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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCATTGAAGTGCATGGAGTTCCAGGAACTCTTTACGCCAATGAAACTTACCAACTTCAAGTTGAGTTCCCTGAGCATTATCCTATGGAAGCTCCACAGgttcgtcctctaactccttttgttaatacttaacgatacttaatcatcgcatcaatctcataacccgatggttccacatataaaacag

Basic information

species Arabidopsis thaliana
transcript AT4G36410.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G36410.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G007381_T01 (Zea mays), 5'ss of exon 3
GATCATTGAAGTGCATGGAGTTCCAGGAACTCTTTACGCCAATGAAACTTACCAACTTCAAGTTGAGTTCCCTGAGCATTATCCTATGGAAGCTCCACAGgttcg-tcctctaactccttttgttaatacttaacgatacttaatcatcgcatcaatctcataacccgatggttccacat-ataaaacag-----------
| | ||||| ||    ||||   | || || |||||||||   ||  |||||||  | || ||||| ||||||||||||||||||||||| || || |||||  | |  |||         |   |    |   ||||  ||  || || |||   |||  |   ||     || ||  | ||   ||             
GGTAATTGAGGTCACCGGAGCGGCGGGCACCCTTTACGCCGGCGAGGCTTACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggttttctcgacaaagattgcacctttagtcgattgtttgtcttctcatt--tcttctgttccttccatttcatttgattggactcatcttttccag

upper sequence: AT4G36410.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G018447_T01 (Zea mays), 5'ss of exon 3
GATCATTGAAGTGCATGGAGTTCCAGGAACTCTTTACGCCAATGAAACTTACCAACTTCAAGTTGAGTTCCCTGAGCATTATCCTATGGAAGCTCCACAGgttcg-tcctctaact---ccttttgttaatacttaacgatacttaatcatcgcatcaatctcataacccgatggttccac-atataaaacag--------------------
| | ||||| ||   |||||   | || || |||||||||   || || |||||  | || ||||| ||||||||||||||||||||||| || || |||||  | |  |||         |    |   || | ||  |    || |||||   |    ||      |   || ||  |  ||| | |||                      
GGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGACCTACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggttttctggacaaagatcgcatatttagtcaattacgtctactcatcctttttcccttcatttcatttgattgaatgatacataaccattcacgtcttttgcttccag

upper sequence: AT4G36410.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv04s0023g02620.t01 (Vitis vinifera), 5'ss of exon 3
GATCATTGAAGTGCATGGAGTTCCAGGAACTCTTTACGCCAATGAAACTTACCAACTTCAAGTTGAGTTCCCTGAGCATTATCCTATGGAAGCTCCACAGgt-----------tcgtc-----------ctctaactccttttgttaatacttaacgatacttaatcatcgcatcaatctcataac--ccga--tggttccacatataaaacag
| |||| ||||||||||||| |||||||||||| ||||| || ||| ||||||| ||||| ||||| || ||||||||||| || |||||||||||||||||           |  ||            |||  ||  |||| ||  |  ||  |     ||||   ||   |   | | ||     | ||  |||||      ||   ||||
GGTCATAGAAGTGCATGGAGCTCCAGGAACTCTCTACGCTAACGAATCTTACCAGCTTCAGGTTGATTTTCCTGAGCATTACCCCATGGAAGCTCCACAGgtagccaaaaacattatcaaaatttgcatttctttcttttttttttttttttttgcatgctttaaatttccatttgtttttatgctttctgacttggttggtgtcattggacag

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|86046991|gb|DR342746.1|DR342746
EST:     ACCAACTTCAAGTTGAGTTCCCTGAGCATTATCCTATGGAAGCTCCACAG                         GTTATCTTTCAGCATCCAGCTCCACTTCATCCTCATATTTACAGCAACGGT
genomic: ACCAACTTCAAGTTGAGTTCCCTGAGCATTATCCTATGGAAGCTCCACAGgttcgtcctc ... tataaaacagGTTATCTTTCAGCATCCAGCTCCACTTCATCCTCATATTTACAGCAACGGT
EST: gi|86046992|gb|DR342747.1|DR342747
EST:     ACCAACTTCAAGTTGAGTTCCCTGAGCATTATCCTATGGAAGCTCCACAG                         GTTATCTTTCAGCATCCAGCTCCACTTCATCCTCATATTTACAGCAACGGT
genomic: ACCAACTTCAAGTTGAGTTCCCTGAGCATTATCCTATGGAAGCTCCACAGgttcgtcctc ... tataaaacagGTTATCTTTCAGCATCCAGCTCCACTTCATCCTCATATTTACAGCAACGGT
EST: gi|86046995|gb|DR342750.1|DR342750
EST:     ACCAACTTCAAGTTGAGTTCCCTGAGCATTATCCTATGGAAGCTCCACAG                         GTTATCTTTCAGCATCCAGCTCCACTTCATCCTCATATTTACAGCAACGGT
genomic: ACCAACTTCAAGTTGAGTTCCCTGAGCATTATCCTATGGAAGCTCCACAGgttcgtcctc ... tataaaacagGTTATCTTTCAGCATCCAGCTCCACTTCATCCTCATATTTACAGCAACGGT
EST: gi|86081006|gb|DR376763.1|DR376763
EST:     ACCAACTTCAAGTTGAGTTCCCTGAGCATTATCCTATGGAAGCTCCACAG                         GTTATCTTTCAGCATCCAGCTCCACTTCATCCTCATATTTACAGCAACGGT
genomic: ACCAACTTCAAGTTGAGTTCCCTGAGCATTATCCTATGGAAGCTCCACAGgttcgtcctc ... tataaaacagGTTATCTTTCAGCATCCAGCTCCACTTCATCCTCATATTTACAGCAACGGT
EST: gi|86046993|gb|DR342748.1|DR342748
EST:     ACCAACTTCAAGTTGAGTTCCCTGAGCATTATCCTATGGAAGCTCCACAG                         GTTATCTTTCAGCATCCAGCTCCACTTCATCCTCATATTTACAGCAACGGT
genomic: ACCAACTTCAAGTTGAGTTCCCTGAGCATTATCCTATGGAAGCTCCACAGgttcgtcctc ... tataaaacagGTTATCTTTCAGCATCCAGCTCCACTTCATCCTCATATTTACAGCAACGGT
EST: gi|86046996|gb|DR342751.1|DR342751
EST:     ACCAACTTCAAGTTGAGTTCCCTGAGCATTATCCTATGGAAGCTCCACAG                         GTTATCTTTCAGCATCCAGCTCCACTTCATCCTCATATTTACAGCAACGGT
genomic: ACCAACTTCAAGTTGAGTTCCCTGAGCATTATCCTATGGAAGCTCCACAGgttcgtcctc ... tataaaacagGTTATCTTTCAGCATCCAGCTCCACTTCATCCTCATATTTACAGCAACGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATCATTGAAGTGCATGGAGTTCCAGGAACTCTTTACGCCAATGAAACTTACCAACTTCAAGTTGAGTTCCCTGAGCATTATCCTATGGAAGCTCCACAGgttcgtcctctaactccttttgttaatacttaacgatacttaatcatcgcatcaatctcataacccgatggttccacatataaaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG