RetrogeneDB ID: retro_btau_783

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 19:11526153..11526422(-)
• Located in intron of: ENSBTAG00000012068

Retrocopy information

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

Parental gene information

• Parental gene symbol: LYRM4
• Ensembl ID: ENSBTAG00000031432
• Aliases: None
• Description: LYR motif-containing protein 4 [Source:UniProtKB/Swiss-Prot;Acc:Q0VCG0]

Sequence

>retro_btau_783
ATGGCACCCTCAGCCCGACACAAGTTCTGGATCTGTACCCAGCAATGCTGAAGAAGGGCAAACACTTCAGCACCTACAAC
TACACAACTTACACCATCAGGAGGATATGAATTGCCTTCAGAGAAAATAAGAATGTAGAGGATCCTATAAAAATTCAAGC
CCTAATGAATAAAGCCAAAAGAGATATTAGAATAAGTCTGTCCACAGGTCATAATGGCCAACTGTATTCAACTGACAATC
TTGTCACTGAGAATCAAGAGAAGTCCAGG

Alignment

ORF - retro_btau_783 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.93 %
• Parental protein coverage: 98.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAASSR-AQVLDLYRAMLRESKRFGAYNYRTYAIRRIRDAFRENKNVKDPVEIQALVNKAKRDLGIIRRQ
          MA.S.R..QVLDLY.AML...K.F..YNY.TY.IRRI..AFRENKNV.DP..IQAL.NKAKRD..I....
Retrocopy MAPSAR<TQVLDLYPAMLKKGKHFSTYNYTTYTIRRI*IAFRENKNVEDPIKIQALMNKAKRDIRISLST

Parental  VHIGQMYSTDKLVIENQEKPR
          .H.GQ.YSTD.LV.ENQEK.R
Retrocopy GHNGQLYSTDNLVTENQEKSR

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	3.24 RPM
ERP005899_muscle	0.00 RPM	11.98 RPM
SRP017611_brain	0.00 RPM	10.60 RPM
SRP017611_kidney	0.00 RPM	12.33 RPM
SRP017611_liver	0.00 RPM	6.95 RPM
SRP030211_testis	0.03 RPM	53.10 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_783 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_783 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_783 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031432	1 retrocopy	retro_btau_783 ,
Callithrix jacchus	ENSCJAG00000021370	1 retrocopy	retro_cjac_1371,
Homo sapiens	ENSG00000214113	1 retrocopy	retro_hsap_194,
Macropus eugenii	ENSMEUG00000005958	1 retrocopy	retro_meug_656,
Myotis lucifugus	ENSMLUG00000028065	1 retrocopy	retro_mluc_394,
Mustela putorius furo	ENSMPUG00000000532	1 retrocopy	retro_mputfur_1459,
Mus musculus	ENSMUSG00000046573	1 retrocopy	retro_mmus_2374,
Nomascus leucogenys	ENSNLEG00000011472	1 retrocopy	retro_nleu_1002,
Rattus norvegicus	ENSRNOG00000047970	2 retrocopies	retro_rnor_1862, retro_rnor_2052,
Tursiops truncatus	ENSTTRG00000007073	1 retrocopy	retro_ttru_552,