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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaattgctagatctttcatttttttttaaaaatgcaaaaaccttatacgacttttaaactatatgctcaagttctagttgcagatggttaacttttttagtagtaccaatagcttaatttctgtttgtttgcagCCCAATTGTATCATATTGGCTATATCTCCTGCCAACCAAGACATTGCCACATCAGATGCAATTAAGCTCGCAAAAGATGTCGATCCAACAG

Basic information

species Arabidopsis thaliana
transcript AT3G60190.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G60190.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os09g39960.1 (Oryza sativa), 3'ss of exon 6
gtgagaattgctagatctttcatttttttttaaaaatgcaaaaaccttatacgacttttaaactatatgctcaagttctagt-tgcagatggttaacttttttagtagtaccaatagcttaatttctgt--ttgtttgcagCCCAATTGTATCATATTGGCTATATCTCCTGCCAACCAAGACATTGCCACATCAGATGCAATTAAGCTCGCAAAAGATGTCGATCCAACAG
                                      |||| | |||       | ||| | | | |  | || |||| || | || ||  || |    ||    |   | ||||| ||| ||| | |  |  ||||||||||||||||||||| |||||||||||||| || ||||| ||||||||||| || ||||| ||||||||  | || || || || ||| |||
------------------------------------cccaaataactt---taggtgttatattgtttaattaatttctggtgttcaaat--ttgagaacttatacaaggctaataggttactttgtatgatattttgcagCCCAATTGTATCATTTTGGCTATATCTCCAGCAAACCAGGACATTGCCACTTCTGATGCCATTAAGCTTTCGAAGGAGGTTGACCCATCAG

upper sequence: AT3G60190.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os10g41820.1 (Oryza sativa), 3'ss of exon 6
gtgagaattgctagatctttcatttttttttaaaaatgcaaaaaccttatacgacttttaaactatatgctcaagttctagttgcagatggttaactttttta-gtagtaccaatagcttaatttctgtttgtttgcagCCCAATTGTATCATATTGGCTATATCTCCTGCCAACCAAGACATTGCCACATCAGATGCAATTAAGCTCGCAAAAGATGTCGATCCAACAG
                                ||  | ||| |     |||   |||   |||  |       | |   |  ||   ||   |   |   ||| | |||  || |    || |||||     |||| |||| || || |||||| | ||||||||||||||||| ||||| || || ||||| ||||| |||||||| ||   |||||| |||||||| |
--------------------------------aagctccaagatgaccatat--cttaacaacattgcaggagactatgaagtgtgcatttgtgtgtaccttatgcagtgacatttttgtattttct-----tttgtagCCAAACTGCATCATACTTGCTATATCTCCTGCCAATCAAGATATAGCAACATCTGATGCTATTAAGCTTGCTCGAGATGTTGATCCAACTG

upper sequence: AT3G60190.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G070899_T01 (Zea mays), 3'ss of exon 6
gtgagaattgctagatctttcatttttttttaaaaatgcaaaaaccttatacgacttttaaactatatgctcaagttctagttgcagatggttaacttttttagtagtaccaatag-----cttaa--tttctgtttgtttgcagCCCAATTGTATCATATTGGCTATATCTCCTGCCAACCAAGACATTGCCACATCAGATGCAATTAAGCTCGCAAAAGATGTCGATCCAACAG
                                            | |  ||   ||  |  |   | ||      | ||  ||||| | | |||   || | | |   |  || |      ||| |  ||| | ||| ||||||||| |||||||| ||||||||||||||||||||||| ||||| || || |||||||||||||| ||||| ||    || || |||||||| |
--------------------------------------------cttcctatacctactctatgttttggcactttgcttattgcatacgatta-tattctcaatcacattaacaaggcgtcttgaattttgtatttctttgcagCCGAATTGTATTATATTGGCTATATCTCCTGCCAATCAAGATATAGCGACATCAGATGCAATCAAGCTTGCCCGGGAAGTGGATCCAACTG

upper sequence: AT3G60190.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G055883_T02 (Zea mays), 3'ss of exon 4
gtgagaatt--gctagatc---tttcatttttttttaaaaatgcaaaaaccttatacgactttta-aactatatgctcaagttctagttgcagatggttaacttttttagtagtaccaat---agcttaatttctgtttg-----tttgcagCCCAATTGTATCATATTGGCTATATCTCCTGCCAACCAAGACATTGCCACATCAGATGCAATTAAGCTCGCAAAAGATGTCGATCCAACAG
|| | || |   ||  ||    ||  ||   |  || || |||||  | |      |  ||  || ||| ||| ||     |    | ||    |  ||   |||     | ||| | |    ||  ||| || | | |      |||||||||||| ||||| || |||||||||||||| || || || || ||||| || || ||||||||||||||| ||||||| || ||||||||||
gtaacaaattaacttaatactgttctatcactgattcaatatgcatgaccaaccacctgctgatataacaataggcctggctgtgtggtggtattctttcgttttcaccttggtatccaagtgagaataagttttttatacatgttttgcagCCCAACTGTATTATTTTGGCTATATCTCCAGCAAATCAGGATATTGCAACTTCTGATGCAATTAAGCTCTCAAAAGAAGTTGATCCAACAG

upper sequence: AT3G60190.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA07G12850.1 (Glycine max), 3'ss of exon 6
gtgagaattgctagatctttcatttttttttaaaaatgcaaaaaccttatacgacttttaaactatatgctcaagttctagttgcagatggttaacttttttagtagtaccaatagcttaatttctgtttgtttgcagCCCAATTGTATCATATTGGCTATATCTCCTGCCAACCAAGACATTGCCACATCAGATGCAATTAAGCTCGCAAAAGATGTCGATCCAACAG
                               | | ||     ||   | ||| | |  |||| || ||    ||||  |  | |||    | || | | |||  |   |||||||      ||  || || ||  ||||| |||||||| ||| |||| |||||||| |||||||||||||| || || || ||||| ||||| ||  | |  || || |||||  |||
------------------------------aatacatttgtgaagtgtttactaatgataaatta-atcaggaagtggtgatggcatcaagata-catatttgctttaaccaatac-----ttgttgctt-ttgacagCCTAATTGTATTATACTGGCAATATCTCCAGCCAACCAAGACATAGCAACTTCTGATGCTATTAAACTTTCGAGGGAGGTGGATCCCTCAG

upper sequence: AT3G60190.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA03G24610.1 (Glycine max), 3'ss of exon 6
gtgagaattgctagatctttcatttttttttaaaaatgcaaaaaccttatacgacttttaaactatatgctcaagttctagttgcagatggttaacttttttagtagtaccaatagcttaatttctgtttgtttgcagCCCAATTGTATCATATTGGCTATATCTCCTGCCAACCAAGACATTGCCACATCAGATGCAATTAAGCTCGCAAAAGATGTCGATCCAACAG
                              | | | ||   ||   || ||| | |  |||| ||       ||||  |  | ||     |||| | | |||  |   ||||| |       || |   | ||  ||||| |||||||| ||| |||| |||||||| |||||||||||||| || || || ||||| ||||| ||  | |  || || |||||  |||
-----------------------------attacattgttgaagtgtt-tactattgataaattaggcagg-aagtggtgatggcgtcaagtta-catatttgctttaaccaaca------cttgttacttttgacagCCTAATTGTATTATACTGGCAATATCTCCAGCCAACCAAGACATAGCGACTTCTGATGCTATTAAACTTTCGAGGGAGGTGGATCCCTCAG

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|164061609|gb|ES009388.1|ES009388
EST:     ATGGTTCGCACATATGTTGATAAG                         CCCAATTGTATCATATTGGCTATATCTCCTGCCAACCAAGACATTGCCACA
genomic: ATGGTTCGCACATATGTTGATAAGgtgagaattg ... ttgtttgcagCCCAATTGTATCATATTGGCTATATCTCCTGCCAACCAAGACATTGCCACA
EST: gi|164154345|gb|ES117068.1|ES117068
EST:     AAACCATTGCTGAGGATATCGAATCCATGGTTCGCACATATGTTGATAAG                         CCCAATTGTATC
genomic: AAACCATTGCTGAGGATATCGAATCCATGGTTCGCACATATGTTGATAAGgtgagaattg ... ttgtttgcagCCCAATTGTATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcagatggttaacttttttagtagtaccaatagcttaatttctgtttgtttgcagCCCAATTGTATCATATTGGCTATATCTCCTGCCAACCAAGACATTGCCACATCAGATGCAATTAAGCTCGCAAAAGATGTCGATCCAACAG
                                      tttctgttt  CT-rich tract
        ttaacttttttagta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaattgctagatctttcatttttttttaaaaatgcaaaaaccttatacgacttttaaactatatgctcaagttctagttgcagatggttaacttttttagtagtaccaatagcttaatttctgtttgtttgcagCCCAATTGTATCATATTGGCTATATCTCCTGCCAACCAAGACATTGCCACATCAGATGCAATTAAGCTCGCAAAAGATGTCGATCCAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG