RetrogeneDB ID: retro_btau_1617

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 8:68323699..68325536(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000012266
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SP2
• Ensembl ID: ENSBTAG00000013740
• Aliases: None
• Description: Transcription factor Sp2 [Source:UniProtKB/Swiss-Prot;Acc:Q5E9U0]

Sequence

>retro_btau_1617
ATGAGCGATCCACAGACCAGCATGGCTGCCACTGCCGCTGTCAGTCCCAGTGACTACCTGCAGCCTGCCGCCTCTACCAC
CCAGGACTCCCAGCCATCTCCCTTAGCGCTGCTTGCCGCGACATGTAGCAAAATCGGCCCTCCAGCTGTTGAAGCTGCGG
TGACGCCTCCTGCTCCCCCCCAGCCCACTCCACGGAAACTCGTCCCTATCAAACCCGCCCCTCTCCCTCTCAGCCCCAGC
AAGAATAGTTTTGGAATCTTGTCCTCCAAGGGAAACATACTTCAGATTCAGGGGTCACAGCTGAGCACGTCCTACCCTGG
GGGGCAGCTGGTGTTTGCCATCCAGAATCCCACCGTGGTCAACAAAGGGACCCGATCGAACACCAGTATCCAGTACCAGG
CGGTCCCTCAGATCCAGGCCAGCAGTCCTCAGACCATCCAGGTGCAGCCCAGTCTGACCAACCAGATCCAGATCATCCCT
GGCACCAACCAAGCCATCATCACCCCGTCCCCGTCCAGTCACAAGCCCGTCCCCATCAAGCCAGCCCCTGTCCAGAAGTC
AAGTACGACCACCACTCCGGCACAGAGCGGGGCCAATGTGGTGAAGCTGACAGGTGGCGGTGGCAATGTGACCCTTACTC
TGCCTGTCAACAACCTCGTGAACACCAGCGACCCCGGGGCCGCCACTCAGCTCCTCACGGAGAGCCCCCCTGCCCCACTG
TCTAAGACTAACAAGAAAGCCAGGAAGAAGAGTCTTCCTGCTGCCCAGCCCCCTGTGGCTGTGGCCGAGCAGGTGGAGAC
GGTGCTGATCGAGACCACTGCAGACAACATTATCCAAGCAGGAAACAACCTGCTCATTGTTCAGAGCCCCGGCGGGGGCC
AGCCAGCCGTGGTCCAGCAGGTCCAGGTGGTGCCCCCCAAGGCCGAGCAGCAGCAGGTGGTGCAGATTCCACAGCAGGCC
CTGCGGGTGGTACAGGCAGCGTCCGCCACACTCCCCACCGTCCCCCAGAAGCCCTCCCAGAACTTCCAGATCCAGGCTGC
TGAGCCGTCACCTACTCAGGTCTACATCCGTACGCCTTCTGGTGAGGTACAGACGGTCCTTGTCCAGGACAGCCCCCCAG
CAACAGCTGCGACTGCCTCCACCACCACTTGTAGCAGCCCCGCGTCCCGTGCTGCCCATCTGAGTGGGACCAGCAAAAAG
CACTCGGCTGCAATTCTCCGAAAAGAACGACCCCTGCCAAAGATCGCTCCTGCTGGGAGCATCATCAGCCTGAACGCAGC
ACAGCTGGCAGCGGCGGCCCAGGCCATGCAGACCATCAACATCAACGGTGTCCAGGTCCAGGGCGTGCCCGTCACCATCA
CCAACACTGGCGGACAGCAGCAGCTGACTGCAGAATGTATCTGGAAACAACCTGACCATCAGTGGGCTGAGCCCCACCCA
GATCCAGCTGCAGATGGAACAGGCCCTGGCTGGAGAGACCCAGCCTGGGGAAAAGCGGCGCCGCATGGCCTGCACGTGTC
CCAACTGCAAGGACGGGGACAAGAGGTCTGGAGAGCAGGGCAAGAAGAAGCACGTGTGCCACATCCCCGACTGCGGCAAG
ACCTTCCGTAAGACATCCCTGCTGCGGGCTCACGTGCGCCTGCACACCGGCGAGCGGCCCTTTGTCTGCAACTGGTTCTT
CTGTGGCAAGAGGTTCACACGGAGCGACAAGCTCCAGCGGCATGCCCGCACCCACACAGGGGACAAACGCTTCGAGTGTG
CCCAGTGTCAGAAGCGCTTCATGAGGAGTGACCACCTCACCAAGCATTACAAGACCCACCTGGTCACGAAGAACTTG

Alignment

ORF - retro_btau_1617 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.86 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSDPQTSMAATAAVSPSDYLQPAASTTQDSQPSPLALLAATCSKIGPPAVEAAVTPPAPPQPTPRKLVPI
          MSDPQTSMAATAAVSPSDYLQPAASTTQDSQPSPLALLAATCSKIGPPAVEAAVTPPAPPQPTPRKLVPI
Retrocopy MSDPQTSMAATAAVSPSDYLQPAASTTQDSQPSPLALLAATCSKIGPPAVEAAVTPPAPPQPTPRKLVPI

Parental  KPAPLPLSPSKNSFGILSSKGNILQIQGSQLSTSYPGGQLVFAIQNPTVVNKGTRSNTSIQYQAVPQIQA
          KPAPLPLSPSKNSFGILSSKGNILQIQGSQLSTSYPGGQLVFAIQNPTVVNKGTRSNTSIQYQAVPQIQA
Retrocopy KPAPLPLSPSKNSFGILSSKGNILQIQGSQLSTSYPGGQLVFAIQNPTVVNKGTRSNTSIQYQAVPQIQA

Parental  SSPQTIQVQPSLTNQIQIIPGTNQAIITPSPSSHKPVPIKPAPVQKSSTTTTPAQSGANVVKLTGGGGNV
          SSPQTIQVQPSLTNQIQIIPGTNQAIITPSPSSHKPVPIKPAPVQKSSTTTTPAQSGANVVKLTGGGGNV
Retrocopy SSPQTIQVQPSLTNQIQIIPGTNQAIITPSPSSHKPVPIKPAPVQKSSTTTTPAQSGANVVKLTGGGGNV

Parental  TLTLPVNNLVNTSDPGAATQLLTESPPAPLSKTNKKARKKSLPAAQPPVAVAEQVETVLIETTADNIIQA
          TLTLPVNNLVNTSDPGAATQLLTESPPAPLSKTNKKARKKSLPAAQPPVAVAEQVETVLIETTADNIIQA
Retrocopy TLTLPVNNLVNTSDPGAATQLLTESPPAPLSKTNKKARKKSLPAAQPPVAVAEQVETVLIETTADNIIQA

Parental  GNNLLIVQSPGGGQPAVVQQVQVVPPKAEQQQVVQIPQQALRVVQAASATLPTVPQKPSQNFQIQAAEPS
          GNNLLIVQSPGGGQPAVVQQVQVVPPKAEQQQVVQIPQQALRVVQAASATLPTVPQKPSQNFQIQAAEPS
Retrocopy GNNLLIVQSPGGGQPAVVQQVQVVPPKAEQQQVVQIPQQALRVVQAASATLPTVPQKPSQNFQIQAAEPS

Parental  PTQVYIRTPSGEVQTVLVQDSPPATAATASTTTCSSPASRAAHLSGTSKKHSAAILRKERPLPKIAPAGS
          PTQVYIRTPSGEVQTVLVQDSPPATAATASTTTCSSPASRAAHLSGTSKKHSAAILRKERPLPKIAPAGS
Retrocopy PTQVYIRTPSGEVQTVLVQDSPPATAATASTTTCSSPASRAAHLSGTSKKHSAAILRKERPLPKIAPAGS

Parental  IISLNAAQLAAAAQAMQTININGVQVQGVPVTITNTGGQQQLT-VQNVSGNNLTISGLSPTQIQLQMEQA
          IISLNAAQLAAAAQAMQTININGVQVQGVPVTITNT.G.QQ....QNVSGNNLTISGLSPTQIQLQMEQA
Retrocopy IISLNAAQLAAAAQAMQTININGVQVQGVPVTITNT-GGQQQL>LQNVSGNNLTISGLSPTQIQLQMEQA

Parental  LAGETQPGEKRRRMACTCPNCKDGDKRSGEQGKKKHVCHIPDCGKTFRKTSLLRAHVRLHTGERPFVCNW
          LAGETQPGEKRRRMACTCPNCKDGDKRSGEQGKKKHVCHIPDCGKTFRKTSLLRAHVRLHTGERPFVCNW
Retrocopy LAGETQPGEKRRRMACTCPNCKDGDKRSGEQGKKKHVCHIPDCGKTFRKTSLLRAHVRLHTGERPFVCNW

Parental  FFCGKRFTRSDELQRHARTHTGDKRFECAQCQKRFMRSDHLTKHYKTHLVTKNL
          FFCGKRFTRSD.LQRHARTHTGDKRFECAQCQKRFMRSDHLTKHYKTHLVTKNL
Retrocopy FFCGKRFTRSDKLQRHARTHTGDKRFECAQCQKRFMRSDHLTKHYKTHLVTKNL

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	2.52 RPM
ERP005899_muscle	0.05 RPM	6.02 RPM
SRP017611_brain	0.27 RPM	5.62 RPM
SRP017611_kidney	0.06 RPM	6.34 RPM
SRP017611_liver	0.15 RPM	2.49 RPM
SRP030211_testis	1.52 RPM	30.98 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_btau_1617 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
DY157173	68324550	68324895	99.8	344	0	342

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1617 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1617 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013740	1 retrocopy	retro_btau_1617 ,
Bos taurus	ENSBTAG00000017488	1 retrocopy	retro_btau_271,
Bos taurus	ENSBTAG00000020355	1 retrocopy	retro_btau_521,
Bos taurus	ENSBTAG00000038055	1 retrocopy	retro_btau_1360,
Ictidomys tridecemlineatus	ENSSTOG00000015926	1 retrocopy	retro_itri_569,