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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCGAGAGATGGCGAAGACGGCCGCGTGGAGCGTCAGTTCCTGCAAGGCCGGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggatcacctttttttttctttgtcgaattagttgaagctagaaggtcagagttggtgattcgggtcctgcgatttggtttcag

Basic information

species Zea mays
transcript GRMZM2G054247_T04
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G054247_T03 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os05g50360.1 (Oryza sativa), 5'ss of exon 1
TGCGAGAGATGGCGAAGACGGCCGCGTGGAGCGTCAGTTCCTGCAAGGCCGGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggatcacctt-----------tttttttctttgtcgaattagttgaagctagaaggtcagagttggtgattcgggtcctgcgatttggtttcag------
|||| |||||||||||||||||||| ||||||||||| ||||||||| ||||||||||||||||  |||| |||||||||||||||||||||||||||||||||||  | | |  |           ||| ||| |   ||   ||  |   ||  || || |      || ||||| ||||  ||  ||||  |||  |      
TGCGGGAGATGGCGAAGACGGCCGCCTGGAGCGTCAGCTCCTGCAAGCCCGGCAACGGCGTCGCCTCCCTCCGCGACGACAACCTCGACACCTACTGGCAgtcagtaaaacccgctccaaatctccatttgtttttccttcttctttttccgagggaggagattgttaatg-tgatttgggttttgacattttttttttgggttag

upper sequence: GRMZM2G054247_T03 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA02G06190.3 (Glycine max), 5'ss of exon 2
TGCGAGAGATGGCGAAGACGGCCGCGTGGAGCGTCAGTTCCTGCAAGGCCGGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggatcaccttttttt-ttctttgtcgaattagttgaagctagaa--ggtcagagttggtgattcgggtcctgcgatttggtttcag--------
|    || ||||  ||||  ||||| ||||||||||||||||||||  |||| ||||||||  |  | || || |||||||| ||||| ||||| ||||||| | |   || |    | ||  |   |||     |  | |  | |||||  | |        |  |||| ||     |  |||  | | |         
TAACGGAAATGGGAAAGAAAGCCGCTTGGAGCGTCAGTTCCTGCAAACCCGGTAACGGCGTTTCCTCTCTCCGTGACGACAATCTCGAAACCTATTGGCAgtaactccctccctcactcttactgcgtgtttggatgatggctgatagaattgattttgaagtgaaattcaggataaactttttcatctaatgctgaaac
















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|12045796|gb|BF727935.1|BF727935
EST:     GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCA                         GTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
genomic: GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggat ... ttggtttcagGTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
EST: gi|91873254|gb|EB403211.1|EB403211
EST:     GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCA                         GTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
genomic: GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggat ... ttggtttcagGTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
EST: gi|89252141|gb|DY623927.1|DY623927
EST:     GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCA                         GTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
genomic: GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggat ... ttggtttcagGTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
EST: gi|74244865|gb|DT652779.1|DT652779
EST:     GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCA                         GTCTGATGGGGCGCAGCCG
genomic: GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggat ... ttggtttcagGTCTGATGGGGCGCAGCCG
EST: gi|211282122|gb|FL372019.1|FL372019
EST:     GGCAACGGCGTCGCGGCCCTGCGCGACGACAAC-TCGACACCTACTGGCA                         GTCTGATGGGGCGCAGC
genomic: GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggat ... ttggtttcagGTCTGATGGGGCGCAGC
EST: gi|211201873|gb|FL396465.1|FL396465
EST:     GGCAACGGCGTCGCGGCCCTGCGCGACGACNACCTCGACACCTACTGGCA                         GTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
genomic: GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggat ... ttggtttcagGTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
EST: gi|71432068|gb|DR813118.1|DR813118
EST:     GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCA                         GTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
genomic: GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggat ... ttggtttcagGTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
EST: gi|149073064|gb|EE161334.2|EE161334
EST:     GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCA                         GTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
genomic: GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggat ... ttggtttcagGTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
EST: gi|211341306|gb|FL394252.1|FL394252
EST:     GGCAACGGCGTCGCGGCC-TGCGCGACGACAACCTCGACACCTACTGGCA                         GTCTGATGGGGCGCAGC
genomic: GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggat ... ttggtttcagGTCTGATGGGGCGCAGC
EST: gi|71427966|gb|DR809016.1|DR809016
EST:     GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCA                         GTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
genomic: GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggat ... ttggtttcagGTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
EST: gi|78180912|gb|DV551285.1|DV551285
EST:     GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCA                         GTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
genomic: GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggat ... ttggtttcagGTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
EST: gi|71297610|gb|DR784754.1|DR784754
EST:     GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCA                         GTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
genomic: GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggat ... ttggtttcagGTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT

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: 49 (upstream exon), 44 (downstream exon)
Score: 24

TGCGAGAGATGGCGAAGACGGCCGCGTGGAGCGTCAGTTCCTGCAAGGCCGGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggat ... ttggtttcagGTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAG


Block sizes: 48 (upstream exon), 16 (downstream exon)
Score: 24

TGCGAGAGATGGCGAAGACGGCCGCGTGGAGCGTCAGTTCCTGCAAGGCCGGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggat ... ttggtttcagGTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 26

TGCGAGAGATGGCGAAGACGGCCGCGTGGAGCGTCAGTTCCTGCAAGGCCGGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggat ... ttggtttcagGTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 17

TGCGAGAGATGGCGAAGACGGCCGCGTGGAGCGTCAGTTCCTGCAAGGCCGGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggat ... ttggtttcagGTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAG