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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAAGCTTCTGTCAGTGAAAAACTAACATTTGCTGCAAAAGGAGTTCTATCAAAAGTATTCCCAAAGCCTCGTAGAGCTTGGTTGCCCACCGGCTGCTTGgtatggctttccaaaactttagctttgtgaggttagagcatctccaagagatcccaaaaaaaaatctcccaatacaaaggaattagaatctccctaaatc...

Basic information

species Zea mays
transcript GRMZM2G101217_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101217_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os01g68390.1 (Oryza sativa), 5'ss of exon 9
CAAAGCTTCTGTCAGTGAAAAACTAACATTTGCTGCAAAAGGAGTTCTATCAAAAGTATTCCCAAAGCCTCGTAGAGCTTGGTTGCCCACCGGCTGCTTGgtatggctttccaaaac-tttagctttgtgaggttagagca------tctccaagagatcccaaa--aaaaaatctcccaatacaaaggaattagaatctccctaaatc------------------
 ||||  ||||| || || ||| || || ||||||||||||||||| | ||||||||||||||||||||||| ||||||||||| || || || ||||||||||| ||||  ||  |  ||    |||| |||||| |         |||  | | ||||  |     |  | | |  ||    |  |     ||||||||   ||                     
GAAAGTGTCTGTGAGAGACAAATTATCACTTGCTGCAAAAGGAGTTGTGTCAAAAGTATTCCCAAAGCCTCGGAGAGCTTGGTTACCAACTGGATGCTTGgtatgtcttttgaacccacttccacttgttaggttataaactgttattctatatgtgatcatatgctgatgagtttgtcagcttactg---ccagaatctctgaaatatgtgttatgacatatgcag
















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|76924071|gb|DV169789.1|DV169789
EST:     CAAAAGTATTCCCAAAGCCTCGTAGAGCTTGGTTGCCCACCGGCTGCTTG                         AAACTAATGGATACTCTACATCAAGCTTTACCGAGCATGTCCCTTATTGCT
genomic: CAAAAGTATTCCCAAAGCCTCGTAGAGCTTGGTTGCCCACCGGCTGCTTGgtatggcttt ... cctttcgcagAAACTAATGGATACTCTACATCAAGCTTTACCGAGCATGTCCCTTATTGCT
EST: gi|71418851|gb|DR804567.1|DR804567
EST:     CAAAAGTATTCCCAAAGCCTCGTAGAGCTTGGTTGCCCACCGGCTGCTTG                         AAACTAATGGATACTCTACATCAAGCTTTACCGAGCATGTCCCTTATTGCT
genomic: CAAAAGTATTCCCAAAGCCTCGTAGAGCTTGGTTGCCCACCGGCTGCTTGgtatggcttt ... cctttcgcagAAACTAATGGATACTCTACATCAAGCTTTACCGAGCATGTCCCTTATTGCT
EST: gi|76281531|gb|DV021099.1|DV021099
EST:     CAAAAGTATTCCCAAAGCCTCGTAGAGCTTGGTTGCCCACCGGCTGCTTG                         AAACTAATGGATACTCTACATCAAGCTTTACCGAGCATGTCCCTTATTGCT
genomic: CAAAAGTATTCCCAAAGCCTCGTAGAGCTTGGTTGCCCACCGGCTGCTTGgtatggcttt ... cctttcgcagAAACTAATGGATACTCTACATCAAGCTTTACCGAGCATGTCCCTTATTGCT
EST: gi|93012640|gb|EB638160.1|EB638160
EST:     CAAAAGTATTCCCAAAGCCTCGTAGAGCTTGGTTGCCCACCGGCTGCTTG                         AAACTAATGGATACTCTACATCAAGCTTTACCGAGCATGTCCCTTATTGCT
genomic: CAAAAGTATTCCCAAAGCCTCGTAGAGCTTGGTTGCCCACCGGCTGCTTGgtatggcttt ... cctttcgcagAAACTAATGGATACTCTACATCAAGCTTTACCGAGCATGTCCCTTATTGCT
EST: gi|71763051|gb|DR960988.1|DR960988
EST:     CAAAAGTATTCCCAAAGCCTCGTAGAGCTTGGTTGCCCACCGGCTGCTTG                         AAACTAATGGATACTCTACATCAAGCTTTACCGAGCATGTCCCTTATTGCT
genomic: CAAAAGTATTCCCAAAGCCTCGTAGAGCTTGGTTGCCCACCGGCTGCTTGgtatggcttt ... cctttcgcagAAACTAATGGATACTCTACATCAAGCTTTACCGAGCATGTCCCTTATTGCT
EST: gi|71418854|gb|DR804568.1|DR804568
EST:     AAA-GTATTCCCAAAGCCTCGTAGAGCTTGGTTGCCCCACCG-CTGCTTG                         AAACTAATGGATACTCTACATCAAGCTTTACCGAGCATGTCCCTTA
genomic: AAAAGTATTCCCAAAGCCTCGTAGAGCTTGGTTGCCC-ACCGGCTGCTTGgtatggcttt ... cctttcgcagAAACTAATGGATACTCTACATCAAGCTTTACCGAGCATGTCCCTTA
EST: gi|148960596|gb|EE011218.2|EE011218
EST:     CAAAAGTATTCCCAAAGCCTCGTAGAGCTTGGTTGCCCACCGGCTGCTTG                         AAACTAATGGATACTCTACATCAAGCTTTACCGAGCATGTCCCTTATTGCT
genomic: CAAAAGTATTCCCAAAGCCTCGTAGAGCTTGGTTGCCCACCGGCTGCTTGgtatggcttt ... cctttcgcagAAACTAATGGATACTCTACATCAAGCTTTACCGAGCATGTCCCTTATTGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAAGCTTCTGTCAGTGAAAAACTAACATTTGCTGCAAAAGGAGTTCTATCAAAAGTATTCCCAAAGCCTCGTAGAGCTTGGTTGCCCACCGGCTGCTTGgtatggctttccaaaactttagctttgtgaggttagagcatctccaagagatcccaaaaaaaaatctcccaatacaaaggaattagaatctccctaaatc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT