RetrogeneDB ID: retro_btau_91

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 27:16630108..16630996(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000044139
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: YY1
• Ensembl ID: ENSBTAG00000020819
• Aliases: None
• Description: transcriptional repressor protein YY1 [Source:RefSeq peptide;Acc:NP_001091550]

Sequence

>retro_btau_91
ATGGACCAGCAACTGAAGAAAAGGGGAACGACACCTAGCCAGAAAGGCCTGGGGAGAAGAGCTACCAGCACAGACAAGTC
ACTGCCAGCCCAGCAGGAACCTCCTGACACAACGTGCATCTTATATGATGAGGATGTGTGCTATGAGGCTAGCTTCCGGG
TTGTCAAAGATGATACCTTCTCTGACTGTTACATAGAATGCATAATAAGAGGTGAGTTTTCTGAACCTATTGTGGAAGAG
GACCCACTCCTTCAGTCCTTTGAACGTCTGAAAGAAGGATCAGAACAAGACCTTTCTCAACAGGTTCTTGCGGCAAGCTC
ACTTCTTGAATCTTCCTTGGAATACATGAAAAGGGACGCAAAACAAGAATTTCCTCAACAGGTGGTTGGAGAGAATCCAC
TTCTTGAGTTTTCTGAGTACAAGACAAGCAAGAAGCTTCCTCCCGGAGGAATACCCAACATGGACTTTCCAGAATCTAAA
CAGCTCACAGGATGCACTAGGAGGCCAAGTACAAATAAAGAATATGGTGCTCCTGAAAGACATGCCTGTCCTCACAACGG
ATGCACAAGAGAGTTCCAGAATAAAAGATCCCTGAGGAAGCATCTTCGAGTTCATAATCCCCGAGATCATGTGTGTGCAG
AATGTGGGAAAGCCTTCAAGGAGAGTGCAAAGCTAAAAAGACATTTTCTGGTTCATACTGGAGAGAAGCCATTTCCGTGC
ACTTTCCAAGGGTGCGGAAAACGCTTTTCCCTGTCCTTCAACTTGCGCACACACGTGCGCACCCACACTGGGGAGAAGCC
TTTTGTGTGTCCTTTTGTAGGCTGCCGCAAGAAGTTTATTCAGTCAAACAACATGAAAGCCCACCTCCTGACTCATGGAA
AGGCCAAT

Alignment

ORF - retro_btau_91 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.29 %
• Parental protein coverage: 54.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SSDEKKDIDHETVVEEQIIGENSPPDYSEYMTGKKLPPGGIPGIDLSDPKQLAEFARMKPRKIKEDDAPR
          SS.E....D.......Q..GEN.....SEY.T.KKLPPGGIP..D....KQL....R..P...KE..AP.
Retrocopy SSLEYMKRDAKQEFPQQVVGENPLLEFSEYKTSKKLPPGGIPNMDFPESKQLTGCTR-RPSTNKEYGAPE

Parental  TIACPHKGCTKMFRDNSAMRKHLHTHGPRVHVCAECGKAFVESSKLKRHQLVHTGEKPFQCTFEGCGKRF
          ..ACPH.GCT..F......RKHL..H.PR.HVCAECGKAF.ES.KLKRH.LVHTGEKPF.CTF.GCGKRF
Retrocopy RHACPHNGCTREFQNKRSLRKHLRVHNPRDHVCAECGKAFKESAKLKRHFLVHTGEKPFPCTFQGCGKRF

Parental  SLDFNLRTHVRIHTGDRPYVCPFDGCNKKFAQSTNLKSHILTHAKA
          SL.FNLRTHVR.HTG..P.VCPF.GC.KKF.QS.N.K.H.LTH.KA
Retrocopy SLSFNLRTHVRTHTGEKPFVCPFVGCRKKFIQSNNMKAHLLTHGKA

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	24.87 RPM
ERP005899_muscle	0.32 RPM	30.41 RPM
SRP017611_brain	0.00 RPM	28.23 RPM
SRP017611_kidney	0.00 RPM	31.24 RPM
SRP017611_liver	0.00 RPM	17.67 RPM
SRP030211_testis	0.07 RPM	52.57 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

2 EST(s) were mapped to retro_btau_91 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
GO351493	16630122	16630526	99.6	402	2	400
GO353286	16630100	16630526	99.1	422	4	418

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_91 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_91 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011146	1 retrocopy	retro_amel_2,
Bos taurus	ENSBTAG00000020819	1 retrocopy	retro_btau_91 ,
Callithrix jacchus	ENSCJAG00000016853	2 retrocopies	retro_cjac_1931, retro_cjac_4045,
Cavia porcellus	ENSCPOG00000020809	2 retrocopies	retro_cpor_1220, retro_cpor_1522,
Equus caballus	ENSECAG00000005805	1 retrocopy	retro_ecab_97,
Homo sapiens	ENSG00000100811	2 retrocopies	retro_hsap_106, retro_hsap_97,
Gorilla gorilla	ENSGGOG00000026332	2 retrocopies	retro_ggor_190, retro_ggor_2,
Mustela putorius furo	ENSMPUG00000002931	1 retrocopy	retro_mputfur_867,
Mus musculus	ENSMUSG00000021264	1 retrocopy	retro_mmus_190,
Oryctolagus cuniculus	ENSOCUG00000026938	1 retrocopy	retro_ocun_1871,