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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccttttttattctaaagggagaccactgtttgaaatatttcgtgcggtgtttttaaatgatctgttatggcagGTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTGATGCTTGGTATTCTGACCGGAGTGGTTCCGTGGAGAGCACCGCTGCTTA

Basic information

species Zea mays
transcript GRMZM2G348675_T02
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G348675_T02 (Zea mays), 3'ss of exon 21
lower sequence: LOC_Os11g42420.1 (Oryza sativa), 3'ss of exon 21
gtacc-ttttttattctaaagggagaccactgtttgaaatatttcgtgcggtgtttttaaatgatctgttatggcagGTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTGATGCTTGGTATTCTGACCGGAGTGGTTCCGTGGAGAGCACCGCTGCTTA
||| | ||| |           || ||     |||| |||| |  ||    | | | | ||| ||   |||||||||||||||||| ||| || |||||||||||||| || | ||| ||||||||||||||||||||||||||  |   |||||| || || ||||| ||||| ||
gtatcatttatcgacactttatgatactgtgatttggaatagtctgtaatatttatgtgaataattcattatggcagGTGAACTCAATCGATTTCAACCTGGAGTTTCAATTGAAATATCACGGCTTGATGCTTGGTATTCTGATGGTCATGGTTCAGTAGAAAGCACTGCTGCATA
















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|60401356|gb|DN234163.1|DN234163
EST:     AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAG                         GTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
genomic: AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAGgtaccttttt ... gttatggcagGTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
EST: gi|89106042|gb|DY576259.1|DY576259
EST:     AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAG                         GTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
genomic: AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAGgtaccttttt ... gttatggcagGTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
EST: gi|6564229|gb|AW231851.1|AW231851
EST:     AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAG                         GTGAACTCAGTCGGTTCCAACCTG
genomic: AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAGgtaccttttt ... gttatggcagGTGAACTCAGTCGGTTCCAACCTG
EST: gi|33098458|gb|CF058418.1|CF058418
EST:     AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAG                         GTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
genomic: AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAGgtaccttttt ... gttatggcagGTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
EST: gi|71444755|gb|DR825805.1|DR825805
EST:     AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAG                         GTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
genomic: AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAGgtaccttttt ... gttatggcagGTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
EST: gi|60338136|gb|DN205109.1|DN205109
EST:     AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAG                         GTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
genomic: AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAGgtaccttttt ... gttatggcagGTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
EST: gi|31611836|gb|CD568458.1|CD568458
EST:     AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAG                         GTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
genomic: AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAGgtaccttttt ... gttatggcagGTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
EST: gi|211241122|gb|FL071392.1|FL071392
EST:     AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAG                         GTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
genomic: AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAGgtaccttttt ... gttatggcagGTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
EST: gi|71769927|gb|DR967864.1|DR967864
EST:     AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAG                         GTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
genomic: AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAGgtaccttttt ... gttatggcagGTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
EST: gi|60337110|gb|DN204083.1|DN204083
EST:     AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAG                         GTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
genomic: AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAGgtaccttttt ... gttatggcagGTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
EST: gi|91056201|gb|EB166619.1|EB166619
EST:     AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAG                         GTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
genomic: AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAGgtaccttttt ... gttatggcagGTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
EST: gi|6021399|gb|AW066327.1|AW066327
EST:     AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAG                         GTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
genomic: AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAGgtaccttttt ... gttatggcagGTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
EST: gi|60394400|gb|DN227270.1|DN227270
EST:     AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAG                         GTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
genomic: AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAGgtaccttttt ... gttatggcagGTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
EST: gi|78077107|gb|DV505541.1|DV505541
EST:     AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAG                         GTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
genomic: AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAGgtaccttttt ... gttatggcagGTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
EST: gi|21843367|gb|BQ703948.1|BQ703948
EST:     GATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAG                         GTGAACTCAGTCGGTTCCACCCTGGAGTTTCGATGGCAATTTCACGGCTTG
genomic: GATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAGgtaccttttt ... gttatggcagGTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
EST: gi|6526938|gb|AW216185.1|AW216185
EST:     GATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAG                         GTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCNCGGCTTG
genomic: GATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAGgtaccttttt ... gttatggcagGTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
EST: gi|211426538|gb|FL064839.1|FL064839
EST:     AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAG                         GTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
genomic: AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAGgtaccttttt ... gttatggcagGTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
EST: gi|6012524|gb|AW061961.1|AW061961
EST:     GTCATGGCT-CTGGCTTTAAAG                         GTGAANTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCNCGGCTTG
genomic: GTCATGGCTGCTGGCTTTAAAGgtaccttttt ... gttatggcagGTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
EST: gi|60342258|gb|DN209231.1|DN209231
EST:     AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAG                         GTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
genomic: AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAGgtaccttttt ... gttatggcagGTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
EST: gi|211436987|gb|FL183985.1|FL183985
EST:     -GCCAACGATGGAGGTCTTCTTGCTGCAATCATGGCTGCTGGCTTTAAAG                         GTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
genomic: AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAGgtaccttttt ... gttatggcagGTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
EST: gi|31406262|gb|CD484994.1|CD484994
EST:     AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAG                         GTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
genomic: AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAGgtaccttttt ... gttatggcagGTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
EST: gi|60358719|gb|DN225692.1|DN225692
EST:     AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAG                         GTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
genomic: AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAGgtaccttttt ... gttatggcagGTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
EST: gi|60398909|gb|DN231725.1|DN231725
EST:     AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAG                         GTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
genomic: AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAGgtaccttttt ... gttatggcagGTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
EST: gi|87157582|gb|DY402371.1|DY402371
EST:     AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAG                         GTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
genomic: AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAGgtaccttttt ... gttatggcagGTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
EST: gi|33095636|gb|CF055630.1|CF055630
EST:     GGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAG                         GTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
genomic: GGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAGgtaccttttt ... gttatggcagGTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
EST: gi|21432401|gb|BQ547891.1|BQ547891
EST:     CTTGCTGCAGTCATGGCTGCTGGCTTTAAAG                         GTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
genomic: CTTGCTGCAGTCATGGCTGCTGGCTTTAAAGgtaccttttt ... gttatggcagGTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
EST: gi|33095263|gb|CF055257.1|CF055257
EST:     AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAG                         GTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG
genomic: AGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAGgtaccttttt ... gttatggcagGTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTG

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), 46 (downstream exon)
Score: 182

GTCGCTCTTCGCTGCTTAGCAGCAGAAGGTGATGGATATGGGCTTCATGAAGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAGgtaccttttt ... gttatggcagGTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTGATGCTTGGTATTCTGACCGGAGTGGTTCCGTGGAGAGCACCGCTGCTTA


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

GTCGCTCTTCGCTGCTTAGCAGCAGAAGGTGATGGATATGGGCTTCATGAAGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAGgtaccttttt ... gttatggcagGTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTGATGCTTGGTATTCTGACCGGAGTGGTTCCGTGGAGAGCACCGCTGCTTA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 107

GTCGCTCTTCGCTGCTTAGCAGCAGAAGGTGATGGATATGGGCTTCATGAAGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAGgtaccttttt ... gttatggcagGTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTGATGCTTGGTATTCTGACCGGAGTGGTTCCGTGGAGAGCACCGCTGCTTA


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 58

GTCGCTCTTCGCTGCTTAGCAGCAGAAGGTGATGGATATGGGCTTCATGAAGCCAACGATGGAGGTCTTCTTGCTGCAGTCATGGCTGCTGGCTTTAAAGgtaccttttt ... gttatggcagGTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTGATGCTTGGTATTCTGACCGGAGTGGTTCCGTGGAGAGCACCGCTGCTTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagaccactgtttgaaatatttcgtgcggtgtttttaaatgatctgttatggcagGTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTGATGCTTGGTATTCTGACCGGAGTGGTTCCGTGGAGAGCACCGCTGCTTA
        tgtttgaaatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccttttttattctaaagggagaccactgtttgaaatatttcgtgcggtgtttttaaatgatctgttatggcagGTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTGATGCTTGGTATTCTGACCGGAGTGGTTCCGTGGAGAGCACCGCTGCTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT