RetrogeneDB ID: retro_btau_1527

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 7:32166983..32167193(+)
• Located in intron of: ENSBTAG00000031069

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEPW1
• Ensembl ID: ENSBTAG00000008203
• Aliases: None
• Description: selenoprotein W [Source:RefSeq peptide;Acc:NP_001156697]

Sequence

>retro_btau_1527
AAGTATCTTCAGCTCAAAAAGAAGTTAGAAGATGGGTTCCCTGGATGCTTGGACATTTGCAGCAAGGGGACTCACCAGGT
CACTGGCTTCTTTGAAGTGTTCGTAGCAGGGAAGCCGGTTCATTCCAAGAAGGGAGGTGATGGCTACATGGACATGGAGA
GCAAGTTTCTGAAGCTGGTGGCCGCCATCAAAGCTGCTCTGGCTCAGGCC

Alignment

ORF - retro_btau_1527 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.14 %
• Parental protein coverage: 94.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KYLQLKKKLEDEFPSRLDICGEGTPQVTGFFEVFVAGKLVHSKKGGDGYVDTESKFLKLVAAIKAALAQA
          KYLQLKKKLED.FP..LDIC..GT.QVTGFFEVFVAGK.VHSKKGGDGY.D.ESKFLKLVAAIKAALAQA
Retrocopy KYLQLKKKLEDGFPGCLDICSKGTHQVTGFFEVFVAGKPVHSKKGGDGYMDMESKFLKLVAAIKAALAQA

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	0.07 RPM	9.59 RPM
ERP005899_muscle	0.00 RPM	69.00 RPM
SRP017611_brain	0.05 RPM	186.55 RPM
SRP017611_kidney	0.00 RPM	72.73 RPM
SRP017611_liver	0.00 RPM	27.86 RPM
SRP030211_testis	0.00 RPM	40.32 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1527 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1527 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1527 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015208	1 retrocopy	retro_amel_1135,
Bos taurus	ENSBTAG00000008203	2 retrocopies	retro_btau_1527 , retro_btau_756,
Canis familiaris	ENSCAFG00000004074	1 retrocopy	retro_cfam_1368,
Choloepus hoffmanni	ENSCHOG00000013206	2 retrocopies	retro_chof_1486, retro_chof_61,
Felis catus	ENSFCAG00000015176	2 retrocopies	retro_fcat_108, retro_fcat_186,
Mustela putorius furo	ENSMPUG00000004433	1 retrocopy	retro_mputfur_326,
Rattus norvegicus	ENSRNOG00000013548	2 retrocopies	retro_rnor_1819, retro_rnor_688,
Ictidomys tridecemlineatus	ENSSTOG00000001294	1 retrocopy	retro_itri_578,