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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaccttataaatttatgatatatcttttttgttcctctagagttctgttttcgcattacctgcatgtagttctgctgacaaaggcaaataagcgactagttagatgtatcttatggtaaactctctccatctttgtctcatatatattttttttaatcagGATTGTGCAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCACTTCAG

Basic information

species Zea mays
transcript GRMZM2G052630_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052630_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os05g03480.4 (Oryza sativa), 3'ss of exon 12
gtaaccttataaatttatgatatatcttttttgttcctctagagttctgttttcgcattacctgcatgtagttctgctgacaa-aggcaaataagcgactagttagatg--tatctta-tggtaaactctctccatctttgtct-catat--atattttttttaat---cagGATTGTGCAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCACTTCAG
                                                                        |||  | |||| |      |   |  ||  |   ||   |||| |  ||||||||| ||| ||||||  |||  |||   |||||||||||| |   ||||||||||| || || |||||||||||||||||||  |||||||| || |||||||||
------------------------------------------------------------------------tctattcacaacaaaactgtcttcatctcatctaataattatcatggtggtaaactgtcttcatcttcatctatataataatattttttttattattcagGATTGTGCTGGTGTGATTCTCTTTGCTGCTGAAAGGGCAACCCAGGTTGCACTTCAG
















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|45847870|gb|CN071813.1|CN071813
EST:     GCGATAATGGCAAAGTTGATCGCAAG                         GATTGTGCAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCA
genomic: GCGATAATGGCAAAGTTGATCGCAAGgtaaccttat ... ttttaatcagGATTGTGCAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCA
EST: gi|24769404|gb|CA404533.1|CA404533
EST:     TTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG                         GATTGTGCAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCA
genomic: TTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaaccttat ... ttttaatcagGATTGTGCAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCA
EST: gi|110190881|gb|EC872779.1|EC872779
EST:     TTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG                         GATTGTGCAGGGGTAANNNNNNNNGCTGCTGAAAATGCAACCCAAGTGGCA
genomic: TTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaaccttat ... ttttaatcagGATTGTGCAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCA
EST: gi|31360769|gb|CD445126.1|CD445126
EST:     TTGTATACTCGGCTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG                         GATTGTGCAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCA
genomic: TTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaaccttat ... ttttaatcagGATTGTGCAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCA
EST: gi|60347547|gb|DN214520.1|DN214520
EST:     TTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG                         GATTGTGCAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCA
genomic: TTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaaccttat ... ttttaatcagGATTGTGCAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCA
EST: gi|78027006|gb|DV495393.1|DV495393
EST:     TTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG                         GATTGTGCAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCA
genomic: TTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaaccttat ... ttttaatcagGATTGTGCAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCA
EST: gi|5108421|gb|AI740134.1|AI740134
EST:     TTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG                         GATTGTGCAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCA
genomic: TTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaaccttat ... ttttaatcagGATTGTGCAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCA
EST: gi|74240406|gb|DT648320.1|DT648320
EST:     TTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG                         GATTGTGCAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCA
genomic: TTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaaccttat ... ttttaatcagGATTGTGCAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCA
EST: gi|76936507|gb|DV174755.1|DV174755
EST:     TTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG                         GATTGTGCAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCA
genomic: TTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaaccttat ... ttttaatcagGATTGTGCAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCA
EST: gi|50336352|gb|CO531478.1|CO531478
EST:     TTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG                         GATTGTGCAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCA
genomic: TTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaaccttat ... ttttaatcagGATTGTGCAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCA
EST: gi|78124549|gb|DV542933.1|DV542933
EST:     TTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG                         GATTGTGCAGGGGTAATTTTCTTTGCTGCTGAAAATGCAACCCAAGTGGCA
genomic: TTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaaccttat ... ttttaatcagGATTGTGCAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCA
EST: gi|78105056|gb|DV523474.1|DV523474
EST:     TTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG                         GATTGTGCAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCA
genomic: TTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaaccttat ... ttttaatcagGATTGTGCAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCA
EST: gi|110525230|gb|EE029414.1|EE029414
EST:     TTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG                         GATTGTGCAGGGGTAANNNNNNNNGCTGCTGAAAATGCAACCCAAGTGGCA
genomic: TTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaaccttat ... ttttaatcagGATTGTGCAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCA
EST: gi|149076167|gb|EE164757.2|EE164757
EST:     TTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG                         GATTGTGCAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCA
genomic: TTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaaccttat ... ttttaatcagGATTGTGCAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatcttatggtaaactctctccatctttgtctcatatatattttttttaatcagGATTGTGCAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCACTTCAG
                                       tatttttttt  CT-rich tract
                       atctttgtctcatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaccttataaatttatgatatatcttttttgttcctctagagttctgttttcgcattacctgcatgtagttctgctgacaaaggcaaataagcgactagttagatgtatcttatggtaaactctctccatctttgtctcatatatattttttttaatcagGATTGTGCAGGGGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTGGCACTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT