlineatus	ENSSTOG00000026363	2 retrocopies	retro_itri_1325, retro_itri_682,