RetrogeneDB ID: retro_mmus_190

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:157567631..157568768(-)
• Located in intron of: ENSMUSG00000046873

Retrocopy information

• Ensembl ID: ENSMUSG00000091736
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Yy1
• Ensembl ID: ENSMUSG00000021264
• Aliases: Yy1, AW488674, NF-E1
• Description: YY1 transcription factor [Source:MGI Symbol;Acc:MGI:99150]

Sequence

>retro_mmus_190
ATGGCCTCTGAGACAGAGAAACTTCTGTGTCTTAACACAGAAAGCGCAGAGATTCCTGCTGATTTTGTGGAGCTGCTGCC
ACCGGATAATATCGGTGATATCGAGGCGGTTTCTCTGGAAACCAGCGTAGGCCAAACCATCGAAGTATATGGAGATGTAG
GTGTCGATTGGGCGCATGGTAGCCAATACCACTCTCCTGTTATTGCTCTGCAGCCGCTTGTGGGCAGCAGCCTGAGTAGT
AGAGATCATGATAAGGAAATGTTTGTCGTTCAGACACGAGAGGAGGAGGTGGTGGGCTACCAAGACTCAGACAACCTACT
ATTCAGTCCTGAATTTGGAAGCCAGATGGTTTTGCCAGTTAATGAAGACGACTATCTCCAGCCGACCACTGCCTCTTTTA
CGGGCTTTCTGGCGGCAGAGAATGGTCAAGGTGAGCTCAGCCCCTATGAAGGGAATCTCTGTGGTTTGACGACCTTTATA
GAGGCCGGTGCAGAAGAAAGCGTGAACGCTGACCTGGGTGACAAACAGTGGGAGCAGAAGCAGATCGATGGTCTTGATGG
CGAATTTCCCTTCACCATGTGGGACGATGTTAATGAAAAAGAAGATCCCATAGCTGAAGAACAGGCTGGTGAGTCACCCC
CCGATTATTCTGAGTATATGACAGGAAAGAAATTTCCTCCTGAAGGAATACCTGGCATTGATCTTTCTGATCCCAAACAA
CTGGCAGAATTTACTAGCATGAGACCCAAAAAGCCAAAAGGAGACTTTCCAAGACCTATAGCATGCTCTCATAAAGGCTG
CGAGAAGATGTTCAAAGATAATTCTGCTATGAGAAAGCACTTGCACATCCATGGGCCGAGAGTGCATGTCTGTGCAGAAT
GTGGCAAAGCTTTTGTTGAGAGTTCCAAGCTGAAACGTCATCAGCTTGTTCACACTGGAGAGAAACCCTACCAGTGTACC
TTTGAAGGCTGTGGGAGACGCTTTTCCCTGGATTTCAATTTGCGCACACATGTGCGAATCCATACTGGAGACAAACCTTT
CGTGTGTCCATTTGATGCCTGCAACAAGAAGTTTGCACAGTCAACAAACCTGAAATCGCATATCTTAACCCATGTTAAGA
ACAAGAATGACCAGTAA

Alignment

ORF - retro_mmus_190 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.0 %
• Parental protein coverage: 60.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASSGGGRVKKGGGKKSGKKSYLGGGAGAAGGGGADPGNKKWEQKQVQIKTLEGEFSVTMWSSDEKKDIDH
          A..G.G......G...G........AGA.....AD.G.K.WEQKQ.....L.GEF..TMW.....K....
Retrocopy AENGQGELSPYEGNLCGLTTFIE--AGAEESVNADLGDKQWEQKQID--GLDGEFPFTMWDDVNEKE---

Parental  ETVVEEQIIGENSPPDYSEYMTGKKLPPGGIPGIDLSDPKQLAEFARMKPRKIKEDDAPRTIACPHKGCT
          ....EEQ..GE.SPPDYSEYMTGKK.PP.GIPGIDLSDPKQLAEF..M.P.K.K..D.PR.IAC.HKGC.
Retrocopy DPIAEEQA-GE-SPPDYSEYMTGKKFPPEGIPGIDLSDPKQLAEFTSMRPKKPK-GDFPRPIACSHKGCE

Parental  KMFRDNSAMRKHLHTHGPRVHVCAECGKAFVESSKLKRHQLVHTGEKPFQCTFEGCGKRFSLDFNLRTHV
          KMF.DNSAMRKHLH.HGPRVHVCAECGKAFVESSKLKRHQLVHTGEKP.QCTFEGCG.RFSLDFNLRTHV
Retrocopy KMFKDNSAMRKHLHIHGPRVHVCAECGKAFVESSKLKRHQLVHTGEKPYQCTFEGCGRRFSLDFNLRTHV

Parental  RIHTGDRPYVCPFDGCNKKFAQSTNLKSHILTHAKAKNNQ
          RIHTGD.P.VCPFD.CNKKFAQSTNLKSHILTH.K.KN.Q
Retrocopy RIHTGDKPFVCPFDACNKKFAQSTNLKSHILTHVKNKNDQ

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
SRP007412_brain	0.75 RPM	26.98 RPM
SRP007412_cerebellum	1.04 RPM	24.97 RPM
SRP007412_heart	1.43 RPM	21.67 RPM
SRP007412_kidney	1.39 RPM	33.13 RPM
SRP007412_liver	0.49 RPM	29.55 RPM
SRP007412_testis	1.10 RPM	30.78 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_190 was not detected

EST

No EST(s) were mapped for retro_mmus_190 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_156010	1007 libraries	23 libraries	26 libraries	13 libraries	3 libraries

The graphical summary, for retro_mmus_190 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_190 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_190 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 27 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 ,
Nomascus leucogenys	ENSNLEG00000000999	3 retrocopies	retro_nleu_1092, retro_nleu_116, retro_nleu_2225,
Oryctolagus cuniculus	ENSOCUG00000026938	1 retrocopy	retro_ocun_1871,
Otolemur garnettii	ENSOGAG00000006955	4 retrocopies	retro_ogar_1231, retro_ogar_1804, retro_ogar_1857, retro_ogar_289,
Pongo abelii	ENSPPYG00000025949	3 retrocopies	retro_pabe_145, retro_pabe_3616, retro_pabe_534,
Pan troglodytes	ENSPTRG00000006717	3 retrocopies	retro_ptro_3093, retro_ptro_45, retro_ptro_494,