RetrogeneDB ID: retro_btau_1749

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:79134301..79135102(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000035882
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BT.106043
• Ensembl ID: ENSBTAG00000020981
• Aliases: None
• Description: E3 ubiquitin-protein ligase MARCH5 [Source:UniProtKB/Swiss-Prot;Acc:Q3ZC24]

Sequence

>retro_btau_1749
AGAAGTTGCTGGGTGTGTTTTGCCACTGATGAAGATAATAAAACAGCTGAATGGGTGAGACCATGCAGATGCAGAGGATC
TACAAAATGGGTTCACCAGGCTTGTCTACAGTGCTGGGTGGATGAAAAACAAAGAGGAAACAGTACAGCCAGAGTGGCAT
GTCCTCAGTGCAATGCTGAATACTTAATAGTTTTTCCAAAGTTGGGTCCAGTTGTTTACATCTTGGATCTTGCAGATAGA
CTGATCTCAAAAGCCTGTCCATTTGCTGCAGCAGGAATAATGGTTGGCTCCATCTATTGGACAGCTGTGACTTACGGACA
GGTGACAGTGATGCAGGTTGTAGGCCATAAAGAAGGTCTGGATGTTATGGAGAGAGTTGATCCTTTATTCCTTTTAATTG
GACTTCCTACTATTCCGGTCATGCTGATACTAGGCAAGATGATTCGCTGGGAGGACTATGTGCTTAGACTCTGGCGCAAA
TACTCAAATAAACCACAAATTTTGAACAGTATATTCCCAGGGATTGGTTGTCCTGTTCCTCGAATTCCAGCTGAGGCTAA
TCCTTTAGCAGATCATGTCTCTGCCACCCGAATTTTGTGTGGAGCCCTTGTTTTTCCTACTATTGTGACAATAGTTGGTA
AACTAATGTTCAGTAGTGTTAACTCTAATTTACAAAGGACAATCTTGGGTGGAATTGCTTTTGTTGCCATTAAAGGAGCA
TTCAAGGTTTACTTCAAACAGCAGCAATATTTACGTCAGGCACATCGCAAAATCCTAAATTACCCAGAGCAAGAAGAAGC
A

Alignment

ORF - retro_btau_1749 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RSCWVCFATDEDDRTAEWVRPCRCRGSTKWVHQACLQRWVDEKQRGNSTARVACPQCNAEYLIVFPKLGP
          RSCWVCFATDED..TAEWVRPCRCRGSTKWVHQACLQ.WVDEKQRGNSTARVACPQCNAEYLIVFPKLGP
Retrocopy RSCWVCFATDEDNKTAEWVRPCRCRGSTKWVHQACLQCWVDEKQRGNSTARVACPQCNAEYLIVFPKLGP

Parental  VVYVLDLADRLISKACPFAAAGIMVGSIYWTAVTYGAVTVMQVVGHKEGLDVMERADPLFLLIGLPTIPV
          VVY.LDLADRLISKACPFAAAGIMVGSIYWTAVTYG.VTVMQVVGHKEGLDVMER.DPLFLLIGLPTIPV
Retrocopy VVYILDLADRLISKACPFAAAGIMVGSIYWTAVTYGQVTVMQVVGHKEGLDVMERVDPLFLLIGLPTIPV

Parental  MLILGKMIRWEDYVLRLWRKYSNKLQILNSIFPGIGCPVPRIPAEANPLADHVSATRILCGALVFPTIAT
          MLILGKMIRWEDYVLRLWRKYSNK.QILNSIFPGIGCPVPRIPAEANPLADHVSATRILCGALVFPTI.T
Retrocopy MLILGKMIRWEDYVLRLWRKYSNKPQILNSIFPGIGCPVPRIPAEANPLADHVSATRILCGALVFPTIVT

Parental  IVGKLMFSSVNSNLQRTILGGIAFVAIKGAFKVYFKQQQYLRQAHRKILNYPEQEEA
          IVGKLMFSSVNSNLQRTILGGIAFVAIKGAFKVYFKQQQYLRQAHRKILNYPEQEEA
Retrocopy IVGKLMFSSVNSNLQRTILGGIAFVAIKGAFKVYFKQQQYLRQAHRKILNYPEQEEA

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	12.62 RPM
ERP005899_muscle	0.53 RPM	17.95 RPM
SRP017611_brain	0.50 RPM	11.69 RPM
SRP017611_kidney	0.30 RPM	16.30 RPM
SRP017611_liver	0.30 RPM	10.27 RPM
SRP030211_testis	0.44 RPM	15.49 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1749 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1749 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1749 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020981	1 retrocopy	retro_btau_1749 ,
Macropus eugenii	ENSMEUG00000011031	1 retrocopy	retro_meug_1192,
Mus musculus	ENSMUSG00000023307	3 retrocopies	retro_mmus_1559, retro_mmus_3211, retro_mmus_3373,
Sarcophilus harrisii	ENSSHAG00000018432	1 retrocopy	retro_shar_459,
Xiphophorus maculatus	ENSXMAG00000007675	1 retrocopy	retro_xmac_25,