RetrogeneDB ID: retro_btau_144

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 2:49736039..49736399(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000012376
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SNRPD1
• Ensembl ID: ENSBTAG00000008292
• Aliases: None
• Description: Small nuclear ribonucleoprotein Sm D1 [Source:UniProtKB/Swiss-Prot;Acc:Q3ZC10]

Sequence

>retro_btau_144
ATGAAGCTCGTGAGATTTTTGACGAAATTGAGTCATGAAACTGTAACCATTGAATTAAAGAATGGAACACAGGTCCATGG
AACAATCACAGGTGTAGATGTCAGTATGAACACACATCTTAAAGCAGTGAAAATGACCCTGAAGAACAGAGAACCTGTAC
AGCTGGAAACACTGAGTATTCAAGGAAATAACATTCGGTATTTTATTCTGCCAGACAGCTTACCTCTGGATACACTACTC
GTGGATGTGGAACCAAAGGTGAAGTCTAAGAAAAGGGAAGCTGTTGCAGGAAGAGGCCGAGGCCAAGGAAGAGGACGAGG
CCGAGGCCAAGGAAGAGGACGAGGCCGAGGCCAAGGAAGA

Alignment

ORF - retro_btau_144 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.52 %
• Parental protein coverage: 96.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFIL
          MKLVRFL.KLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSI.GNNIRYFIL
Retrocopy MKLVRFLTKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIQGNNIRYFIL

Parental  PDSLPLDTLLVDVEPKVKSKKREAVAGRGRGRGRGRGRGRGRGRG
          PDSLPLDTLLVDVEPKVKSKKREAVAGRGRG.GRGRGRG.GRGRG
Retrocopy PDSLPLDTLLVDVEPKVKSKKREAVAGRGRGQGRGRGRGQGRGRG

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	11.46 RPM
ERP005899_muscle	0.00 RPM	28.14 RPM
SRP017611_brain	0.00 RPM	11.01 RPM
SRP017611_kidney	0.00 RPM	14.46 RPM
SRP017611_liver	0.00 RPM	7.40 RPM
SRP030211_testis	0.03 RPM	43.17 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_144 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_144 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_144 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000006364	1 retrocopy	retro_acar_129,
Ailuropoda melanoleuca	ENSAMEG00000002576	1 retrocopy	retro_amel_1905,
Bos taurus	ENSBTAG00000008292	3 retrocopies	retro_btau_144 , retro_btau_706, retro_btau_84,
Canis familiaris	ENSCAFG00000018247	1 retrocopy	retro_cfam_373,
Dasypus novemcinctus	ENSDNOG00000018773	4 retrocopies	retro_dnov_1254, retro_dnov_1716, retro_dnov_1832, retro_dnov_2403,
Felis catus	ENSFCAG00000012352	1 retrocopy	retro_fcat_1885,
Homo sapiens	ENSG00000167088	2 retrocopies	retro_hsap_1147, retro_hsap_372,
Macaca mulatta	ENSMMUG00000003992	2 retrocopies	retro_mmul_887, retro_mmul_891,
Mustela putorius furo	ENSMPUG00000005567	1 retrocopy	retro_mputfur_185,
Mus musculus	ENSMUSG00000002477	1 retrocopy	retro_mmus_1996,
Nomascus leucogenys	ENSNLEG00000006822	2 retrocopies	retro_nleu_2824, retro_nleu_945,
Oryctolagus cuniculus	ENSOCUG00000023761	1 retrocopy	retro_ocun_224,
Otolemur garnettii	ENSOGAG00000007833	1 retrocopy	retro_ogar_3085,
Pongo abelii	ENSPPYG00000025874	3 retrocopies	retro_pabe_254, retro_pabe_948, retro_pabe_952,
Pan troglodytes	ENSPTRG00000009909	2 retrocopies	retro_ptro_291, retro_ptro_781,
Pteropus vampyrus	ENSPVAG00000005511	1 retrocopy	retro_pvam_450,
Rattus norvegicus	ENSRNOG00000013714	2 retrocopies	retro_rnor_2671, retro_rnor_2729,
Sarcophilus harrisii	ENSSHAG00000011791	1 retrocopy	retro_shar_147,
Tursiops truncatus	ENSTTRG00000002654	2 retrocopies	retro_ttru_1566, retro_ttru_1890,