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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTTAAGGATGATCCATACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttggatagtcggatcttcctctctcttgttcagaaggacatcacagttatgcctctttttttgtttttctatgtacag

Basic information

species Zea mays
transcript GRMZM2G358059_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G358059_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os07g14270.3 (Oryza sativa), 5'ss of exon 9
ATTTTAAGGATGATCCATACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttggatagt------------cggatct---tcctctctcttgttcagaaggacat-----cacagttatg--cctctttttttgtttttctatgtacag
| || ||||||||||||||||| || || || |||||| |||||||||||||||||||| ||||||||||  ||   | | |||              | |||   |  | |  || | |||| | ||||       | |||||||  | | |   ||   | ||||||  ||||
ACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTGGCATTGAGTTGTGGCAGgttagttaagcaaagtacagtacgcctttagttctgatttattttgctgggtcaggaagacagacataaatagttatgaacttatcccttctctcttctatcaacag
















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|148931875|gb|EC877339.2|EC877339
EST:     ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAG                         GTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
genomic: ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
EST: gi|84980101|gb|DW530450.1|DW530450
EST:     ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAG                         GTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCG
genomic: ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
EST: gi|86467986|gb|DY234356.1|DY234356
EST:     ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAG                         GTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
genomic: ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
EST: gi|149074502|gb|EE162898.2|EE162898
EST:     ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAG                         GTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
genomic: ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
EST: gi|14883658|gb|BI273473.1|BI273473
EST:     ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAG                         GTTAAATCGGGCACTCTGTTCGACAACATCATCATCA
genomic: ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTTGACAACATCATCATCA
EST: gi|14190892|gb|BG833122.1|BG833122
EST:     ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAG                         GTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCG
genomic: ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
EST: gi|7162446|gb|AW520068.1|AW520068
EST:     ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAG                         GTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCG
genomic: ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
EST: gi|14190894|gb|BG833124.1|BG833124
EST:     ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAG                         GTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCG
genomic: ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
EST: gi|37377946|gb|CF625620.1|CF625620
EST:     ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAG                         GTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCG
genomic: ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
EST: gi|33096251|gb|CF056245.1|CF056245
EST:     ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAG                         GTTAAATCGGGCACTCT-TTTCGACAACATCATCATCACTGATGACCCTGC
genomic: ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTT-GACAACATCATCATCACTGATGACCCTGC
EST: gi|31440900|gb|CD510331.1|CD510331
EST:     ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCCTTGAGCTGTGGCAG                         GTTAAATCGGGCACTCTGTTTGACAACATCATCATCCCTGATGACCCTGCC
genomic: ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
EST: gi|149074540|gb|EE162939.2|EE162939
EST:     ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAG                         GTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
genomic: ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
EST: gi|86470502|gb|DY236872.1|DY236872
EST:     ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAG                         GTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
genomic: ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
EST: gi|71442155|gb|DR823205.1|DR823205
EST:     ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAG                         GTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
genomic: ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
EST: gi|37374548|gb|CF623645.1|CF623645
EST:     ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAG                         GTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCG
genomic: ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
EST: gi|14190893|gb|BG833123.1|BG833123
EST:     ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAG                         GTTAAATCGGGCACTCTGNTTGACAACATCATCATCACTGATGACCCTGCG
genomic: ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
EST: gi|84980095|gb|DW530444.1|DW530444
EST:     TTGGCATTGAGCTGTGGCAG                         GTTAAATCGGGCACTCCTGTTTGACAACATCATCATCACTGATGACCCTGC
genomic: TTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACT-CTGTTTGACAACATCATCATCACTGATGACCCTGC
EST: gi|84976665|gb|DW475087.1|DW475087
EST:     ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAG                         GTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCG
genomic: ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
EST: gi|15590491|gb|BI675107.1|BI675107
EST:     ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAG                         GTTAAATCGGGCACTCTGTTCGACAACATCATCATCACTGATGACCCTGCG
genomic: ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
EST: gi|6021565|gb|AW066493.1|AW066493
EST:     ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGNGGCAG                         GTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCG
genomic: ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
EST: gi|5268655|gb|AI770619.1|AI770619
EST:     ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAG                         GTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCG
genomic: ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
EST: gi|33093443|gb|CF053437.1|CF053437
EST:     ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAG                         GTTAAATCGGGCACTCT-TTTCGACAACATCATCATCACTGATGACCCTGC
genomic: ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTT-GACAACATCATCATCACTGATGACCCTGC
EST: gi|148937046|gb|EC881219.2|EC881219
EST:     ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAG                         GTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
genomic: ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
EST: gi|21088786|gb|BQ401099.1|BQ401099
EST:     ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAG                         GTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCG
genomic: ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
EST: gi|4647548|gb|AI622623.1|AI622623
EST:     ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAG                         GTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
genomic: ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
EST: gi|211100469|gb|FL191950.1|FL191950
EST:     ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAG                         GTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
genomic: ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
EST: gi|33103536|gb|CF063496.1|CF063496
EST:     GTACATTGGCATTGAGCTGTGGCAG                         GTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
genomic: GTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
EST: gi|32912239|gb|CF017051.1|CF017051
EST:     ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAG                         GTTAAATCGGGCACTCT-TTTCGACAACATCAT
genomic: ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTT-GACAACATCAT
EST: gi|84980708|gb|DW531057.1|DW531057
EST:     ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAG                         GTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCG
genomic: ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
EST: gi|29544799|gb|CB605407.1|CB605407
EST:     ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAG                         GTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
genomic: ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
EST: gi|37382092|gb|CF627969.1|CF627969
EST:     ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAG                         GTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCG
genomic: ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
EST: gi|88750940|gb|DY535081.1|DY535081
EST:     ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAG                         GTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
genomic: ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
EST: gi|7216518|gb|AW562640.1|AW562640
EST:     ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTG-GGCAG                         GTTAAATCGGGC
genomic: ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGC
EST: gi|71759740|gb|DR957677.1|DR957677
EST:     ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAG                         GTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
genomic: ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
EST: gi|7162466|gb|AW520088.1|AW520088
EST:     ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAG                         GTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCG
genomic: ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
EST: gi|148963936|gb|EE015057.2|EE015057
EST:     ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAG                         GTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
genomic: ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
EST: gi|71432522|gb|DR813572.1|DR813572
EST:     ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAG                         GTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC
genomic: ACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCC

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: 1245

ATTTTAAGGATGATCCATACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 1014

ATTTTAAGGATGATCCATACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 1165

ATTTTAAGGATGATCCATACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 4368

ATTTTAAGGATGATCCATACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttg ... ctatgtacagGTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTTAAGGATGATCCATACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAGgtcggtgttggatagtcggatcttcctctctcttgttcagaaggacatcacagttatgcctctttttttgtttttctatgtacag

- - - - - - - - - - - - - - - - - - - TTGAAG