RetrogeneDB ID: retro_btau_1101

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 26:21057819..21058836(+)
• Located in intron of: ENSBTAG00000010742

Retrocopy information

• Ensembl ID: ENSBTAG00000027715
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BT.64608
• Ensembl ID: ENSBTAG00000011635
• Aliases: CENPN, CENP-N
• Description: centromere protein N [Source:RefSeq peptide;Acc:NP_001033188]

Sequence

>retro_btau_1101
ATGGATGAAACTCTTGCCGAATTTTTCAGGAGGACCATCTTGAAAATCCCAATGACTGAAATGATGACAATCCTAAAAAC
CTGGAATTTTTTGTCTGAAAATCAACTGCAGACCGTAAACTTTCGGCAGAGAAAGGAATCTATTGTTCAGGACTTGGTTC
TGCTTTGTGAGGAGAACCGTGCGAGTCTCAATGACGCAGCCCATTTAGACATCATTTATACTCAGTTTCATCGGCACCAG
AAAATTTGGGATGTTTTTCAGATGAGTAAAGCACCAGGTGACGACATTGATCTTTTTGATATGGAACAATTCAAAAGTTC
ATTCAAGAAAATTCTTCAGAGAGCATTAAAAAATGTGACAGTCAGCTTCAGAGACGCCGAGGAGAACTCGGTATGGATTC
GAATTGCCTGGGGAACACAGTATAAAAAGCCAAACCAGTACAAACCTGCTTACGTGGTATACTATTCCCAAACTCCATAT
GCCTTCACTTCGTCCTCCCGACTGAAGAGCAATCTACCCCTTCTGGGTCAGGCACTGACAGTTGCTAGCAAACACCATCA
GATTGTGAAAATGGACCTCAGAAGCCGATATCTGGACTCTCTTAAGGCTATTGTTTTTAAACAGTATAATCAGAGCTTTG
AAACTCACAACTGTACTACATCTCTACAAGAAGGAAGCCTTGGGCTAGATATAAATATGGATTCAAGGATCATTCATGAA
AACAAAGTTGAAAAAGAAAGAGTGCAGAGAGTGACTCAAGAAATTTTTGGAGACTATCCTCAACCAAGACTAGAATTTGC
ACAATATAAGCTTGAAACGAAATTCAAAAGTGACTTAAACGGGGGCATCCTGGCTGAGAGAGAAGAGCCCCTCCGGTGCC
TGGTAAAGTTCTCTAGCCCGCATCTTCTGGAAGCGCTGAAATCCCTGGCCCCAGCCGGTATTGCAGATGCACCACTTTCT
CCACTGCTCACTTGCATACCCAATAAGGGAAAGAATTATTTTAAAATTAGAGATAAA

Alignment

ORF - retro_btau_1101 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.71 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDETLAEFFRRTILKIPMTEMMTILKTWNFLSENQLQTVNFRQRKESIVQDLVLLCEENHASLNDAAHLD
          MDETLAEFFRRTILKIPMTEMMTILKTWNFLSENQLQTVNFRQRKESIVQDLVLLCEEN.ASLNDAAHLD
Retrocopy MDETLAEFFRRTILKIPMTEMMTILKTWNFLSENQLQTVNFRQRKESIVQDLVLLCEENRASLNDAAHLD

Parental  IIYTQFHRHQKIWDVFQMSKAPGDDIDLFDMEQFKSSFKKILQRALKNVTVSFRDAEENSVWIRIAWGTQ
          IIYTQFHRHQKIWDVFQMSKAPGDDIDLFDMEQFKSSFKKILQRALKNVTVSFRDAEENSVWIRIAWGTQ
Retrocopy IIYTQFHRHQKIWDVFQMSKAPGDDIDLFDMEQFKSSFKKILQRALKNVTVSFRDAEENSVWIRIAWGTQ

Parental  YKKPNQYKPAYVVYYSQTPYAFTSSSRLKSNLPLLGQALTVASKHHQIVKMDLRSRYLDSLKAIVFKQYN
          YKKPNQYKPAYVVYYSQTPYAFTSSSRLKSNLPLLGQALTVASKHHQIVKMDLRSRYLDSLKAIVFKQYN
Retrocopy YKKPNQYKPAYVVYYSQTPYAFTSSSRLKSNLPLLGQALTVASKHHQIVKMDLRSRYLDSLKAIVFKQYN

Parental  QSFETHNCTTSLQEGSLGLDINMDSRIIHENKVEKERVQRVTQEIFGDYPQPRLEFAQYKLETKFKSDLN
          QSFETHNCTTSLQEGSLGLDINMDSRIIHENKVEKERVQRVTQEIFGDYPQPRLEFAQYKLETKFKSDLN
Retrocopy QSFETHNCTTSLQEGSLGLDINMDSRIIHENKVEKERVQRVTQEIFGDYPQPRLEFAQYKLETKFKSDLN

Parental  GGILAEREEPLRCLVKFSSPHLLEALKSLAPAGIADAPLSPLLTCIPNKGKNYFKIRDK
          GGILAEREEPLRCLVKFSSPHLLEALKSLAPAGIADAPLSPLLTCIPNKGKNYFKIRDK
Retrocopy GGILAEREEPLRCLVKFSSPHLLEALKSLAPAGIADAPLSPLLTCIPNKGKNYFKIRDK

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	0.43 RPM
ERP005899_muscle	0.00 RPM	2.01 RPM
SRP017611_brain	0.00 RPM	0.37 RPM
SRP017611_kidney	0.00 RPM	0.71 RPM
SRP017611_liver	0.00 RPM	0.30 RPM
SRP030211_testis	0.37 RPM	21.58 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1101 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1101 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1101 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011635	1 retrocopy	retro_btau_1101 ,
Felis catus	ENSFCAG00000004978	1 retrocopy	retro_fcat_1852,
Homo sapiens	ENSG00000166451	2 retrocopies	retro_hsap_2146, retro_hsap_2291,
Oryctolagus cuniculus	ENSOCUG00000000024	3 retrocopies	retro_ocun_1676, retro_ocun_1806, retro_ocun_528,
Sarcophilus harrisii	ENSSHAG00000002111	1 retrocopy	retro_shar_331,
Ictidomys tridecemlineatus	ENSSTOG00000007345	1 retrocopy	retro_itri_1431,
Tupaia belangeri	ENSTBEG00000000039	2 retrocopies	retro_tbel_2049, retro_tbel_3055,