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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatttctgatcgattgtggttgccatatattcagtatggcttatgtttatttttagtacattttgaatagcttttgtatttcaatcatttctttaccagCGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGCTAAGCGCAGAAGGGAGAAGTACCAAAAACAATCATCTCTCCTGTCAAAA

Basic information

species Zea mays
transcript GRMZM2G157462_T01
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 20
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 20
-atatttctgatcgattgtggttgccatatattcagtatggcttatgtttatttttagtacattttgaatagcttttgtatttcaatcatttctttaccagCGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGCTAAGCGCAGAAGGGAGAAGTACCAAAAACAATCATCTCTCCTGTCAAAA
 |  |   | |  | |      |    ||| |  | |||    | | |||| |   | ||   | | |      ||  | |     |  | || ||||||| |||||||||||||| || ||||||||||| || |||||||||||||||||||| || |||||||| || ||||||||||||||||||||| ||||||| 
gacttgcttaaatggt-acacctaagctatttatactatatgctgtttttaatgccattattatctaatcttaattcctttgctttttttgtcattaccagTGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGCTAAACGTAGAAGGGAAAAATACCAAAAACAATCATCTCTCTTGTCAAAG

upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 20
lower sequence: GLYMA09G00430.2 (Glycine max), 3'ss of exon 20
-----atatttctgatcg--attgtggttgccatatattcagtatggcttatgtttatttttagtacattttgaatagcttttgtatttcaatcatttctttaccagCGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGCTAAGCGCAGAAGGGAGAAGTACCAAAAACAATCATCTCTCCTGTCAAAA
     || || | | |    ||  |  |  | || | ||   | | | |    |||  | || ||   | || || |  ||||     |  ||  || | | |  || |  |||||||  ||||||||||| || ||||||| ||| || || |||| |||||||||||||||      ||| ||||||||||| || || || |||
tctgtatgttacagttttgtatgataataacaattttttacatttagttgc--tttgatgttggtctctgtttaacatttttt-----tgtatgtttccgtgattagTGCTCAAAGCACGGCTAAGATTGAGGAACTGCTTCTAGAAGATCAAAATGTTAAGCGCAGAAGGGATCGAATCCAGAAACAATCATCCCTTCTCTCGAAA
















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|4314677|gb|AI438584.2|AI438584
EST:     AGCAAAGGAAGGCATGCTTAGCCAGCTATACAGCTCGATAAG                         CGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
genomic: AGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgatgttc ... tctttaccagCGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
EST: gi|78543683|gb|DV621181.1|DV621181
EST:     GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG                         CGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
genomic: GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgatgttc ... tctttaccagCGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
EST: gi|19821990|gb|BQ048014.1|BQ048014
EST:     GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG                         CGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
genomic: GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgatgttc ... tctttaccagCGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
EST: gi|24768960|gb|CA404089.1|CA404089
EST:     GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG                         CGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
genomic: GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgatgttc ... tctttaccagCGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
EST: gi|78180891|gb|DV551264.1|DV551264
EST:     GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG                         CGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
genomic: GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgatgttc ... tctttaccagCGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
EST: gi|71773970|gb|DR971858.1|DR971858
EST:     GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG                         CGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
genomic: GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgatgttc ... tctttaccagCGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
EST: gi|149108496|gb|EE189682.2|EE189682
EST:     AAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG                         CGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
genomic: AAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgatgttc ... tctttaccagCGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
EST: gi|14243758|gb|BG841389.2|BG841389
EST:     AGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG                         CGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
genomic: AGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgatgttc ... tctttaccagCGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
EST: gi|26455909|gb|CA827492.1|CA827492
EST:     GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG                         CGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
genomic: GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgatgttc ... tctttaccagCGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
EST: gi|31355296|gb|CD439653.1|CD439653
EST:     GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG                         CGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
genomic: GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgatgttc ... tctttaccagCGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
EST: gi|56382295|gb|CV984964.1|CV984964
EST:     GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG                         CGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
genomic: GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgatgttc ... tctttaccagCGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
EST: gi|31357385|gb|CD441742.1|CD441742
EST:     GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG                         CGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
genomic: GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgatgttc ... tctttaccagCGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
EST: gi|22491320|gb|BU051243.1|BU051243
EST:     GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG                         CGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
genomic: GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgatgttc ... tctttaccagCGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
EST: gi|149096022|gb|EE181696.2|EE181696
EST:     GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG                         CGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
genomic: GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgatgttc ... tctttaccagCGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
EST: gi|32940832|gb|CF045651.1|CF045651
EST:     GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG                         CGGGCAAAGCAATGCTAAGATTGACGAGCTGCTTCAAGAGGACCATAATGC
genomic: GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgatgttc ... tctttaccagCGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
EST: gi|67026008|gb|CO454757.1|CO454757
EST:     GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG                         CGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
genomic: GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgatgttc ... tctttaccagCGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
EST: gi|87151847|gb|DY396636.1|DY396636
EST:     GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG                         CGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
genomic: GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgatgttc ... tctttaccagCGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
EST: gi|24769886|gb|CA405015.1|CA405015
EST:     AGAAAGCAAAGGAAGACATGCTTACCCAGCTATACAGCTCGATAAG                         CGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGCCCATAATGC
genomic: AGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgatgttc ... tctttaccagCGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
EST: gi|32857965|gb|CD997646.1|CD997646
EST:     GGGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG                         CGGGCAAAGCAA
genomic: GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgatgttc ... tctttaccagCGGGCAAAGCAA
EST: gi|211132361|gb|FK982428.1|FK982428
EST:     GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG                         CGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
genomic: GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgatgttc ... tctttaccagCGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
EST: gi|109637318|gb|EC590863.1|EC590863
EST:     GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG                         CGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
genomic: GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgatgttc ... tctttaccagCGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC

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), 49 (downstream exon)
Score: 424

GCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgatgttc ... tctttaccagCGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGCTAAGCGCAGAAGGGAGAAGTACCAAAAACAATCATCTCTCCTGTCAAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 492

GCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgatgttc ... tctttaccagCGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGCTAAGCGCAGAAGGGAGAAGTACCAAAAACAATCATCTCTCCTGTCAAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 729

GCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgatgttc ... tctttaccagCGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGCTAAGCGCAGAAGGGAGAAGTACCAAAAACAATCATCTCTCCTGTCAAAA


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 327

GCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgatgttc ... tctttaccagCGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGCTAAGCGCAGAAGGGAGAAGTACCAAAAACAATCATCTCTCCTGTCAAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttatttttagtacattttgaatagcttttgtatttcaatcatttctttaccagCGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGCTAAGCGCAGAAGGGAGAAGTACCAAAAACAATCATCTCTCCTGTCAAAA
                                        tcatttcttt  CT-rich tract
     tttttagtacatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatttctgatcgattgtggttgccatatattcagtatggcttatgtttatttttagtacattttgaatagcttttgtatttcaatcatttctttaccagCGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGCTAAGCGCAGAAGGGAGAAGTACCAAAAACAATCATCTCTCCTGTCAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- -tttctga
- - - - - - - - -tggttgc
- - - - - - - - - - - - - - - - - - - -gcttatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tacattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttttg