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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagttaccaactttttttttgcaaatctaggttacatatctttatgattttcatcattatactagcgactgtcatgtctaattatgtcttcggtctgcagAGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG

Basic information

species Zea mays
transcript GRMZM2G130034_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130034_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os12g40550.1 (Oryza sativa), 3'ss of exon 10
---------------------------------------------------gagttaccaactttttttttgcaa-atctaggttacatatctttatgattttcat------cattatact-agcgactgtcatgtctaattatgtcttcggtctgcagAGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
                                                     | |  |||  | |          || |   ||   | |  ||||| | ||  |       |  ||  | | | |||  || ||  || |   |||| | |||||||| |||||||||||||||||||||||||||| ||||||||||
gtcaagtactataggccccaacagggttttccacctacaaaccaaataccctggctggcaatctctgaaacatgttatttgctttgtgtctaattatgttctttttgtggggtaacatgtttaccaactaacacgtacaactgcttctttgttctgcagAATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAG

upper sequence: GRMZM2G130034_T02 (Zea mays), 3'ss of exon 11
lower sequence: Vv05s0020g04900.t01 (Vitis vinifera), 3'ss of exon 10
----gagttaccaactttttttttgcaaatctaggttacatatctttatgattttcatcattatactagcgactgtcatgtctaattatgtcttcggtct-gcagAGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
      ||    ||  |||    ||  | |  |  |    |    ||  | ||||| | | |  |  |    |||     |||  | ||||| |    || ||||| |||| |||||||||||||| |||||||| ||||||||||
aatgtggtcttaaagatttcagatggtactgaaaatagtttgctctt--ggttttcttaactgca--aatagctgctg-atcttgtaatgtcatattccttgcagAATATCTCCAATGGGTATGATATTCATTCCATGTTACAAAG
















