Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catttaattgttttttttgaaattttgatgaaagcagcagcagcagtattaatgatctgtactaaaattgacttgttgattacatttaatcttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAG

Basic information

species Zea mays
transcript GRMZM2G056572_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G056572_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os04g56450.2 (Oryza sativa), 3'ss of exon 6
catttaattgttttttttgaaatttt-gatgaaagcagcagcagcagtattaatgatctgtactaaa--attgacttgttgatta-catttaatcttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAG
    ||||   | || || |  |||| |     || |  | || |  |  || | | || |   |||  ||   |||||| | ||    ||      || ||||||||||||| ||||| || | |||||||| || || |||||||||||||||||||||||||| ||  | || |||
----taatatatgttgttaattttttaggcttcagaataatcatcctttatattcacctttcacaaatgatgaccttgttcagtaatgcttttgtgggtcatagGAGGAAGTTATTGATCACTCTCTCGAGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAG

upper sequence: GRMZM2G056572_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 7
-catttaat-tgttttttttgaaattttgatgaaagcagcagcagcagtattaatgatctgtactaaaattgacttgttgat-tacatttaatcttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAG
  | || ||    |  ||    |  ||| |    ||   |   |   | | |    |    | |     || |||  ||    || ||  ||  ||     ||||||||   ||||||  | | ||||||||||| || |||||||||||||| || ||||| || || |||||||||
ttacttgatacaatcattacccacattttagactagtttctagaatggcactttacaaaacttccttcgttcactcattagcataaatggaaaatttc---agGAGGAAAAAGTTGATAGCTCTCTCGAGTTTCTCATTCTTGCAAGTGATGGTCTCTGGGACGTTGTATCTAACGAG

upper sequence: GRMZM2G056572_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv04s0008g07320.t01 (Vitis vinifera), 3'ss of exon 7
--catttaatt---gttttttttgaaattttgatgaaagcagcagcagcagtattaatgatctgtactaaaattgacttgttgattacatttaatcttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAG
  | ||  |||   ||  || ||    || |      |    |   | |  | |  |  ||| | |||||  || | ||  ||   |  |||       |   ||||||||    ||||   | | |||||||||||||||||||| |||||||| ||||||||||| ||| | || |||
tgctttagatttatgtcattctttgccttctccctccatt--ccaaaactttctgcagaatcagcactaa--ttaatttactggc-atttttctgaaaattgcagGAGGAAAAGATTGACAGCTCCCTCGAGTTTCTTATCCTTGCCAGTGATGGACTGTGGGATGTTGTCACAAATGAG

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|87156931|gb|DY401720.1|DY401720
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... cttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
EST: gi|71762691|gb|DR960628.1|DR960628
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... cttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
EST: gi|6095655|gb|AW120322.1|AW120322
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAGGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... cttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
EST: gi|211036167|gb|FL457683.1|FL457683
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... cttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
EST: gi|5124063|gb|AI745904.1|AI745904
EST:     TAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
genomic: TAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... cttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
EST: gi|76016318|gb|DT943488.1|DT943488
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... cttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
EST: gi|5296366|gb|AI783136.1|AI783136
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAGGTTGTTGATGACACACTCGAGTTTCTTATCCTTG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... cttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTG
EST: gi|67024109|gb|CO452858.1|CO452858
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... cttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
EST: gi|76917080|gb|DV166669.1|DV166669
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCCTGCAAGTGAGGGG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... cttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
EST: gi|149106821|gb|EE188718.2|EE188718
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... cttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
EST: gi|211036166|gb|FL457682.1|FL457682
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... cttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
EST: gi|76016319|gb|DT943489.1|DT943489
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... cttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
EST: gi|5901101|gb|AW042201.1|AW042201
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGTATCCGGAGATCCGA                         GAGGAGGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... cttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
EST: gi|94472146|gb|EB701104.1|EB701104
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTTGCA-GTGATGG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... cttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTT-GCAAGTGATGG
EST: gi|5846990|gb|AW000069.1|AW000069
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGNGGATCCGGAGATCCGA                         GAGGAGGTTGNTGATGACACACTCGAGTTTCTTATCCTTGCAA
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... cttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAA
EST: gi|61118718|gb|DN559679.1|DN559679
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACAC
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... cttgtgatagGAGGAAGTTGTTGATGACAC
EST: gi|76290021|gb|DV029589.1|DV029589
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... cttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
EST: gi|76288714|gb|DV028282.1|DV028282
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... cttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
EST: gi|76288715|gb|DV028283.1|DV028283
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATTCTTGCAAGTGATGGG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... cttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
EST: gi|60340995|gb|DN207968.1|DN207968
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... cttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
EST: gi|60357297|gb|DN224270.1|DN224270
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... cttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
EST: gi|50323711|gb|CO518837.1|CO518837
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGA
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... cttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGA
EST: gi|60359261|gb|DN226234.1|DN226234
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... cttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
EST: gi|71448387|gb|DR829437.1|DR829437
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACACTCGAGTTTC
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... cttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTC
EST: gi|60354881|gb|DN221854.1|DN221854
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... cttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
EST: gi|60338245|gb|DN205218.1|DN205218
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... cttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
EST: gi|166605679|gb|EG191128.1|EG191128
EST:     GTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACGCTCGAGTTTCTTATCCTTGCAAGTGATGGG
genomic: GTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... cttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
EST: gi|166705270|gb|EG043028.1|EG043028
EST:     GTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACGCTCGAGTTTCTTATCCTTGCAAGTGATGGG
genomic: GTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... cttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
EST: gi|67021956|gb|CO450705.1|CO450705
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... cttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
EST: gi|31406343|gb|CD485075.1|CD485075
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... cttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
EST: gi|149111015|gb|EE294514.2|EE294514
EST:     TTGGTGACAAACTTTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACCCTCGAGTTTTTTATCCTTGCAAGTGATGGG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... cttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG

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), 48 (downstream exon)
Score: 363

GAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... cttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 426

GAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... cttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 534

GAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... cttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 446

GAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... cttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtattaatgatctgtactaaaattgacttgttgattacatttaatcttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAG
                              ttgattacatttaat  TA-rich tract