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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataattattcttccaagaatctaccaaagttctatattccatctcttcaagatttctgttcaagctttataagccttctgagagtttgttctttttgcagATCCACTGGTTCTCCATCTTTAACTCGTTCATGATGGTTATTTTCCTCACCGGTTTGGTCTCAATGATATTGATGAGGACTCTCAGAAATGATTATGCGA

Basic information

species Arabidopsis thaliana
transcript AT1G10950.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os11g07910.1 (Oryza sativa), 3'ss of exon 6
-----------------------------------------------------------ataa------ttattcttccaagaatctaccaaagttctatattccatct-cttcaagatttctgt----tcaagctttataagccttctgagagtt-------tgttctttttgcagATCCACTGGTTCTCCATCTTTAACTCGTTCATGATGGTTATTTTCCTCACCGGTTTGGTCTCAATGATATTGATGAGGACTCTCAGAAATGATTATGCGA
                                                           ||||      ||  |||     |  | |  ||||||  || | |  || | ||| || | |   |     |  |  |||| |||    || ||   |         |||  | | |||||||| |||||||||||||| || ||||||||||||||||||||| | || || ||||| |||||||||||||||||||| || ||||||||||||||||
gtaatctttgttcgaaccaacattactttttatgtcttttgctggacagtttttgtgctataatttactttgctctgtggtggttttgacaaagtggtagactttattttctttaaaactctcgaggaattgaaatttacaagaaaactaagttctgctgcaaccttccatgttcagATCCATTGGTTCTCCATCTTCAATTCGTTCATGATGGTTATTTTCTTGACTGGATTGGTATCAATGATATTGATGAGGACGCTGAGAAATGATTATGCGA

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os12g07670.1 (Oryza sativa), 3'ss of exon 6
---------------------------------------------------------------------------ataattattcttccaagaatctaccaa-agttctatattccatctcttcaagatttctgttcaagctttataagccttctgagagtttgttctttttgcagATCCACTGGTTCTCCATCTTTAACTCGTTCATGATGGTTATTTTCCTCACCGGTTTGGTCTCAATGATATTGATGAGGACTCTCAGAAATGATTATGCGA
                                                                           | ||  | | ||    | | | ||    || |  ||  ||    ||||   ||    |||||||   || | |    | ||  | ||| |  | ||  ||||| || ||||||||||| || || || ||||||||||||||||||||||| |||||||| ||||||||||||||| ||||  | |||||||| ||||| |
gtaatattttcccactccaaagaaaaaaaaactatgcgtaacatgcagctctcagcttgcttacttatgtgaaagagaaaaaatgttaattgtaacaacagggagctgaatcgtcttgttctttttgaaagttgttcaaaggttctgacttctatgcaaatttctaatgtt--cagATTCATTGGTTCTCCATTTTCAATTCTTTCATGATGGTTATTTTCCTCACTGGTTTGGTTTCAATGATATTGATGCGGACATTGAGAAATGACTATGCAA

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os02g34690.1 (Oryza sativa), 3'ss of exon 6
-----------------------------------------------------------ataattattcttcca-agaatctaccaaagttctatattccatctcttcaagatttctgttcaagctttataagccttctgagagtttgttctttttgcagATCCACTGGTTCTCCATCTTTAACTCGTTCATGATGGTTATTTTCCTCACCGGTTTGGTCTCAATGATATTGATGAGGACTCTCAGAAATGATTATGCGA
                                                            |    | | ||||| | ||   |  |    |  ||  || || ||      || |||        ||  |  | |  | || | |   || || | ||||||||| |||||||| ||||| || || |||||||||||||| || ||||| ||  | || |||||||| |||||| | ||||| |||||||| ||||| |
gtaagaactcagtttctgcaattaaagcctggttctgcaccttggttcttatgtattttgttgccaattttccacataaaaaattatgccttgattctcaatttcccatgtatatcttgcagcatttcctctgaccacagataatccatt-ttatggcagATCCATTGGTTCTCAATCTTCAATTCTTTCATGATGGTTATCTTTCTCACTGGGCTAGTGTCAATGATTTTGATGCGCACTCTAAGAAATGACTATGCAA

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G026231_T01 (Zea mays), 3'ss of exon 6
---ataattattcttccaagaatctaccaaagttctatattccatctcttcaagatttctgttcaagct--ttataagccttctgagagtttgttctt--------tttgcagATCCACTGGTTCTCCATCTTTAACTCGTTCATGATGGTTATTTTCCTCACCGGTTTGGTCTCAATGATATTGATGAGGACTCTCAGAAATGATTATGCGA
   ||| || |  || ||   | | |  ||  |||||  ||| ||           |||  ||  | ||   ||| ||   ||  |   | ||||| |        ||| ||||| |||||||||||||| || ||||| |||||||||||||||||||| || |||||||| || |||||||||||| ||||| | |||||||||||||| |
gtgatactt-tgtttgcagacaaccagaaactttctagtttctattcagctgtatcttcccttttaactaactattagaaatcctaagctctgttcatatttctcattttcagATTCACTGGTTCTCCATTTTCAACTCTTTCATGATGGTTATTTTCCTAACTGGTTTGGTTTCGATGATATTGATGCGGACTTTGAGAAATGATTATGCCA

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G420310_T01 (Zea mays), 3'ss of exon 6
---ataattattcttccaagaatctaccaaagttctatattccatctcttcaagatttctgttcaagct--ttataagccttctgagagtttgttctt--------tttgcagATCCACTGGTTCTCCATCTTTAACTCGTTCATGATGGTTATTTTCCTCACCGGTTTGGTCTCAATGATATTGATGAGGACTCTCAGAAATGATTATGCGA
   ||| ||  | |    | || | || ||  | |||  |||  |           |||  ||  | ||   ||| ||   ||  |   | ||||| |        ||| ||||| |||||||||||||| || ||||| |||||||||||||||||||| || |||||||| || |||||||||||| ||||| | ||||| |||||||| |
gtgatactttgtttgtagacaaccgac-aacttcctagtttctgttcagctgtaccttcccttttaactagctattagaagtcctaagctctgttcatatttctcatttccagATTCACTGGTTCTCCATTTTCAACTCTTTCATGATGGTTATTTTCCTAACTGGTTTGGTTTCGATGATATTGATGCGGACTTTGAGAAACGATTATGCCA

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G087212_T01 (Zea mays), 3'ss of exon 6
ataattattcttccaagaatctaccaaagttctatattccatct-cttcaagatttctgttcaagctttataagccttctgagagtttgttctttttgcagATCCACTGGTTCTCCATCTTTAACTCGTTCATGATGGTTATTTTCCTCACCGGTTTGGTCTCAATGATATTGATGAGGACTCTCAGAAATGATTATGCGA
| | || | |  |   |    | ||   | |||   |    |   | |    || | | |  |    ||| |||    ||||   ||| |||  | |  |||| || |||||||||||||| || || |||||||||||||||||| | || ||||| || |||||||||||||||||||| || |||||||||||||| |
acactt-tgccactttggtctttcctcggctctgactaatgtggaccttgctatctgtctgaagtaattacaagatggctgacccttttttccatgtttagATTCATTGGTTCTCCATCTTCAATTCATTCATGATGGTTATTTTCTTGACTGGTTTAGTGTCAATGATATTGATGAGGACACTAAGAAATGATTATGCAA

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G165631_T01 (Zea mays), 3'ss of exon 5
---------------------------------------------------------------ata-attattcttccaagaatctaccaa-agttctatattccatctcttcaagatttctgttcaagctttataagccttctgagagtttgttctttttgcagATCCACTGGTTCTCCATCTTTAACTCGTTCATGATGGTTATTTTCCTCACCGGTTTGGTCTCAATGATATTGATGAGGACTCTCAGAAATGATTATGCGA
                                                               ||| |  |    |  ||  |  | |||  || |   |  | ||| | |  ||||       |||    || | |   ||||     ||| || |  |||||||| || |||||||| || || || || |||||||||||||| || ||||| ||  | || ||||||||| ||||| ||||||| |||||||||||||| |
gtaatataggtatatatttttgcaattaaggagatctttgcagcttggctcctcgtaattacaatacagaaccagtataattacttcccattagctgcgttctacatgtttgaaagagcctgaatcatatcttcttaat-ttctagttatttcttgtacttgcagATTCATTGGTTCTCAATTTTCAATTCTTTCATGATGGTTATCTTTCTCACTGGACTAGTGTCAATGATACTGATGCGGACTCTAAGAAATGATTATGCAA

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA05G30210.1 (Glycine max), 3'ss of exon 6
----------------------ataattattcttccaagaatctaccaaagttctatat-tccatctcttcaagatttctgttcaagcttta----taagccttctgagagtttgttctttttgc----agATCCACTGGTTCTCCATCTTTAACTCGTTCATGATGGTTATTTTCCTCACCGGTTTGGTCTCAATGATATTGATGAGGACTCTCAGAAATGATTATGCGA
                        |||  |  |    |   | |    || | |||| | | ||||  |    |  | ||     |||| |     | ||  || ||    |||||| | |||      |||| || ||||||||||| |||||||| ||||||||||| || ||||| || |||||||| ||||||||||||||| | ||||| |||||||| ||||| |
gtacagctttgcttttaaaattgaaatggtgttgtttatggtttggtgaattgctatgtattcatccatgttgg--tcctaccatagctctgccactgagaattttgctcctttgttttctttttccctagATTCATTGGTTCTCCATTTTTAACTCTTTCATGATGGTCATCTTCCTTACTGGTTTGGTGTCAATGATATTGATGCGAACTCTGAGAAATGACTATGCAA