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|86468217|gb|DY234587.1|DY234587
EST:     TACAAAAAGATGATTAGCAGAGCCTACCCCGATTCACTCTTCATGGCCAG                         AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
genomic: TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAGgtgaactact ... cggtctgcagAGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
EST: gi|86473058|gb|DY239428.1|DY239428
EST:     TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAG                         AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
genomic: TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAGgtgaactact ... cggtctgcagAGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
EST: gi|31362362|gb|CD446719.1|CD446719
EST:     TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAG                         AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
genomic: TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAGgtgaactact ... cggtctgcagAGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
EST: gi|88749671|gb|DY533812.1|DY533812
EST:     TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAG                         AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
genomic: TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAGgtgaactact ... cggtctgcagAGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
EST: gi|33466598|gb|CF243647.1|CF243647
EST:     TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTTTTCATGGCCAG                         AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
genomic: TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAGgtgaactact ... cggtctgcagAGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
EST: gi|24768371|gb|CA403500.1|CA403500
EST:     TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAG                         AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
genomic: TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAGgtgaactact ... cggtctgcagAGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
EST: gi|78022951|gb|DV491338.1|DV491338
EST:     TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAG                         AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
genomic: TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAGgtgaactact ... cggtctgcagAGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
EST: gi|50333648|gb|CO528774.1|CO528774
EST:     TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTTTTCATGGCCAG                         AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
genomic: TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAGgtgaactact ... cggtctgcagAGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
EST: gi|211502326|gb|FL069735.1|FL069735
EST:     TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAG                         AGTATCACCCAAATGGGGTATGATCTTCATTCCCTGTTACAAAG
genomic: TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAGgtgaactact ... cggtctgcagAGTATCACC-AA-TGGG-TATGATCTTCATTCCCTGTTACAAAG
EST: gi|71775246|gb|DR973124.1|DR973124
EST:     TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAG                         AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
genomic: TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAGgtgaactact ... cggtctgcagAGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
EST: gi|211502325|gb|FL069734.1|FL069734
EST:     TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAG                         AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
genomic: TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAGgtgaactact ... cggtctgcagAGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
EST: gi|91874397|gb|EB404354.1|EB404354
EST:     TACAAAAAGATGATTAGCAGAGCCTACCCCGATTCACTTTTCATGGCCAG                         AGTATCACCAATGGGTATGATTTTCATTCCCTGTTACAAAG
genomic: TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAGgtgaactact ... cggtctgcagAGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
EST: gi|30087001|gb|CB885209.1|CB885209
EST:     TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAG                         AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
genomic: TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAGgtgaactact ... cggtctgcagAGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
EST: gi|71441172|gb|DR822222.1|DR822222
EST:     TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAG                         AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
genomic: TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAGgtgaactact ... cggtctgcagAGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
EST: gi|148944451|gb|EC889566.2|EC889566
EST:     TACAAAAAGATGATTAGCAGAGCCTACCCCGATTCACTCTTCATGGCCAG                         AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
genomic: TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAGgtgaactact ... cggtctgcagAGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
EST: gi|71305488|gb|DR788881.1|DR788881
EST:     TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAG                         AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
genomic: TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAGgtgaactact ... cggtctgcagAGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
EST: gi|78107617|gb|DV526035.1|DV526035
EST:     TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAG                         AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
genomic: TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAGgtgaactact ... cggtctgcagAGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
EST: gi|5714250|gb|AI944235.1|AI944235
EST:     TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAG                         AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
genomic: TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAGgtgaactact ... cggtctgcagAGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
EST: gi|148983477|gb|EE029495.2|EE029495
EST:     TACAAAAAGATGATTAGCAGAGCCTACCCCGATTCACTTTTCATGGCCAG                         AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
genomic: TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAGgtgaactact ... cggtctgcagAGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
EST: gi|71427277|gb|DR808327.1|DR808327
EST:     TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAG                         AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
genomic: TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAGgtgaactact ... cggtctgcagAGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
EST: gi|86468218|gb|DY234588.1|DY234588
EST:     TACAAAAAGATGATTAGAAAAGCCTACCACGATTCACTCTTCAGGGCCAG                         AGTATCACCAAGGGGTATGATCTTCTTTCCCTGTTACAAAG
genomic: TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAGgtgaactact ... cggtctgcagAGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
EST: gi|149103752|gb|EE289158.2|EE289158
EST:     TACAAAAAGATGATTAGCAGAGCCTACCCCGATTCACTCTTCATGGCCAG                         AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
genomic: TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAGgtgaactact ... cggtctgcagAGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
EST: gi|50324879|gb|CO520005.1|CO520005
EST:     TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAG                         AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
genomic: TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAGgtgaactact ... cggtctgcagAGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
EST: gi|50323472|gb|CO518598.1|CO518598
EST:     TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAG                         AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
genomic: TACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAGgtgaactact ... cggtctgcagAGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG

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), 49 (downstream exon)
Score: 97

AATCAGTCGTTGACGCAATGGAATTTGCTGCAAAACAGTTAAACCTGGCATACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAGgtgaactact ... cggtctgcagAGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 96

AATCAGTCGTTGACGCAATGGAATTTGCTGCAAAACAGTTAAACCTGGCATACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAGgtgaactact ... cggtctgcagAGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 122

AATCAGTCGTTGACGCAATGGAATTTGCTGCAAAACAGTTAAACCTGGCATACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAGgtgaactact ... cggtctgcagAGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 77

AATCAGTCGTTGACGCAATGGAATTTGCTGCAAAACAGTTAAACCTGGCATACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAGgtgaactact ... cggtctgcagAGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattttcatcattatactagcgactgtcatgtctaattatgtcttcggtctgcagAGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG
                              gtctaat  putative branch site (score: 77)
                                       tgtcttc  putative PPT
       atcattata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagttaccaactttttttttgcaaatctaggttacatatctttatgattttcatcattatactagcgactgtcatgtctaattatgtcttcggtctgcagAGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG

- - - - - - - - ttttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtcatg