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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggacagtcatggaatcattgtggggtggcagagtgtgtgagattggcaggggttggaatgatggcaattttagtatcttttgcttgttcttttgctccagGTGAGGAAGGAGAAGCTAGGGGATCGAATAACTGCTCTCCACCAGCTTGTCTCCCCGTTTGGAAAG

Basic information

species Zea mays
transcript GRMZM2G105494_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G105494_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g17680.1 (Oryza sativa), 3'ss of exon 3
ggacagtcatggaatcattgtggggtggcagagtgtgtgagattgg--caggggttggaatgatggcaatttta----gtatcttttgcttgttcttttgctccagGTGAGGAAGGAGAAGCTAGGGGATCGAATAACTGCTCTCCACCAGCTTGTCTCCCCGTTTGGAAAG
       |||||||||||||| || |   |||    ||||||| ||    | | | | |||||||||  | |||    |||| |||||||||| ||||| || ||||||||||||||||||||||| ||| |||||||||| || ||||||||||||||||| ||||| |||
------gcatggaatcattgtaggttaagagataaggtgagatggggttggagatggaaatgatggcgttcttaattagtatgttttgcttgtgctttttcttcagGTGAGGAAGGAGAAGCTAGGTGATAGAATAACTGCCCTTCACCAGCTTGTCTCCCCATTTGGGAAG

upper sequence: GRMZM2G105494_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA15G02020.1 (Glycine max), 3'ss of exon 3
ggacagtcatggaatcattgtggggtggcagagtgtgtgagattggcaggggttggaatgatggcaattttagtatcttttgcttgttcttttgctccagGTGAGGAAGGAGAAGCTAGGGGATCGAATAACTGCTCTCCACCAGCTTGTCTCCCCGTTTGGAAAG
   |  ||        | |    | ||| |||| |      ||    |        | | |||  | |  |  | ||  |   |   | || ||   |||||| |||||||||||||||| ||| |||||||  | || ||||| || || |||||||||||||||
attctttctgctggcaaatacttgttggaagagagaaaagcatatatatacaagaaattcatgtaattaatgatttccatgtatgaatattgtgaatcagGTGCGGAAGGAGAAGCTAGGTGATAGAATAACAACCCTTCACCAACTAGTTTCCCCGTTTGGAAAG

upper sequence: GRMZM2G105494_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G21770.2 (Glycine max), 3'ss of exon 3
-ggacagtcatgga--atcattgtggggtggcagagtgtgtgagattggcaggggttggaatgatggcaattttagtatcttttgcttgttcttttgctc-cagGTGAGGAAGGAGAAGCTAGGGGATCGAATAACTGCTCTCCACCAGCTTGTCTCCCCGTTTGGAAAG
 ||  |   ||| |  ||  |||   |   | | |     |||      || |   |    |    ||    |||  || || ||     |||| |  || |||||||| |||||||||||||| ||| ||||||| ||||| |||||||| || ||||| || ||||||
aggtaaaatatgcatgatagttgaaagtgagaaaaacacatgatgaattcatgtactaactt---agcttccttaa-atattatgaaatctcttgtaatcacagGTGAGAAAGGAGAAGCTAGGTGATAGAATAACAGCTCTTCACCAGCTAGTTTCCCCATTCGGAAAG

upper sequence: GRMZM2G105494_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv09s0002g04120.t01 (Vitis vinifera), 3'ss of exon 3
ggacagtcatggaatcattgtggggtggc--agagtgtgtgagattggcaggggttggaatgatggcaattttagtatcttttgcttgttct--tttgctccagGTGAGGAAGGAGAAGCTAGGGGATCGAATAACTGCTCTCCACCAGCTTGTCTCCCCGTTTGGAAAG
  ||||| | | ||  |  | |   |     |||       | | | | |     |  ||   |     ||||  ||| | ||  ||  | |  | ||  ||||||||| ||||||||||| || ||| ||||||| || || |||||| | || ||||| |||||||||
aaacagtaaagaaaaaagagagaaattctctagaaaacagaaaactagtaa----tttaacattctttctttttatatatattaattaatttactctgaaccagGTGAGAAAGGAGAAGCTGGGTGATAGAATAACAGCCCTTCACCAGTTAGTTTCCCCATTTGGAAAG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|78084337|gb|DV512730.1|DV512730
EST:     TCAAGAAGGCTAGGACCCAAGAACCCTCCCCGGCTCAATCTACTGTGAAG                         GTGAGGAAGGAGAAGCTAGGGGATCGAATAACTGCTCTCCACCAGCTTGTC
genomic: TCAAGAAGGCTAGGACCCAAGAACCCTCCCCGGCTCAATCTACTGTGAAGgtcatccctc ... tttgctccagGTGAGGAAGGAGAAGCTAGGGGATCGAATAACTGCTCTCCACCAGCTTGTC
EST: gi|78112567|gb|DV530961.1|DV530961
EST:     TCAAGAAGGCTAGGACCCAAGACCCCTCCCCGGCTCAATCTACTGTGAAG                         GTGAGGAAGGA-AAGCTAGGGGATCGAATAACTGCTCTCCACCAGCTTGTC
genomic: TCAAGAAGGCTAGGACCCAAGAACCCTCCCCGGCTCAATCTACTGTGAAGgtcatccctc ... tttgctccagGTGAGGAAGGAGAAGCTAGGGGATCGAATAACTGCTCTCCACCAGCTTGTC
EST: gi|76929547|gb|DV172057.1|DV172057
EST:     TCAAGAAGGCTAGGACCCAAGAACCCTCCCCGGCTCAATCTACTGTGAAG                         GTGAGGAAGGAGAAGCTAGGGGATCGAATAACTGCTCTCCACCAGCTTGTC
genomic: TCAAGAAGGCTAGGACCCAAGAACCCTCCCCGGCTCAATCTACTGTGAAGgtcatccctc ... tttgctccagGTGAGGAAGGAGAAGCTAGGGGATCGAATAACTGCTCTCCACCAGCTTGTC
EST: gi|71435603|gb|DR816653.1|DR816653
EST:     TCAAGAAGGCTAGGACCCAAGAACCCTCCCCGGCTCAATCTACTGTGAAG                         GTGAGGAAGGAGAAGCTAGGGGATCGAATAACTGCTCTCCACCAGCTTGTC
genomic: TCAAGAAGGCTAGGACCCAAGAACCCTCCCCGGCTCAATCTACTGTGAAGgtcatccctc ... tttgctccagGTGAGGAAGGAGAAGCTAGGGGATCGAATAACTGCTCTCCACCAGCTTGTC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 45 (upstream exon), 44 (downstream exon)
Score: 64

TGCATCAGTACAGTATCTGGATCAGCTTTCAAGAAGGCTAGGACCCAAGAACCCTCCCCGGCTCAATCTACTGTGAAGgtcatccctc ... tttgctccagGTGAGGAAGGAGAAGCTAGGGGATCGAATAACTGCTCTCCACCAGCTTGTCTCCCCGTTTGGAAAG


Block sizes: 45 (upstream exon), 42 (downstream exon)
Score: 37

TGCATCAGTACAGTATCTGGATCAGCTTTCAAGAAGGCTAGGACCCAAGAACCCTCCCCGGCTCAATCTACTGTGAAGgtcatccctc ... tttgctccagGTGAGGAAGGAGAAGCTAGGGGATCGAATAACTGCTCTCCACCAGCTTGTCTCCCCGTTTGGAAAG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 49

TGCATCAGTACAGTATCTGGATCAGCTTTCAAGAAGGCTAGGACCCAAGAACCCTCCCCGGCTCAATCTACTGTGAAGgtcatccctc ... tttgctccagGTGAGGAAGGAGAAGCTAGGGGATCGAATAACTGCTCTCCACCAGCTTGTCTCCCCGTTTGGAAAG


Block sizes: 47 (upstream exon), 36 (downstream exon)
Score: 30

TGCATCAGTACAGTATCTGGATCAGCTTTCAAGAAGGCTAGGACCCAAGAACCCTCCCCGGCTCAATCTACTGTGAAGgtcatccctc ... tttgctccagGTGAGGAAGGAGAAGCTAGGGGATCGAATAACTGCTCTCCACCAGCTTGTCTCCCCGTTTGGAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaggggttggaatgatggcaattttagtatcttttgcttgttcttttgctccagGTGAGGAAGGAGAAGCTAGGGGATCGAATAACTGCTCTCCACCAGCTTGTCTCCCCGTTTGGAAAG
                              tcttttgcttgttctt  CT-rich tract
                    aattttagtatctttt  TA-rich tract