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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTATTGTTGCAGCCTTCTTGATGAAGTCTAGAGGGTGGAGACTTGCACAATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATGgttagcttcataccctttgaagcttgttgactaattaagacaccgtctctattacattatgaatcattggttccttgcctatcaaatgttaacatttttt...

Basic information

species Zea mays
transcript GRMZM2G045404_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G045404_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g48840.1 (Oryza sativa), 5'ss of exon 4
GCTATTGTTGCAGCCTTCTTGATGAAGTCTAGAGGGTGGAGACTTGCACAATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATGgt-tagcttcataccc-----tttgaagcttgttgactaattaagacaccgtctctattacattatgaatcattggt-tccttgcctatcaaatgttaacatttttt
||||||||   || || ||||||||| ||||| || ||||||||| |||| ||||  |||||||||||||| ||  |||||||||| ||||||||||||||| |     ||||||      |||    ||| ||   |   | | | | | |  | |   | |  | ||  |||  | |   ||| |  | |      |  || |||
GCTATTGTAATAGGCTACTTGATGAAATCTAGGGGATGGAGACTTTCACAGTCTTACCAATGGGTGAAAGACCGGCGACCACAGGTGCAACTGACAGATGgtatgatcccataccaaataatttatttcttctttcatgcctgaaaaatctttgccaacccctattcaa--attaatataggtgcttggcgag-----atgttcttt
















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|71327049|gb|DR800171.1|DR800171
EST:     ATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATG                         CTTCTCAGAAGGAGCTTTTGGAGTATGAGCTGAAGCTTTTCGGACCCAGTA
genomic: ATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATGgttagcttca ... ttctatgcagCTTCTCAGAAGGAGCTTTTGGAGTATGAGCTGAAGCTTTTCGGACCCAGTA
EST: gi|5607978|gb|AI901645.1|AI901645
EST:     CAGGTTCAACTGCCAGATG                         CTTCTCAGAAGGAGCTTTTGGAGTATGAGCTGAAGCTTTTCGGACCCAGTA
genomic: CAGGTTCAACTGACAGATGgttagcttca ... ttctatgcagCTTCTCAGAAGGAGCTTTTGGAGTATGAGCTGAAGCTTTTCGGACCCAGTA
EST: gi|71445833|gb|DR826883.1|DR826883
EST:     ATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATG                         CTTCTCAGAAGGAGCTTTTGGAGTATGAGCT
genomic: ATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATGgttagcttca ... ttctatgcagCTTCTCAGAAGGAGCTTTTGGAGTATGAGCT
EST: gi|76018560|gb|DT945730.1|DT945730
EST:     ATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATG                         CTTCTCAGAAGGAGCTTTTGGAGTATGAGCTGAAGCTTTTCGGACCCAGTA
genomic: ATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATGgttagcttca ... ttctatgcagCTTCTCAGAAGGAGCTTTTGGAGTATGAGCTGAAGCTTTTCGGACCCAGTA
EST: gi|31354088|gb|CD438445.1|CD438445
EST:     GTCTTTTCAATGGGTGAAAGACCGAAGACCACAGGTTCAACTGACAGATG                         CTTCTCAGAAGGAGCTTTTGGAGTATGAGCTGAAGCTTTTCGGACCCAGTA
genomic: ATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATGgttagcttca ... ttctatgcagCTTCTCAGAAGGAGCTTTTGGAGTATGAGCTGAAGCTTTTCGGACCCAGTA
EST: gi|76286478|gb|DV026046.1|DV026046
EST:     ATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATG                         CTTCTCAGAAGGAGCTTTTGGAGTATGAGCTGAAGCTTTTCGGACCCAGTA
genomic: ATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATGgttagcttca ... ttctatgcagCTTCTCAGAAGGAGCTTTTGGAGTATGAGCTGAAGCTTTTCGGACCCAGTA
EST: gi|94472551|gb|EB701509.1|EB701509
EST:     ATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATG                         CTTTTCAGAAGGAGCTTTTGGAGTATGAGCTGAAGCTTTTCGGACCCAGTA
genomic: ATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATGgttagcttca ... ttctatgcagCTTCTCAGAAGGAGCTTTTGGAGTATGAGCTGAAGCTTTTCGGACCCAGTA
EST: gi|67020663|gb|CO449412.1|CO449412
EST:     GTCTTTTCAATGGGTGAAAGACCGAAGACCACAGGTTCAACTGACAGATG                         CTTCTNCAGAAG-AGCTTTTGGAGTATGAGTTGAAGCTTTTCGGACCCAGT
genomic: ATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATGgttagcttca ... ttctatgcagCTTCT-CAGAAGGAGCTTTTGGAGTATGAGCTGAAGCTTTTCGGACCCAGT
EST: gi|89251347|gb|DY623133.1|DY623133
EST:     ATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCCACTGACAGATG                         CTTCTCAGAAGGAGCTTTTGGAGTATGAG
genomic: ATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATGgttagcttca ... ttctatgcagCTTCTCAGAAGGAGCTTTTGGAGTATGAG
EST: gi|67011227|gb|CO439976.1|CO439976
EST:     GTCTTTTCAATGGGTGAAAGACCGAAGACCACAGGTTCAACTGACAGATG                         CTTCTCAGAAGGAGCTTTTGGAGTATGAGTTGAAGCTTTTCGGACCCAGTA
genomic: ATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATGgttagcttca ... ttctatgcagCTTCTCAGAAGGAGCTTTTGGAGTATGAGCTGAAGCTTTTCGGACCCAGTA
EST: gi|71422091|gb|DR805613.1|DR805613
EST:     ATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATG                         CTTCTCAGAAGGAGCTTTTGGAGTATGAGCTGAAGCTTTTCGGACCCAGTA
genomic: ATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATGgttagcttca ... ttctatgcagCTTCTCAGAAGGAGCTTTTGGAGTATGAGCTGAAGCTTTTCGGACCCAGTA
EST: gi|89760803|gb|DY689068.1|DY689068
EST:     ATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATG                         CTTCTCAGAAGGAGCTTTTGGAGTATGAGCTGAAGCTTTTCGGACCCAGTA
genomic: ATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATGgttagcttca ... ttctatgcagCTTCTCAGAAGGAGCTTTTGGAGTATGAGCTGAAGCTTTTCGGACCCAGTA
EST: gi|74236962|gb|DT644876.1|DT644876
EST:     ATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATG                         CTTCTCAGAAGGAGCTTTTGGAGTATGAGCTGAAGCTTTTCGGACCCAGTA
genomic: ATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATGgttagcttca ... ttctatgcagCTTCTCAGAAGGAGCTTTTGGAGTATGAGCTGAAGCTTTTCGGACCCAGTA
EST: gi|76286477|gb|DV026045.1|DV026045
EST:     ATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATG                         CTTCTCAGAAGGAGCTTTTGGAGTATGAGCTGAAGCTTTTCGGACCCAGTA
genomic: ATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATGgttagcttca ... ttctatgcagCTTCTCAGAAGGAGCTTTTGGAGTATGAGCTGAAGCTTTTCGGACCCAGTA
EST: gi|78113628|gb|DV532019.1|DV532019
EST:     ATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATG                         CTTCTCAGAAGGAGCTTTTGGAGTATGAGCTGAAGCTTTTCGGACCCAGTA
genomic: ATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATGgttagcttca ... ttctatgcagCTTCTCAGAAGGAGCTTTTGGAGTATGAGCTGAAGCTTTTCGGACCCAGTA
EST: gi|78109343|gb|DV527759.1|DV527759
EST:     TCTTTTTCA-TGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATG                         CTTCTCAGAAGGAGCTTTTGGAGTATGAGCTGAA
genomic: TCTTTT-CAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATGgttagcttca ... ttctatgcagCTTCTCAGAAGGAGCTTTTGGAGTATGAGCTGAA
EST: gi|76922423|gb|DV168996.1|DV168996
EST:     ATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATG                         CTTCTCAGAAGGAGCTTTTGGAGTATGAGCTGAAGCTTTTCGGACCCAGTA
genomic: ATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATGgttagcttca ... ttctatgcagCTTCTCAGAAGGAGCTTTTGGAGTATGAGCTGAAGCTTTTCGGACCCAGTA
EST: gi|71327044|gb|DR800170.1|DR800170
EST:     ATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATG                         CTTCTCAGAAGGAGCTTTTGGAGTATGAGCTGAAGCTTTTCGGACCCAGTA
genomic: ATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATGgttagcttca ... ttctatgcagCTTCTCAGAAGGAGCTTTTGGAGTATGAGCTGAAGCTTTTCGGACCCAGTA
EST: gi|74244123|gb|DT652037.1|DT652037
EST:     ATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATG                         CTTCTCAGAAGGAGCTTTTGGAGTATGAGCTGAAGCTTTTCGGACCCAGTA
genomic: ATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATGgttagcttca ... ttctatgcagCTTCTCAGAAGGAGCTTTTGGAGTATGAGCTGAAGCTTTTCGGACCCAGTA

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: 48 (upstream exon), 49 (downstream exon)
Score: 113

GCTATTGTTGCAGCCTTCTTGATGAAGTCTAGAGGGTGGAGACTTGCACAATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATGgttagcttca ... ttctatgcagCTTCTCAGAAGGAGCTTTTGGAGTATGAGCTGAAGCTTTTCGGACCCAGTACTCAAACCTTGGTTCCCACTGAATCATTTGCTTCTCTTGGATTTGGTTA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 50

GCTATTGTTGCAGCCTTCTTGATGAAGTCTAGAGGGTGGAGACTTGCACAATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATGgttagcttca ... ttctatgcagCTTCTCAGAAGGAGCTTTTGGAGTATGAGCTGAAGCTTTTCGGACCCAGTACTCAAACCTTGGTTCCCACTGAATCATTTGCTTCTCTTGGATTTGGTTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 76

GCTATTGTTGCAGCCTTCTTGATGAAGTCTAGAGGGTGGAGACTTGCACAATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATGgttagcttca ... ttctatgcagCTTCTCAGAAGGAGCTTTTGGAGTATGAGCTGAAGCTTTTCGGACCCAGTACTCAAACCTTGGTTCCCACTGAATCATTTGCTTCTCTTGGATTTGGTTA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 69

GCTATTGTTGCAGCCTTCTTGATGAAGTCTAGAGGGTGGAGACTTGCACAATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATGgttagcttca ... ttctatgcagCTTCTCAGAAGGAGCTTTTGGAGTATGAGCTGAAGCTTTTCGGACCCAGTACTCAAACCTTGGTTCCCACTGAATCATTTGCTTCTCTTGGATTTGGTTA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTATTGTTGCAGCCTTCTTGATGAAGTCTAGAGGGTGGAGACTTGCACAATCTTTTCAATGGGTGAAAGATCGAAGACCACAGGTTCAACTGACAGATGgttagcttcataccctttgaagcttgttgactaattaagacaccgtctctattacattatgaatcattggttccttgcctatcaaatgttaacatttttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG