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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttaatgttacggtctcaaatagatctttgcaatgtacgcaatgtgttcaaatcaatcataaactttatatgctctatgttcattatagGAGATCAACCATGCTGGTGCCGGTGGATTATGGGCCGAACTTGTTAGCAACAGAG

Basic information

species Arabidopsis thaliana
transcript AT3G10740.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G10740.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 2
-----------------------------------------------gtttgttaatgttacggtctcaaatagatctttgcaatgtacgcaatgtgttcaaatcaatcataaacttta-tatgctct-atg-----ttc---------attatagGAGATCAACCATGCTGGTGCCGGTGGATTATGGGCCGAACTTGTTAGCAACAGAG
                                                | |     |||      |||    |  |  ||   ||||    |||  || ||  |  |  | |   || | ||||  || |||     |||         ||| ||||| ||||||||||| || || |||||| ||||||| ||||||||||| |||||||
gtaaaccgtaagatacatatagtaattttgttttgcacaattgcattatatcactttgtcctttcctctggcactttgttagcatgtctagaataagt-caggtagactacatgtttcactatgtcctgatggcaatttcttggctaatattgtagGAAATCAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG

upper sequence: AT3G10740.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os11g03730.2 (Oryza sativa), 3'ss of exon 2
----------------------------------------------------------------------gtttgttaatgttacggt-ctcaaatagatc--tttgc-------aatgtacgcaatgtgttcaaat-caatcataaact--ttata-tgctctatgtt--cattatagGAGATCAACCATGCTGGTGCCGGTGGATTATGGGCCGAACTTGTTAGCAACAGAG
                                                                      |    ||  ||||| | | ||||| |  ||     |||       |||  | | |   | | ||  | | | |||   ||  | ||| || |||  | |   ||| ||||| ||||||||||| || || |||||| ||||||| ||||||||||| |||||||
gtaagccgtgagacatatacagtaattctgtttttcacaattgcactgtatcactatatcctttcctctggcacttttttgttaggatgctcaagtgcattagcatgcccagaataatccaggtagattatacatgttccaccatgtcctgatgataatgatcttggctaatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG

upper sequence: AT3G10740.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os07g48750.1 (Oryza sativa), 3'ss of exon 3
------------gtttgt-taatgttacggtctcaaat-agatctttgcaatgtacgcaatgtgttcaaatcaatcataaactttatatgctctatgttcattatagGAGATCAACCATGCTGGTGCCGGTGGATTATGGGCCGAACTTGTTAGCAACAGAG
             | | | || |       | |||||| || |   | | |  |        || |   | |    ||| | ||| |  | ||||      || |||||||||||||||||||| || ||||| || ||||| || ||||| || |||||||
tgcaacattttcctatatatagtacctgcatatcaaatgaggttgcttcgacttctattccatgctgggagcttgaatata-tttgtg-gttctac-----ttgtagGAGATCAACCATGCTGGGGCTGGTGGGTTGTGGGCAGAGCTTGTAAGTAACAGAG

upper sequence: AT3G10740.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G077299_T01 (Zea mays), 3'ss of exon 2
---------------------gtttgttaatgttac-ggtctcaaatagatctttgcaatgtacgcaatgtgttcaaatcaatcataaac-----tttatatgctc----tatgttcattatagGAGATCAACCATGCTGGTGCCGGTGGATTATGGGCCGAACTTGTTAGCAACAGAG
                            |   |||  | ||| | |  ||| | | || |||| ||    || || || ||  | |   |      | | ||   |    |   |||| |  |||||||||||||||| || || |||||  ||||||| ||||||||||| |||||||
gtgagacagtgatttcttggtacacaccagccttattgatcttacaaggatttgtcca-tgtaagcggaatggtccaaacacacttggtcgtgttctcagataaccaggttgctttcactgcagGAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAG

upper sequence: AT3G10740.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G27490.1 (Glycine max), 3'ss of exon 1
------gtttgttaatgttacggtc----tcaaatagatctttgcaatgtacgcaatgtgttcaaatcaatcataaactttatatgctctatgttcattatagGAGATCAACCATGCTGGTGCCGGTGGATTATGGGCCGAACTTGTTAGCAACAGAG
       |||   ||||  | |||     | || |||||  |  |  | |     || |||| ||||   ||| ||    |  | | | ||   |  |   |||||||||||||||| ||||| |||||||| ||||| || ||||||| ||||||||
agtttcctttcacaatgc-atggttatttttaactagatgatatctttttttattat-tgttaaaatgtttcaaaagtgatcaaagttttaaacttgt-gcagGAGATCAACCATGCCGGTGCTGGTGGATTGTGGGCAGAGCTTGTTAACAACAGAG

upper sequence: AT3G10740.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 3
-gtttgtt---aatgttacggtctcaaatagatctttgcaatgtacgca---atgtgttcaaatcaatcat-aaactttatatgctctatgttcattatagGAGATCAACCATGCTGGTGCCGGTGGATTATGGGCCGAACTTGTTAGCAACAGAG
 | |||||   |||  |  |   | |   |  |  |  || ||||       || |||| |  |  |  ||  | |||| | ||   | | ||  |  ||||||||||||||||| || || |||||| | ||||| || ||||| ||||||||||
gggttgtttcgaattctgagcaattagcaatttactgccactgtaattgtgtatatgttgattttgaagattgagctttgtttgaaatgtctttgt-gtagGAGATCAACCATGCAGGAGCTGGTGGACTGTGGGCAGAGCTTGTCAGCAACAGAG

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|116444622|gb|EG487214.1|EG487214
EST:     ATGGAGGTGGACGACCCATTCCTGAAACGCTATTTGGGATTTTCTTCGAG                         GAGATCAACCATGCTGGTGCCGGTGGATTATGGGTCGAACTTGTTAGCAAC
genomic: ATGGAGGTGGACGACCCATTCCTGAAACGCTATTTGGGATTTTCTTCGAGgtttgttaat ... ttcattatagGAGATCAACCATGCTGGTGCCGGTGGATTATGGGCCGAACTTGTTAGCAAC
EST: gi|124941761|gb|EL018086.1|EL018086
EST:     GATTTTCTTCGAG                         GAGATCAACCATGCTGGTGCCGGTGGATTATGGGCCGAACTTGTTAGTAAC
genomic: GATTTTCTTCGAGgtttgttaat ... ttcattatagGAGATCAACCATGCTGGTGCCGGTGGATTATGGGCCGAACTTGTTAGCAAC
EST: gi|124815264|gb|EH900130.1|EH900130
EST:     ATGGAGGTGGACGACCCATTCCTGAAACGCTATTTGGGATTTTCTTCGAG                         GAGATCAACCATGCTGGTGCCGGTGGATTATGGGCCG
genomic: ATGGAGGTGGACGACCCATTCCTGAAACGCTATTTGGGATTTTCTTCGAGgtttgttaat ... ttcattatagGAGATCAACCATGCTGGTGCCGGTGGATTATGGGCCG
EST: gi|124930720|gb|EL008143.1|EL008143
EST:     ATGGAGGTGGACGACCCATTCCTGAAACGCTATTTGGGATTTTCTTCGAG                         GAGATCAACCATGCTGG
genomic: ATGGAGGTGGACGACCCATTCCTGAAACGCTATTTGGGATTTTCTTCGAGgtttgttaat ... ttcattatagGAGATCAACCATGCTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacgcaatgtgttcaaatcaatcataaactttatatgctctatgttcattatagGAGATCAACCATGCTGGTGCCGGTGGATTATGGGCCGAACTTGTTAGCAACAGAG
               aaatcaatcataaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttaatgttacggtctcaaatagatctttgcaatgtacgcaatgtgttcaaatcaatcataaactttatatgctctatgttcattatagGAGATCAACCATGCTGGTGCCGGTGGATTATGGGCCGAACTTGTTAGCAACAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA