RetrogeneDB ID: retro_btau_429

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 11:29905014..29905534(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.49063
• Ensembl ID: ENSBTAG00000009345
• Aliases: None
• Description: archaemetzincin-2 [Source:RefSeq peptide;Acc:NP_001029653]

Sequence

>retro_btau_429
CTTTTGATGGAAGACTTCCAGGCAGACAATGGTCTTTTTGGATCCATTACTTTGCATTTACATCAGATTGGGTCACCTCC
CATCTCGGGGCTCCCCAAGACTTTGAACACTTTTTCAGTAACCCTTACAGAAAGACATCCTCTTCTGAGAAATGCAGCAT
GGTTACACAGTGCAATGGATCTCTTGGGGAACACCAGAGTTATCAGTGAAAAATATATTAAATGACTCAAGGGCTACTTT
GAAGCATTTTGCTATGGCTAGATAGTAAAACTCCTAGAACTAGTTCTTATCTCTGTAACAGAGTGTTCCTTTAGTGCAAT
GAGAACACATAAAGCCCACAATTCATGCAGGACACATTCTGAAGTTCTTAAAAGAGAAGGAACCTGAAGATGCCTTCTGT
GTTGTGACAGTAACAATGGTCGATCTTTATCCAAGAGGATCTTAGCATTTTGTCTTTGGACAGGCCTCTTTGACAGCTGG
ATGGGCAAGCTTTGCCAGGTATGACAGTGATTTTATATCT

Alignment

ORF - retro_btau_429 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.67 %
• Parental protein coverage: 53.01 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LLNEAFRPRSDLFGPITLHS-PSDWIISHPEAPQDFEQFFSNLHRKSPSPGKQTIYIQCIG-LLGNTRSI
          LL.E.F.....LFG.ITLH...SDW..SH..APQDFE.FFSN..RK..S..K.....QC.G.LLGNTR.I
Retrocopy LLMEDFQADNGLFGSITLHL<TSDWVTSHLGAPQDFEHFFSNPYRKTSSSEKCSMVTQCNG>LLGNTRVI

Parental  SEEYLKWLKGYCEAFFYGLTVKLLEPIPVSATRCSFRI-NDSTLNLQ-IHAGQILTFLKKKKPEDAFCVV
          SE.Y.K.LKGY.EAF.YG..VKLLE....S.T.CSF...N..T...Q.IHAG.IL.FLK.K.PEDAFCVV
Retrocopy SEKYIK*LKGYFEAFCYG*IVKLLELVLISVTECSFSA<NENT*SPQ<IHAGHILKFLKEKEPEDAFCVV

Parental  GVTMIDLYPRESWNFVFGQASLTEGVGIFSFARYGTDFYS
          .VTM.DLYPR.S..FVFGQASLT.G....SFARY..DF.S
Retrocopy TVTMVDLYPRGS*HFVFGQASLTAGWA--SFARYDSDFIS

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	29.27 RPM
ERP005899_muscle	0.05 RPM	58.60 RPM
SRP017611_brain	0.00 RPM	62.81 RPM
SRP017611_kidney	0.00 RPM	77.17 RPM
SRP017611_liver	0.00 RPM	41.68 RPM
SRP030211_testis	0.00 RPM	406.93 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_429 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_429 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_429 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009345	1 retrocopy	retro_btau_429 ,
Choloepus hoffmanni	ENSCHOG00000000493	1 retrocopy	retro_chof_2462,
Callithrix jacchus	ENSCJAG00000000254	1 retrocopy	retro_cjac_2798,
Cavia porcellus	ENSCPOG00000013061	1 retrocopy	retro_cpor_1226,
Equus caballus	ENSECAG00000011450	2 retrocopies	retro_ecab_440, retro_ecab_864,
Felis catus	ENSFCAG00000019195	1 retrocopy	retro_fcat_760,
Myotis lucifugus	ENSMLUG00000006771	2 retrocopies	retro_mluc_1540, retro_mluc_2056,
Mustela putorius furo	ENSMPUG00000014570	1 retrocopy	retro_mputfur_1224,