RetrogeneDB ID: retro_btau_496

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 12:36491416..36491611(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000025383
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NDUFC1
• Ensembl ID: ENSBTAG00000039582
• Aliases: NDUFC1, CI-KFYI
• Description: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q02376]

Sequence

>retro_btau_496
AAGCTGCTGGCCCCGGCTAGGTTCCCGAGTGTCTCTTCATCTCGGTCAAAGTTCTACATTCAGGAACCGCCACATGGCAG
TCCTAACTGGCTGAAAGTTGGCTTGACCTTGGGCACCTCCGTTTTTTTGTGGATCTATCTCATCAAACAACATAACGAAG
ATGTTTTAGAGTATAAAAGAAGAAATGGGTTGGAA

Alignment

ORF - retro_btau_496 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 85.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KLLAPARFPSVSSSRSKFYIQEPPHGSPNWLKVGLTLGTSVFLWIYLIKQHNEDVLEYKRRNGLE
          KLLAPARFPSVSSSRSKFYIQEPPHGSPNWLKVGLTLGTSVFLWIYLIKQHNEDVLEYKRRNGLE
Retrocopy KLLAPARFPSVSSSRSKFYIQEPPHGSPNWLKVGLTLGTSVFLWIYLIKQHNEDVLEYKRRNGLE

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	0.65 RPM	11.68 RPM
ERP005899_muscle	0.00 RPM	17.74 RPM
SRP017611_brain	0.05 RPM	7.81 RPM
SRP017611_kidney	0.00 RPM	19.86 RPM
SRP017611_liver	0.08 RPM	8.83 RPM
SRP030211_testis	0.23 RPM	16.61 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_496 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_496 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_496 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011040	2 retrocopies	retro_amel_282, retro_amel_805,
Bos taurus	ENSBTAG00000039582	2 retrocopies	retro_btau_1578, retro_btau_496 ,
Dasypus novemcinctus	ENSDNOG00000015639	1 retrocopy	retro_dnov_28,
Echinops telfairi	ENSETEG00000004800	11 retrocopies	retro_etel_1014, retro_etel_1025, retro_etel_135, retro_etel_1735, retro_etel_195, retro_etel_1966, retro_etel_214, retro_etel_670, retro_etel_700, retro_etel_701, retro_etel_87,
Felis catus	ENSFCAG00000008548	1 retrocopy	retro_fcat_146,
Loxodonta africana	ENSLAFG00000010459	5 retrocopies	retro_lafr_1034, retro_lafr_191, retro_lafr_77, retro_lafr_834, retro_lafr_869,
Microcebus murinus	ENSMICG00000006836	1 retrocopy	retro_mmur_771,
Myotis lucifugus	ENSMLUG00000009082	2 retrocopies	retro_mluc_1603, retro_mluc_1660,
Ictidomys tridecemlineatus	ENSSTOG00000023590	3 retrocopies	retro_itri_1087, retro_itri_1109, retro_itri_1202,
Tursiops truncatus	ENSTTRG00000001107	2 retrocopies	retro_ttru_142, retro_ttru_586,
Vicugna pacos	ENSVPAG00000007703	1 retrocopy	retro_vpac_161,