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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataaattcttttaaggttattgtgtccacattcactgtgatcttttttggaccctgaagcagaaaatcctagaataacaaactgcattatacttgaacagATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGGAGGATGGTTGGCTATGCTTCTATGAGATTCTTGCCAATCATTTTGTTAG

Basic information

species Zea mays
transcript GRMZM5G871336_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G871336_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g05830.1 (Oryza sativa), 3'ss of exon 2
ataaattcttttaaggttattgtgtccacattcactgtgatcttttttggaccctgaagcagaaaatcctagaata--acaaactgcattatacttgaacagATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGGAGGATGGTTGGCTATGCTTCTATGAGATTCTTGCCAATCATTTTGTTAG
 |    |   ||    ||||  |       |      | ||  |  |   | | ||   ||     |  |   ||   ||| |||  |||    || ||||||||  ||| | ||   ||  |||||||| |||||||||| |||||| || || |||    || | |||||||||||||||||||| || |||||||||| 
ctgtccttacttccttttatgatcaatgtttgggtcataatactactca-atcttgttacaagtgtttttgctatgttacatact-tatttctttttaacagATGTGATTTTAAGCACGAACGATGATGGTATTGCTCCAGTAGATGAGCGAGAAGATACCCGGTTGTGCTTCTATGAGATTCTTGCTAACCATTTTGTTAA
















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|71430125|gb|DR811175.1|DR811175
EST:     TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAG                         ATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGG
genomic: TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAGgtgccatatc ... acttgaacagATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGG
EST: gi|211068146|gb|FL037286.1|FL037286
EST:     TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGACCGCGCTCGAG                         ATGCAATTATGAGTGAGAATGATGATGGCATTGCTCCAGCAGATGAACGGG
genomic: TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAGgtgccatatc ... acttgaacagATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGG
EST: gi|211070875|gb|FL037292.1|FL037292
EST:     TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAG                         ATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGG
genomic: TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAGgtgccatatc ... acttgaacagATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGG
EST: gi|71432140|gb|DR813190.1|DR813190
EST:     TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAG                         ATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGG
genomic: TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAGgtgccatatc ... acttgaacagATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGG
EST: gi|211068145|gb|FL037285.1|FL037285
EST:     TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGACCGCGCTCGAG                         ATGCAATTATGAGTGAGAATGATGATGGCATTGCTCCAGCAGATGAACGGG
genomic: TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAGgtgccatatc ... acttgaacagATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGG
EST: gi|211070876|gb|FL037293.1|FL037293
EST:     TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGACCGCGCTCGAG                         ATGCAATTATGAGTGAGAATGATGATGGCATTGCTCCAGCAGATGAACGGG
genomic: TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAGgtgccatatc ... acttgaacagATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGG
EST: gi|211070877|gb|FL037294.1|FL037294
EST:     TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGACCGCGCTCGAG                         ATGCAATTATGAGTGAGAATGATGATGGCATTGCTCCAGCAGATGAACGGG
genomic: TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAGgtgccatatc ... acttgaacagATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGG
EST: gi|211073615|gb|FL037307.1|FL037307
EST:     TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGACCGCGCTCGAG                         ATGCAATTATGAGTGAGAATGATGATGGCATTGCTCCAGCAGATGAACGGG
genomic: TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAGgtgccatatc ... acttgaacagATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGG
EST: gi|71311972|gb|DR792494.1|DR792494
EST:     TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAG                         ATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGG
genomic: TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAGgtgccatatc ... acttgaacagATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGG
EST: gi|148950551|gb|EC896128.2|EC896128
EST:     TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAG                         ATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGG
genomic: TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAGgtgccatatc ... acttgaacagATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGG
EST: gi|211070883|gb|FL037300.1|FL037300
EST:     TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGACCGCGCTCGAG                         ATGCAATTATGAGTGAGAATGATGATGGCATTGCTCCAGCAGATGAACGGG
genomic: TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAGgtgccatatc ... acttgaacagATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGG
EST: gi|13381878|gb|BG458553.1|BG458553
EST:     TCAGCATTTGNNNNNNNNCATCGCATTGAAGGTGGATGATCGCGCTCGAG                         ATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGG
genomic: TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAGgtgccatatc ... acttgaacagATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGG
EST: gi|211070880|gb|FL037297.1|FL037297
EST:     TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGACCGCGCTCGAG                         ATGCAATTATGAGTGAGAATGATGATGGCATTGCTCCAGCAGATGAACGGG
genomic: TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAGgtgccatatc ... acttgaacagATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGG
EST: gi|93012464|gb|EB637984.1|EB637984
EST:     TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAG                         ATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGG
genomic: TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAGgtgccatatc ... acttgaacagATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGG
EST: gi|211070870|gb|FL037287.1|FL037287
EST:     TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGACCGCGCTCGAG                         ATGCAATTATGAGTGAGAATGATGATGGCATTGCTCCAGCAGATGAACGGG
genomic: TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAGgtgccatatc ... acttgaacagATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGG
EST: gi|211073617|gb|FL037309.1|FL037309
EST:     TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGACCGCGCTCGAG                         ATGCAATTATGAGTGAGAATGATGATGGCATTGCTCCAGCAGATGAACGGG
genomic: TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAGgtgccatatc ... acttgaacagATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGG
EST: gi|211070874|gb|FL037291.1|FL037291
EST:     TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGACCGCGCTCGAG                         ATGCAATTATGAGTGAGAATGATGATGGCATTGCTCCAGCAGATGAACGGG
genomic: TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAGgtgccatatc ... acttgaacagATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGG
EST: gi|149059964|gb|EE157094.2|EE157094
EST:     TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAG                         ATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGG
genomic: TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAGgtgccatatc ... acttgaacagATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGG
EST: gi|149045945|gb|EE047943.2|EE047943
EST:     TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAG                         ATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGG
genomic: TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAGgtgccatatc ... acttgaacagATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGG
EST: gi|94474109|gb|EB703067.1|EB703067
EST:     TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAG                         ATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGG
genomic: TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAGgtgccatatc ... acttgaacagATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGG
EST: gi|211070882|gb|FL037299.1|FL037299
EST:     TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGACCGCGCTCGAG                         ATGCAATTATGAGTGAGAATGATGATGGCATTGCTCCAGCAGATGAACGGG
genomic: TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAGgtgccatatc ... acttgaacagATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGG
EST: gi|211070884|gb|FL037301.1|FL037301
EST:     TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAG                         ATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGG
genomic: TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAGgtgccatatc ... acttgaacagATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGG
EST: gi|211070878|gb|FL037295.1|FL037295
EST:     TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGACCGCGCTCGAG                         ATGCAATTATGAGTGAGAATGATGATGGCATTGCTCCAGCAGATGAACGGG
genomic: TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAGgtgccatatc ... acttgaacagATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGG
EST: gi|211073610|gb|FL037302.1|FL037302
EST:     TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGACCGCGCTCGAG                         ATGCAATTATGAG
genomic: TCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAGgtgccatatc ... acttgaacagATGCAATTATGAG

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: 47 (upstream exon), 44 (downstream exon)
Score: 68

GCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAGgtgccatatc ... acttgaacagATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGGAGGATGGTTGGCTATGCTTCTATGAGATTCTTGCCAATCATTTTGTTAG


Block sizes: 45 (upstream exon), 45 (downstream exon)
Score: 48

GCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAGgtgccatatc ... acttgaacagATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGGAGGATGGTTGGCTATGCTTCTATGAGATTCTTGCCAATCATTTTGTTAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 45

GCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAGgtgccatatc ... acttgaacagATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGGAGGATGGTTGGCTATGCTTCTATGAGATTCTTGCCAATCATTTTGTTAG


Block sizes: 43 (upstream exon), 45 (downstream exon)
Score: 37

GCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAGgtgccatatc ... acttgaacagATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGGAGGATGGTTGGCTATGCTTCTATGAGATTCTTGCCAATCATTTTGTTAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggaccctgaagcagaaaatcctagaataacaaactgcattatacttgaacagATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGGAGGATGGTTGGCTATGCTTCTATGAGATTCTTGCCAATCATTTTGTTAG
                          gaataac  putative branch site (score: 37)
                           aataacaaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataaattcttttaaggttattgtgtccacattcactgtgatcttttttggaccctgaagcagaaaatcctagaataacaaactgcattatacttgaacagATGCAATTATGAGTGAGAGTGATGATGGCATTGCTCCAGCAGATGAACGGGAGGATGGTTGGCTATGCTTCTATGAGATTCTTGCCAATCATTTTGTTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - cattcac
- - - - - - - - - - - - - - - - - - - - - - - - - - -ctgaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgcatt