RetrogeneDB ID: retro_ecab_139

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:112756536..112757238(+)
• Located in intron of: ENSECAG00000018053

Retrocopy information

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

Parental gene information

• Parental gene symbol: SERPINE2
• Ensembl ID: ENSECAG00000016075
• Aliases: None
• Description: serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2 [Source:HGNC Symbol;Acc:8951]

Sequence

>retro_ecab_139
TATGTTAAAAATGAAACAGGGATTTGATTAACAATCTCCTTTCCCTGGATCTTATCAATGGTGTGTTCACTGGACTGGTC
CTTGTCAGTGCAGTGCATTTTAAAGGTTTAGAGAAATCAAAGTTTCAACCTGAGAACACAAAGAAATATATGTTTTTGAC
AGCTGATAGAAAATCCTATCAGTGCTGATGCTAGTTCAGCTCTGCATGTTCTGGTGGGGGGCAGCAAGCACCCCTAATGA
TTTATGGTACAACTTCATTGAATGCCCTACCGTGGGGAAAATATCAGTATGCTGATTCTGCTATCCACCTCCACTCCACT
GTCGGCCATCACCCGCCACATCAGCATGCAAACCATAGACCACTGATGTGAGCACCATGGCACCAAGAGCACACAGCTGA
TCCTGCCCAAGTTCACAGCCATAGAACAAACTGATTTGAAGGAGCCGCTGAAAGTTCTTGGTGTTACTGAGATACTTAAT
CTATCAAAGGCAAATTTTGCAAAGATAACAAGGTCAGAAAACCTTCATGTTTCTCATGTCTTGCAGAAAGCAAAGGTTGA
AGTCAATGTAGACAGAACCAAAGCTTCAGCAGCAACAACTAGGAATCTAATCACAAGAGCATCACCTTGGTTTATAGAAG
ACAGAACTTTTTTATCTTTCATCCTACATAATCCCACAAGTGCTGTCTTACTCAGGGGCAGA

Alignment

ORF - retro_ecab_139 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.55 %
• Parental protein coverage: 59.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  WVKNET-RGMIDNLLSPDLIDGVLTRLVLVNAVYFKGLWKSRFQPENTKKRTFVAADGKSYQ-VPMLAQL
          .VKNET.R..I.NLLS.DLI.GV.T.LVLV.AV.FKGL.KS.FQPENTKK..F..AD.KSYQ.V.ML.QL
Retrocopy YVKNET<RDLINNLLSLDLINGVFTGLVLVSAVHFKGLEKSKFQPENTKKYMFLTADRKSYQ<VLMLVQL

Parental  SVFRCGSTSTPSDLWYNFIE-LPYHGESISMLIALPTESSTPLSAIIPHISTKTID-SWMSTMVP-KRVQ
          ..F..G..STP.DLWYNFIE..PY.GE.ISMLI.L.T..STPLSAI..HIS..TID....STM.P.K..Q
Retrocopy CMFWWGAASTPNDLWYNFIE<MPYRGENISMLILLST--STPLSAITRHISMQTID>TDVSTMAP<KSTQ

Parental  VILPKFTAVAQTDLKEPLKVLGITEMFEPSKANFAKITRSENLHVSHILQKAKIEVSEDGTKASAATTAI
          .ILPKFTA..QTDLKEPLKVLG.TE....SKANFAKITRSENLHVSH.LQKAK.EV..D.TKASAATT..
Retrocopy LILPKFTAIEQTDLKEPLKVLGVTEILNLSKANFAKITRSENLHVSHVLQKAKVEVNVDRTKASAATTRN

Parental  LIARSSPPWFIVDRPFLFFIRHNPTGAVLFMGQ
          LI.R.S.PWFI.DR.FL.FI.HNPT.AVL..G.
Retrocopy LITRAS-PWFIEDRTFLSFILHNPTSAVLLRGR

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	726.78 RPM
SRP021940_cerebellum	0.00 RPM	128.07 RPM
SRP021940_embryo	0.00 RPM	65.75 RPM
SRP021940_placental_villous	0.00 RPM	92.81 RPM
SRP021940_synovial_membrane	0.00 RPM	137.10 RPM
SRP021940_testis	0.00 RPM	78.07 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_139 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_139 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_139 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	ENSECAG00000016075	1 retrocopy	retro_ecab_139 ,
Mustela putorius furo	ENSMPUG00000016691	1 retrocopy	retro_mputfur_1510,