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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTGATGAAGAGCCAAATTATGCCAAGCTTATCTCTATTTTTGATGGTTTGATTGAAGCACCTGCGTCGAGACCAGTCAGAATTGATGGGGCCCTCAAGgtctgtactaactattccctccatatatatttatatttcttcgtccttatctttatttgttcccgtactatag

Basic information

species Zea mays
transcript GRMZM2G164265_T02
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164265_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os07g07560.2 (Oryza sativa), 5'ss of exon 11
ATTTGATGAAGAGCCAAATTATGCCAAGCTTATCTCTATTTTTGATGGTTTGATTGAAGCACCTGCGTCGAGACCAGTCAGAATTGATGGGGCCCTCAAGgtctgtactaactattccctccatatatatttatatttc--ttcgtccttatctttatttgttcccgtactatag-------------
||||||||||||||||||||| ||||| || || ||| | |||||| |||||||||| | |||||| || |||||  ||||||||||||| || || ||||||||||| | | |  |  |  |   |  |  ||||||   || |  ||  ||  ||| ||| |  | ||  |               
ATTTGATGAAGAGCCAAATTACGCCAAACTGATTTCTCTCTTTGATAGTTTGATTGAGGTACCTGCCTCAAGACCTATCAGAATTGATGGCGCTCTTAAGgtctgtaccacccac-cattttactcacttccatattttgtttaggtctgctccatatctgtccatgaacccttctcttaaattatag

upper sequence: GRMZM2G164265_T02 (Zea mays), 5'ss of exon 11
lower sequence: AT3G03940.1 (Arabidopsis thaliana), 5'ss of exon 11
ATTTGATGAAGAGCCAAATTATGCCAAGCTTATCTCTATTTTTGATGGTTTGATTGAAGCACCTGC---GTCGAGACCAGTCAGAATTGATGGGGCCCTCAAGgtctgtactaactattccctccatatatatttatatttcttcgtccttatctttatttgttcccgtactatag--------------
   |||||| ||||| || ||||||||||||||||| |||||||||  | | || ||  ||  |||    || |||||| | |||||||||||||| || |||||     || ||| |       || | ||||| |   | ||  |   ||     ||  || |   || | ||               
---TGATGAGGAGCCCAACTATGCCAAGCTTATCTCGATTTTTGATACTCTTATCGAGCCATGTGCTATATCTAGACCAATTAGAATTGATGGGGCTCTAAAGgt----gctgactttggttcatatgtttatttttcactatttataaataatacaataagtactgatattttacttttgcatcaatag
















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|32912903|gb|CF017715.1|CF017715
EST:     TGATTGAAGCACCTGCGTCGAGACCAGTCAGAATTGATGGGGCCCTCAAG                         GTTGGACAGAAACGTGGAAGATTGCATGCAAATCTAGAAGATGAACAACCT
genomic: TGATTGAAGCACCTGCGTCGAGACCAGTCAGAATTGATGGGGCCCTCAAGgtctgtacta ... cgtactatagGTTGGACAGAAACGTGGAAGATTGCATGCAAATCTAGAAGATGAACAACCT
EST: gi|149031683|gb|EE154868.2|EE154868
EST:     GAAGCACCTGCGTCGAGACCAGTCAGAA-TGATGGGGGCCCTCAAG                         GTTGGACAGAAACGTGGAAGATTGCATGCAAATCTAGAAGATGACCAACCT
genomic: GAAGCACCTGCGTCGAGACCAGTCAGAATTGAT-GGGGCCCTCAAGgtctgtacta ... cgtactatagGTTGGACAGAAACGTGGAAGATTGCATGCAAATCTAGAAGATGAACAACCT
EST: gi|211391059|gb|FL093738.1|FL093738
EST:     TGATTGAAGCACCTGCGTCGAGACCAGTCAGAATTGATGGGGCCCTCAAG                         GTTGGACAGAAACGTGGAAGATTGCATGCAAATCTAGAAGATGAACAACCT
genomic: TGATTGAAGCACCTGCGTCGAGACCAGTCAGAATTGATGGGGCCCTCAAGgtctgtacta ... cgtactatagGTTGGACAGAAACGTGGAAGATTGCATGCAAATCTAGAAGATGAACAACCT
EST: gi|71300241|gb|DR786191.1|DR786191
EST:     TGATTGAAGCACCTGCGTCGAGACCAGTCAGAATTGATGGGGCCCTCAAG                         GTTGGACAGAAACGTGGAAGATTGCATGCAAATCTAGAAGATGAACAACCT
genomic: TGATTGAAGCACCTGCGTCGAGACCAGTCAGAATTGATGGGGCCCTCAAGgtctgtacta ... cgtactatagGTTGGACAGAAACGTGGAAGATTGCATGCAAATCTAGAAGATGAACAACCT
EST: gi|148950556|gb|EC896133.2|EC896133
EST:     TGATTGAAGCACCTGGGTCGAGACCAGTCAGAATTGATGGGGCCCTCAAG                         GTTGGACAGAAACGTGGAAGATTGCATGCAAATCTAGAAGATGAACAACCT
genomic: TGATTGAAGCACCTGCGTCGAGACCAGTCAGAATTGATGGGGCCCTCAAGgtctgtacta ... cgtactatagGTTGGACAGAAACGTGGAAGATTGCATGCAAATCTAGAAGATGAACAACCT
EST: gi|37423723|gb|CF649590.1|CF649590
EST:     TGATTGAAGCACCTGCGTCGAGACCAGTCAGAATTGATGGGGCCCTCAAG                         GTTGGACAGAAACGGTGGAAGATTGCATGCAAATCTAGAAGATGAACAACC
genomic: TGATTGAAGCACCTGCGTCGAGACCAGTCAGAATTGATGGGGCCCTCAAGgtctgtacta ... cgtactatagGTTGGACAGAAAC-GTGGAAGATTGCATGCAAATCTAGAAGATGAACAACC
EST: gi|32913238|gb|CF018050.1|CF018050
EST:     TGATTGAAGCACCTGCGTCGAGACCAGTCAGAATTGATGGGGCCCTCAAG                         GTTGGACAGAAACGTGGAAGATTGCATGCAAATCTAGAAGATGAACAACCT
genomic: TGATTGAAGCACCTGCGTCGAGACCAGTCAGAATTGATGGGGCCCTCAAGgtctgtacta ... cgtactatagGTTGGACAGAAACGTGGAAGATTGCATGCAAATCTAGAAGATGAACAACCT
EST: gi|71430775|gb|DR811825.1|DR811825
EST:     TGATTGAAGCACCTGCGTCGAGACCAGTCAGAATTGATGGGGCCCTCAAG                         GTTGGACAGAAACGTGGAAGATTGCATGCAAATCTAGAAGATGAACAACCT
genomic: TGATTGAAGCACCTGCGTCGAGACCAGTCAGAATTGATGGGGCCCTCAAGgtctgtacta ... cgtactatagGTTGGACAGAAACGTGGAAGATTGCATGCAAATCTAGAAGATGAACAACCT
EST: gi|67043197|gb|CO469452.1|CO469452
EST:     TGATTGAAGCACCTGCGTCGAGACCAGTCAGAATTGATGGGGCCCTCAAG                         GTTGGACAGAAACGTGGAAGATTGCATGCAAATCTAGAAGATGAACAACCT
genomic: TGATTGAAGCACCTGCGTCGAGACCAGTCAGAATTGATGGGGCCCTCAAGgtctgtacta ... cgtactatagGTTGGACAGAAACGTGGAAGATTGCATGCAAATCTAGAAGATGAACAACCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTGATGAAGAGCCAAATTATGCCAAGCTTATCTCTATTTTTGATGGTTTGATTGAAGCACCTGCGTCGAGACCAGTCAGAATTGATGGGGCCCTCAAGgtctgtactaactattccctccatatatatttatatttcttcgtccttatctttatttgttcccgtactatag

- - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC