RetrogeneDB ID: retro_btau_642

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 16:25739193..25739650(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC35E3
• Ensembl ID: ENSBTAG00000031919
• Aliases: None
• Description: Solute carrier family 35 member E3 [Source:UniProtKB/Swiss-Prot;Acc:A4IFK2]

Sequence

>retro_btau_642
CCAGTGGCTGTCACCATCCAGACCATCTGTCACAAGAAGCAGTTCACCGGAGTACTCAACTCAACGCAGCTTCTGGAAAT
TTTAGGGGCAATCTCCAATTCTTTTGATGTGAAGTTTAATGACTTTGTGTTTGCAGCTCTGGCTGTTTAGCTGCATCCTT
TATCCAGTGTGTACAGGAGCCCAGCGGCATGGGCTGGGTGTGAACACCAGTTACCTGCAGTGCTACCAGGCGCTGGTGTC
TTCTGCTGTGTTGGTGGTGGTTGTGCCCTTCTTTGAGTCAGCATGTGGAACACAAATCTATGGTCTCTGGTTAGTTTCTG
CTTTGCTTATGATGCTGCTATCTGGAATCAGAGTTGTCAGGGTGGACTTCTCAATTTACTGGATCAGTGGGTACACTTCA
ACAGTCACCCATGACATATTCGGGCACTTCAAGTTCTGACTTGCTTCGTTTGAAGGC

Alignment

ORF - retro_btau_642 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.2 %
• Parental protein coverage: 50.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PVIIVIQTLCYKKTFSTKIRLTLIPITLGVILNSYYDVKFNFLGTVFAAL-GVLVTS-LYQVWVGAKQHE
          PV...IQT.C.KK.F......T.....LG.I.NS..DVKFN....VFAAL.G.L..S.LY.V..GA..H.
Retrocopy PVAVTIQTICHKKQFTGVLNSTQLLEILGAISNSF-DVKFNDF--VFAAL<GCLAAS<LYPVCTGAQRHG

Parental  LQVNSMQLLYYQAPMSSAMLLVAVPFFEPVFAEGGIFGPWSVSALLMVLLSGVIAFMVNLSIYWIIGNTS
          L.VN...L..YQA..SSA.L.V.VPFFE.......I.G.W.VSALLM.LLSG.....V..SIYWI.G.TS
Retrocopy LGVNTSYLQCYQALVSSAVLVVVVPFFESACGTQ-IYGLWLVSALLMMLLSGIRVVRVDFSIYWISGYTS

Parental  PVTYNMFGHFKFCITLFGG
          .VT...FGHFKF....F.G
Retrocopy TVTHDIFGHFKF*LASFEG

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	43.76 RPM
ERP005899_muscle	0.00 RPM	16.00 RPM
SRP017611_brain	0.00 RPM	26.13 RPM
SRP017611_kidney	0.00 RPM	24.66 RPM
SRP017611_liver	0.00 RPM	25.97 RPM
SRP030211_testis	0.00 RPM	13.81 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_642 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_642 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_642 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_513
Pan troglodytes	retro_ptro_383
Gorilla gorilla	retro_ggor_473

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031919	1 retrocopy	retro_btau_642 ,
Choloepus hoffmanni	ENSCHOG00000013347	1 retrocopy	retro_chof_2348,
Cavia porcellus	ENSCPOG00000004322	3 retrocopies	retro_cpor_1404, retro_cpor_1487, retro_cpor_339,
Homo sapiens	ENSG00000175782	1 retrocopy	retro_hsap_513,
Gorilla gorilla	ENSGGOG00000012605	1 retrocopy	retro_ggor_473,
Mus musculus	ENSMUSG00000060181	1 retrocopy	retro_mmus_287,
Pan troglodytes	ENSPTRG00000005201	1 retrocopy	retro_ptro_383,
Pteropus vampyrus	ENSPVAG00000002545	1 retrocopy	retro_pvam_710,