RetrogeneDB ID: retro_btau_1534

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 7:42576466..42577279(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STX17
• Ensembl ID: ENSBTAG00000008016
• Aliases: None
• Description: Syntaxin-17 [Source:UniProtKB/Swiss-Prot;Acc:Q5E9Y2]

Sequence

>retro_btau_1534
ATGTCTGAAGATGAAGAAAAAGTGAAATTATGCCTTCCTGAACCAGCTATCCAGAAATTTACTAAAATGGCAATCCCAAC
AGACCTGGAGATGTTACAAAAGTGCCAGATAAATATTGAGAAGTATTAGAGGTGCTGAACATGGGACCAGTACATGAAGA
GCATGTCAATGCAGGACGTACAGTTCAGCAACTCTGCTGCAATATTGGAGGAATGGAGAAGCTTTGTTTTAAAGTCCAAA
AGGGTGACCTAAGACTTCTAAAGAGAATGATAGATTCTGTTGAAAACGCGTCAGCTGCAACAGCAGGATTTTTCCAACTC
CATCTAGCATCTGTAGAAGAACTTAAGAAACAATTTAATGATGAAGAAACTTTATTACAGCCTTCTTTAGATCCATGACT
GACAACATTTCATACTACTGAAGATGAAGCTGATCCTCAGAGTATGACTCAGATGTATGCGTTGCCTGAAACGCCTCAAG
ATTAAAATACTGCAGAATCATGGGAGACCTTAGAAGCGGACTTAAATGAACTTAACCAACTGGTCCCACTGATTTCTCTC
TCCTAGTGAATTTTCAGCAGGAGAAGATTGACAGCACTGAAGACCATGTCAACAGTGCTGCTGTGAATATTGAAGAGGGA
ACCAAAACATGGGGGAAGGCTGAAAAATACAAGTTGGCAGCCCTACCTGTGGCAGGCGCACTCAGAGGAGGAGTGGTGAA
GGGTCAGATTGGCCTCCTTGATGCTTCAAAGCGTCAGAAATTGCAGCTGCACTTGGTGGTGGGGTGTTGCGCTTCACAGG
TGGAAAAGTGATA

Alignment

ORF - retro_btau_1534 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.84 %
• Parental protein coverage: 91.06 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSEDEEKVKLRRLEPAIQKFTKIVIPTDLERLRKHQINIEKYQRCRVWDK-LHEEHINAGRTVQQLRSNI
          MSEDEEKVKL...EPAIQKFTK..IPTDLE.L.K.QINIEKY.RC..WD...HEEH.NAGRTVQQL..NI
Retrocopy MSEDEEKVKLCLPEPAIQKFTKMAIPTDLEMLQKCQINIEKY*RC*TWDQ<VHEEHVNAGRTVQQLCCNI

Parental  REMEKLCLKVRKDDLGLLKRMIDPVKEEASAATAEFLQLHLESVEELKKQFNDEETFLQPSLTRSMTVGG
          ..MEKLC.KV.K.DL.LLKRMID.V.E.ASAATA.F.QLHL.SVEELKKQFNDEET.LQPSL....T...
Retrocopy GGMEKLCFKVQKGDLRLLKRMIDSV-ENASAATAGFFQLHLASVEELKKQFNDEETLLQPSLDP*LT---

Parental  TFHSTEDEADPQSMTQIYALPEIPRDQNAAESWETLEADLIELSQLVTDFSL-LVNSQQEK-IDSIEDHV
          TFH.TEDEADPQSMTQ.YALPE.P.D.N.AESWETLEADL.EL.QLV...SL.L....Q...IDS.EDHV
Retrocopy TFHTTEDEADPQSMTQMYALPETPQD*NTAESWETLEADLNELNQLVPLISL<LLVNFQQEKIDSTEDHV

Parental  NTAAVNVEEGTKNLGKAAKYKLAALPVAGALIGGVVGGPIGLLAG-FKVAGIAAALGGGVLGFTGGKLI
          N.AAVN.EEGTK..GKA.KYKLAALPVAGAL.GGVV.G.IGLL...FK...IAAALGGGVL.FTGGK.I
Retrocopy NSAAVNIEEGTKTWGKAEKYKLAALPVAGALRGGVVKGQIGLLDA<FKASEIAAALGGGVLRFTGGKVI

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
ERP005899_liver	0.00 RPM	6.78 RPM
ERP005899_muscle	0.00 RPM	13.46 RPM
SRP017611_brain	0.00 RPM	6.03 RPM
SRP017611_kidney	0.00 RPM	9.60 RPM
SRP017611_liver	0.00 RPM	4.91 RPM
SRP030211_testis	0.00 RPM	5.67 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1534 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1534 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1534 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
Bos taurus	ENSBTAG00000008016	1 retrocopy	retro_btau_1534 ,
Choloepus hoffmanni	ENSCHOG00000013030	1 retrocopy	retro_chof_131,
Myotis lucifugus	ENSMLUG00000011745	1 retrocopy	retro_mluc_760,
Tursiops truncatus	ENSTTRG00000016920	1 retrocopy	retro_ttru_899,