RetrogeneDB ID: retro_btau_629

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 16:52997838..52998273(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000005722
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BT.61911
• Ensembl ID: ENSBTAG00000003358
• Aliases: None
• Description: multiple coagulation factor deficiency protein 2 precursor [Source:RefSeq peptide;Acc:NP_001035685]

Sequence

>retro_btau_629
ATGAGATCTCTGCGACTGCTCAGAATCCCCTTCCTGTGTGGCTTGCTCTGGGCCTTTTGTGCCCCAGGTGCCAGGGCCGA
GGAGCCCGGGGCCAGCTCCTCCCATCACGGCAGCATGGGCCTGGATAAGAACACAGTGCATGACCAAGAGCATATCATGG
AGCATCTCGAAGGTGTCATCAACAAACCAGAGGCGGAGATGTCCCCACAAGAGCTGCAGCTCCATTATTTCAAAATGCAT
GATTATGATGGCAATAATCTGCTTGACAGCCTAGAACTCTCCACGGCCATCACTCAGGTTCACAAGGAGGAGGAAAGTGA
GCAGGCACCAATGAACGAAGATGAGCTGATCAACTTAATAGATGGTGTTTTGAGAGACGATGACAAGAACAATGATGGAT
ACATCGACTATGCCGAATTTGCAAAATCCCTGCAG

Alignment

ORF - retro_btau_629 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.93 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRSLRLLRIPFLCGLLWAFCAPGARAEEPGASSSHHGSMGLDKNTVHDQEHIMEHLEGVINKPEAEMSPQ
          MRSLRLLRIPFLCGLLWAFCAPGARAEEPGASSSHHGSMGLDKNTVHDQEHIMEHLEGVINKPEAEMSPQ
Retrocopy MRSLRLLRIPFLCGLLWAFCAPGARAEEPGASSSHHGSMGLDKNTVHDQEHIMEHLEGVINKPEAEMSPQ

Parental  ELQLHYFKMHDYDGNNLLDGLELSTAITHVHKEEGSEQAPMNEDELINLIDGVLRDDDKNNDGYIDYAEF
          ELQLHYFKMHDYDGNNLLD.LELSTAIT.VHKEE.SEQAPMNEDELINLIDGVLRDDDKNNDGYIDYAEF
Retrocopy ELQLHYFKMHDYDGNNLLDSLELSTAITQVHKEEESEQAPMNEDELINLIDGVLRDDDKNNDGYIDYAEF

Parental  AKSLQ
          AKSLQ
Retrocopy AKSLQ

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	0.87 RPM	232.37 RPM
ERP005899_muscle	0.21 RPM	26.24 RPM
SRP017611_brain	0.27 RPM	41.75 RPM
SRP017611_kidney	0.53 RPM	39.71 RPM
SRP017611_liver	0.76 RPM	223.35 RPM
SRP030211_testis	0.20 RPM	58.87 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_629 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_629 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_629 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003358	1 retrocopy	retro_btau_629 ,
Choloepus hoffmanni	ENSCHOG00000003286	6 retrocopies	retro_chof_110, retro_chof_1840, retro_chof_2447, retro_chof_3, retro_chof_41, retro_chof_581,
Felis catus	ENSFCAG00000009220	1 retrocopy	retro_fcat_42,
Macropus eugenii	ENSMEUG00000010002	1 retrocopy	retro_meug_2119,
Myotis lucifugus	ENSMLUG00000004210	1 retrocopy	retro_mluc_2396,
Ictidomys tridecemlineatus	ENSSTOG00000003692	1 retrocopy	retro_itri_1118,