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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccatgagacacagatacctgtaaactgacaccaggctcaactgcgactcggtattcctttctcttcgtactgatatgactcctccgttgtgtctgttgtagGTTCTCGTCGGGGAATCCCTCATCAAGCAGGAGGATCCAGGGAAAGCAATCGCTGGGCTTTTCGGCAAAGATATCTCGCATGCTGGTGCTACCTAGAGAC

Basic information

species Zea mays
transcript GRMZM2G169516_T05
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169516_T05 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os04g39270.1 (Oryza sativa), 3'ss of exon 9
gtaagccatgagacac-agatacctgtaaactgacaccaggctcaactg-cgactcggtattcctttctcttcgtactgatatgactcctccgttgtgtctgttgtagGTTCTCGTCGGGGAATCCCTCATCAAGCAGGAGGATCCAGGGAAAGCAATCGCTGGGCTTTTCGGCAAAGATATCTCGCATGCTGGTGCTACCTAGAGAC
|||||   |||| ||  ||| || |  |||    ||||| |||  || | | |   || ||||| |  | |   | |||   |||||||||| ||  |  || ||||||||||||| ||||| || |||||||||||||||||||| || ||||||||||||||||||||||||||||| ||||| | ||   ||||| | || || |
gtaag---tgagccatgagacacttccaaatgagcaccaagctgtaccgacaatctggcattccctgatttc--ttctgcgctgactcctcccttacga-tgctgtagGTTCTCGTTGGGGAGTCTCTCATCAAGCAGGAGGATCCTGGCAAAGCAATCGCTGGGCTTTTCGGCAAAGACATCTCACCTGTGAGTGCTGCGTAAAGTC
















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|71430054|gb|DR811104.1|DR811104
EST:     TGTTCACTCCTGATGATATTTCGTTCGTTCAAAACGCTGGGGTCAAAGCG                         GTTTTCGTCGGGGAATCCCTCATCAAGCAGGAGGATCCAGGGAAAGCAATC
genomic: TGTTCACTCCTGATGATATCTCGTTCGTTCAAAACGCTGGGGTCAAAGCGgtaagccatg ... tctgttgtagGTTCTCGTCGGGGAATCCCTCATCAAGCAGGAGGATCCAGGGAAAGCAATC
EST: gi|71759609|gb|DR957546.1|DR957546
EST:     TGTTCACTCCTGATGATATCTCGTTCGTTCAAAACGCTGGGGTCAAAGCG                         GTTCTCGTCGGGGAATCCCTCATCAAGCAGGAGGATCCAGGGAAAGCAATC
genomic: TGTTCACTCCTGATGATATCTCGTTCGTTCAAAACGCTGGGGTCAAAGCGgtaagccatg ... tctgttgtagGTTCTCGTCGGGGAATCCCTCATCAAGCAGGAGGATCCAGGGAAAGCAATC
EST: gi|15214479|gb|BI431015.1|BI431015
EST:     TGTTCACTCCTGGTGATATTTCGTTCGTTCAAAACGCTGGAGTCAAAGCG                         GTTCTCGTCGGGGAATCCCTCATCAAGCAGGAGGATCCAGGGAAAGCAATC
genomic: TGTTCACTCCTGATGATATCTCGTTCGTTCAAAACGCTGGGGTCAAAGCGgtaagccatg ... tctgttgtagGTTCTCGTCGGGGAATCCCTCATCAAGCAGGAGGATCCAGGGAAAGCAATC
EST: gi|71324170|gb|DR798788.1|DR798788
EST:     TGTTCACTCCTGATGATATCTCGTTCGTTCAAAACGCTGGGGTCAAAGCG                         GTTCTCGTCGGGGAATCCCTCATCAAGCAGGAGGATCCAGGGAAAGCAATC
genomic: TGTTCACTCCTGATGATATCTCGTTCGTTCAAAACGCTGGGGTCAAAGCGgtaagccatg ... tctgttgtagGTTCTCGTCGGGGAATCCCTCATCAAGCAGGAGGATCCAGGGAAAGCAATC
EST: gi|211501402|gb|FL138828.1|FL138828
EST:     TGCTCACTCCTGGTGATATTTCGTTCGTTCAAAACGCTGGAGTCAAAGCG                         GTTCTCGTCGGGGAATCCCTCATCAAGCAGGAAGATCCAGGGAAAGCAATC
genomic: TGTTCACTCCTGATGATATCTCGTTCGTTCAAAACGCTGGGGTCAAAGCGgtaagccatg ... tctgttgtagGTTCTCGTCGGGGAATCCCTCATCAAGCAGGAGGATCCAGGGAAAGCAATC
EST: gi|71433347|gb|DR814397.1|DR814397
EST:     TGTTCACTCCTGATGATATCTCGTTCGTTCAAAACGCTGGGGTCAAAGCG                         GTTCTCGTCGGGGAATCCCTCATCAAGCAGGAGGATCCAGGGAAAGCAATC
genomic: TGTTCACTCCTGATGATATCTCGTTCGTTCAAAACGCTGGGGTCAAAGCGgtaagccatg ... tctgttgtagGTTCTCGTCGGGGAATCCCTCATCAAGCAGGAGGATCCAGGGAAAGCAATC
EST: gi|71759019|gb|DR956956.1|DR956956
EST:     TGTTCACTCCTGATGATATCTCGTTCGTTCAAAACGCTGGGGTCAAAGCG                         GTTCTCGTCGGGGAATCCCTCATCAAGCAGGAGGATCCAGGGAAAGCAATC
genomic: TGTTCACTCCTGATGATATCTCGTTCGTTCAAAACGCTGGGGTCAAAGCGgtaagccatg ... tctgttgtagGTTCTCGTCGGGGAATCCCTCATCAAGCAGGAGGATCCAGGGAAAGCAATC
EST: gi|211073093|gb|FL464915.1|FL464915
EST:     TGTTCACTCCTGATGATATCTCGTTCGTTCAAAACGCTGGGGTCAAAGCG                         GTTCTCGTCGGGGAATCCCTCATCAAGCAGGAGGATCCAGGGAAAGCAATC
genomic: TGTTCACTCCTGATGATATCTCGTTCGTTCAAAACGCTGGGGTCAAAGCGgtaagccatg ... tctgttgtagGTTCTCGTCGGGGAATCCCTCATCAAGCAGGAGGATCCAGGGAAAGCAATC
EST: gi|94473827|gb|EB702785.1|EB702785
EST:     TGTTCACTCCTGATGATATCTCGTTCGTTCAAAACGCTGGGGTCAAAGCG                         GTTCTCGTCGGGGAATCCCTCATCAAGCAGGAGGATCCAGGGAAAGCAATC
genomic: TGTTCACTCCTGATGATATCTCGTTCGTTCAAAACGCTGGGGTCAAAGCGgtaagccatg ... tctgttgtagGTTCTCGTCGGGGAATCCCTCATCAAGCAGGAGGATCCAGGGAAAGCAATC
EST: gi|91870855|gb|EB401116.1|EB401116
EST:     TGTTCACTCCTGATGATATCTCGTTCGTTCAAAACGCTGGGGTCAAAGCG                         GTTTTCGTCGGGGAATCCCTCATCAAGCAGGAGGATCCAGGGAAAGCAATC
genomic: TGTTCACTCCTGATGATATCTCGTTCGTTCAAAACGCTGGGGTCAAAGCGgtaagccatg ... tctgttgtagGTTCTCGTCGGGGAATCCCTCATCAAGCAGGAGGATCCAGGGAAAGCAATC
EST: gi|24765189|gb|CA400348.1|CA400348
EST:     TGTTCACTCCTGGTGATATTTCGTTCGTTCAAA-CGCTGGAGTCAAAGCG                         GTTCTCGTCGGGGAATCCCTCATCAAGCAGGAGGAT
genomic: TGTTCACTCCTGATGATATCTCGTTCGTTCAAAACGCTGGGGTCAAAGCGgtaagccatg ... tctgttgtagGTTCTCGTCGGGGAATCCCTCATCAAGCAGGAGGAT
EST: gi|88752600|gb|DY536741.1|DY536741
EST:     TGTTCACTCCTGATGATATCTCGTTCGTTCAAAACGCTGGGGTCAAAGCG                         GTTCTCGTCGGGGAATCCCTCATCAAGCAGGAGGATCCAGGGAAAGCAATC
genomic: TGTTCACTCCTGATGATATCTCGTTCGTTCAAAACGCTGGGGTCAAAGCGgtaagccatg ... tctgttgtagGTTCTCGTCGGGGAATCCCTCATCAAGCAGGAGGATCCAGGGAAAGCAATC
EST: gi|84969902|gb|DV170843.2|DV170843
EST:     TGTTCACTCCTGATGATATCTCGTTCGTTCAAAACGCTGGGGTCAAAGCG                         GTTCTCGTCGGGGAATCCCTCATCAAGCAGGAGGATCCAGGGAAAGCAATC
genomic: TGTTCACTCCTGATGATATCTCGTTCGTTCAAAACGCTGGGGTCAAAGCGgtaagccatg ... tctgttgtagGTTCTCGTCGGGGAATCCCTCATCAAGCAGGAGGATCCAGGGAAAGCAATC
EST: gi|6973599|gb|AW438335.1|AW438335
EST:     TGTTCACTCCTGGTGATATTTCGTTCGTTCAAAACGCTGGAGTCAAAGCG                         GCTCTCGTCGGGGAATCCCTCATCAAGCAGGACGATCCAGGGAAAGCAATC
genomic: TGTTCACTCCTGATGATATCTCGTTCGTTCAAAACGCTGGGGTCAAAGCGgtaagccatg ... tctgttgtagGTTCTCGTCGGGGAATCCCTCATCAAGCAGGAGGATCCAGGGAAAGCAATC
EST: gi|71431465|gb|DR812515.1|DR812515
EST:     TGTTCACTCCTGATGATATCTCGTTCGTTCAAAACGCTGGGGTCAAAGCG                         GTTCTCGTCGGGGAATCCCTCATCAAGCAGGAGGATCCAGGGAAAGCAATC
genomic: TGTTCACTCCTGATGATATCTCGTTCGTTCAAAACGCTGGGGTCAAAGCGgtaagccatg ... tctgttgtagGTTCTCGTCGGGGAATCCCTCATCAAGCAGGAGGATCCAGGGAAAGCAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcggtattcctttctcttcgtactgatatgactcctccgttgtgtctgttgtagGTTCTCGTCGGGGAATCCCTCATCAAGCAGGAGGATCCAGGGAAAGCAATCGCTGGGCTTTTCGGCAAAGATATCTCGCATGCTGGTGCTACCTAGAGAC
                     tactgat  putative branch site (score: 2)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagccatgagacacagatacctgtaaactgacaccaggctcaactgcgactcggtattcctttctcttcgtactgatatgactcctccgttgtgtctgttgtagGTTCTCGTCGGGGAATCCCTCATCAAGCAGGAGGATCCAGGGAAAGCAATCGCTGGGCTTTTCGGCAAAGATATCTCGCATGCTGGTGCTACCTAGAGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG