RetrogeneDB ID: retro_mmus_185

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:67534752..67535706(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000051397
• Aliases: Tacstd2, C80403, EGP-1, GA733-1, Ly97, TROP2
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Epcam
• Ensembl ID: ENSMUSG00000045394
• Aliases: Epcam, CD326, EGP, EGP-2, Egp314, Ep-CAM, EpCAM1, GA733-2, Ly74, TROP1, Tacsd1, Tacstd1, gp40
• Description: epithelial cell adhesion molecule [Source:MGI Symbol;Acc:MGI:106653]

Sequence

>retro_mmus_185
ATGGCGAGGGGCTTGGATCTAGCACCGCTGCTACTGCTACTGCTGGCGATGGCGACCCGCTTTTGCACGGCTCAGAGCAA
CTGTACATGCCCCACCAACAAGATGACGGTCTGCGACACAAATGGCCCAGGCGGGGTCTGCCAATGTCGGGCAATGGGCT
CACAGGTATTGGTCGACTGCTCCACGCTAACTTCCAAGTGCCTGCTGCTCAAGGCGCGCATGAGCGCCCGGAAGAGCGGC
CGCAGCCTGGTGATGCCGAGCGAGCACGCGATACTGGACAACGATGGCCTCTACGACCCGGAGTGTGACGACAAGGGCCG
CTTCAAGGCGCGCCAGTGCAACCAGACCTCGGTGTGCTGGTGCGTAAACTCGGTGGGCGTGCGCCGCACGGACAAGGGAG
ACCAAAGCCTGCGCTGCGACGAAGTGGTGCGAACCCACCACATCCTCATTGAGTTGCGCCACCGCCCGACCGACCGAGCC
TTCAACCACTCTGACCTAGACTCCGAGCTGCGGCGGCTCTTCCAAGAACGCTACAAGCTGCACCCCAGCTTCCTATCCGC
GGTACACTATGAGGAGCCCACCATTCAGATAGAGCTTCGGCAGAACGCGTCGCAGAAGGGCTTGAGAGACGTGGACATCG
CTGATGCCGCCTACTACTTCGAAAGGGACATTAAAGGCGAGTCACTGTTCATGGGCCGCCGCGGCCTGGACGTGCAGGTG
CGTGGGGAACCCCTGCATGTGGAGCGGACGCTCATCTACTACCTGGACGAGAAGCCCCCCCAGTTCTCCATGAAGCGCCT
CACCGCCGGCGTCATTGCCGTCATCGCTGTCGTCTCGGTAGCGGTAGTGGCTGGTGTGGTGGTCTTGGTGGTCACCAAAC
GGAGGAAGTCGGGCAAATACAAAAAGGTGGAGCTTAAGGAGCTGGGGGAGATGAGAAGCGAACCTAGCTTGTAG

Alignment

ORF - retro_mmus_185 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.8 %
• Parental protein coverage: 95.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLLAVVTATLAAAQRDCVCDNYKLATSCSLNEYGECQCTSYGTQNTVICSKLASKCLAMKAEMTHSKSGR
          LLL.........AQ..C.C...K..........G.CQC...G.Q..V.CS.L.SKCL..KA.M...KSGR
Retrocopy LLLLAMATRFCTAQSNCTCPTNKMTVCDTNGPGGVCQCRAMGSQVLVDCSTLTSKCLLLKARMSARKSGR

Parental  RI--KPEGAIQNNDGLYDPDCDEQGLFKAKQCNGTATCWCVNTAGVRRTDK-DTEITCSERVRTYWIIIE
          ......E.AI..NDGLYDP.CD..G.FKA.QCN.T..CWCVN..GVRRTDK.D....C.E.VRT..I.IE
Retrocopy SLVMPSEHAILDNDGLYDPECDDKGRFKARQCNQTSVCWCVNSVGVRRTDKGDQSLRCDEVVRTHHILIE

Parental  LKHKERESPYDHQSLQTALQEAFTSRYKLNQKFIKNIMYENNVITIDLMQNSSQKTQDDVDIADVAYYFE
          L.H........H..L...L...F..RYKL...F.....YE...I.I.L.QN.SQK...DVDIAD.AYYFE
Retrocopy LRHRPTDRAFNHSDLDSELRRLFQERYKLHPSFLSAVHYEEPTIQIELRQNASQKGLRDVDIADAAYYFE

Parental  KDVKGESLFHSSKSMDLRVNGEPLDLDPGQTLIYYVDEKAPEFSMQGLTAGIIAVIVVVSLAVIAGIVVL
          .D.KGESLF......D..V.GEPL......TLIYY.DEK.P.FSM..LTAG.IAVI.VVS.AV.AG.VVL
Retrocopy RDIKGESLFMGRRGLDVQVRGEPLHVE--RTLIYYLDEKPPQFSMKRLTAGVIAVIAVVSVAVVAGVVVL

Parental  VISTRKKSAKYEKAEIKEMGEIHRE
          V...R.KS.KY.K.E.KE.GE...E
Retrocopy VVTKRRKSGKYKKVELKELGEMRSE

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	0.07 RPM	0.14 RPM
SRP007412_cerebellum	0.00 RPM	0.09 RPM
SRP007412_heart	0.03 RPM	0.09 RPM
SRP007412_kidney	17.56 RPM	70.53 RPM
SRP007412_liver	0.03 RPM	1.69 RPM
SRP007412_testis	0.00 RPM	24.20 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_185 was not detected

EST

No EST(s) were mapped for retro_mmus_185 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_124077	954 libraries	63 libraries	39 libraries	16 libraries	0 libraries
TSS #2	TSS_124078	729 libraries	98 libraries	63 libraries	46 libraries	136 libraries
TSS #3	TSS_124079	848 libraries	121 libraries	50 libraries	49 libraries	4 libraries

The graphical summary, for retro_mmus_185 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_185 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_185 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_252

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006474	1 retrocopy	retro_btau_66,
Choloepus hoffmanni	ENSCHOG00000013834	1 retrocopy	retro_chof_258,
Callithrix jacchus	ENSCJAG00000000624	1 retrocopy	retro_cjac_3006,
Dasypus novemcinctus	ENSDNOG00000011799	1 retrocopy	retro_dnov_345,
Erinaceus europaeus	ENSEEUG00000009462	1 retrocopy	retro_eeur_151,
Macropus eugenii	ENSMEUG00000015074	2 retrocopies	retro_meug_1984, retro_meug_474,
Microcebus murinus	ENSMICG00000000151	1 retrocopy	retro_mmur_739,
Macaca mulatta	ENSMMUG00000012390	1 retrocopy	retro_mmul_34,
Monodelphis domestica	ENSMODG00000001077	1 retrocopy	retro_mdom_104,
Mus musculus	ENSMUSG00000045394	1 retrocopy	retro_mmus_185 ,
Ochotona princeps	ENSOPRG00000004301	1 retrocopy	retro_opri_1225,
Pelodiscus sinensis	ENSPSIG00000015680	1 retrocopy	retro_psin_22,
Pan troglodytes	ENSPTRG00000011902	1 retrocopy	retro_ptro_92,
Rattus norvegicus	ENSRNOG00000015667	1 retrocopy	retro_rnor_252,
Sus scrofa	ENSSSCG00000008429	1 retrocopy	retro_sscr_69,
Ictidomys tridecemlineatus	ENSSTOG00000008631	1 retrocopy	retro_itri_106,
Tursiops truncatus	ENSTTRG00000004235	2 retrocopies	retro_ttru_21, retro_ttru_394,