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G13370.1 (Glycine max), 3'ss of exon 6
----------------------ataattattcttccaagaatctaccaaagttctatat-tccatctcttcaagatttctgttcaagctttat----aagccttctgagagtttgttctttttgc----agATCCACTGGTTCTCCATCTTTAACTCGTTCATGATGGTTATTTTCCTCACCGGTTTGGTCTCAATGATATTGATGAGGACTCTCAGAAATGATTATGCGA
                        |||  |  |    |   | |    || | |||| | | ||||  |    |  | ||     | || | |     ||  || ||    |||||| | |||      |||| || ||||||||||| |||||||| ||||||||||| || ||||| || || ||||| ||||||||||||||| | ||||| |||||||| ||||| |
gtacaactttgcttttaaaattgaaatggtgttgtttatggtttggtgaattgctatgtattcatccatgttgg--tcctaccatatctctgtcactgagtattttgctcctttgttttctttttccctagATTCATTGGTTCTCCATTTTTAACTCTTTCATGATGGTCATCTTCCTTACTGGATTGGTGTCAATGATATTGATGCGAACTCTGAGAAATGACTATGCAA

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 6
--------------------ataattattct---tccaagaatctaccaaagtt--ctatattccatctcttca------agatttctgttcaagctttat----aagccttctgagagt-ttgttctttttgcagATCCACTGGTTCTCCATCTTTAACTCGTTCATGATGGTTATTTTCCTCACCGGTTTGGTCTCAATGATATTGATGAGGACTCTCAGAAATGATTATGCGA
                    ||   |||| |   |  ||||       |  |||   ||  | | |  | ||||       |  | || |   |||  | |     |||   ||  ||   || |||||| || |||| |||||||||||||| ||||| || || |||||||| || ||||| || || ||||| ||||||||||| ||| | ||  | |||||||| ||||| |
gtgaaaatcattgctgctagatttgtattttagattgaagaggtgtttattgttggttacctgctacgtgttcattcatgtggatcctatcttagccatgtcactgagcgaactttgatcatttttctttctgtagATTCACTGGTTCTCCATTTTTAATTCTTTTATGATGGTCATCTTCCTTACTGGATTGGTGTCAATGATATTAATGCGAACGTTGAGAAATGACTATGCAA

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 6
-----------------------ataattattcttccaagaatctaccaaagtt--ctatattccatctcttcaag-atttctgttcaagctttataagccttctgagag---tttg-------ttctttttgcagATCCACTGGTTCTCCATCTTTAACTCGTTCATGATGGTTATTTTCCTCACCGGTTTGGTCTCAATGATATTGATGAGGACTCTCAGAAATGATTATGCGA
                          ||| |   |  ||||       |  |||   ||  | | || | ||||   || |   | | | |||    |     |||||||   ||||       |||||| || |||| |||||||||||||| ||||| || || |||||||| || ||||| || || ||||| ||||||||||| ||| | ||  | |||||||| ||||| |
gtgaaaatcattgctgctagctttgtattttagattgaagaggtgtttattgttggttacctgctatgtgttcagtcatgtggatcctatcttagccatgtcactgagagaactttgatccgttttctttctgtagATTCACTGGTTCTCCATTTTTAATTCTTTTATGATGGTCATCTTCCTTACTGGATTGGTGTCAATGATATTAATGCGAACATTGAGAAATGACTATGCAA

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 6
ataattattcttccaagaatctaccaaagttctatattccatctcttcaagatttctgttcaagctttataagcctt-ctgagagtttgttctt---tttgcagATCCACTGGTTCTCCATCTTTAACTCGTTCATGATGGTTATTTTCCTCACCGGTTTGGTCTCAATGATATTGATGAGGACTCTCAGAAATGATTATGCGA
 |||  ||| | |  | | | ||    | ||| ||| ||    | ||       | |  | ||  |  | |        || || |   ||||    | ||||||| || ||||||||||| ||||| || |||||||||||||| |||||||| |||||||| |||||||| || ||| | || || |||||||| ||||| |
ttaaggattgt-cttatattttatatgaattcaataatct---tattttgttcatttaataaacttccacatattgagttgtgaatgcattctgcaatgtgcagATTCATTGGTTCTCCATTTTTAATTCTTTCATGATGGTTATCTTCCTCACTGGTTTGGTGTCAATGATCTTAATGCGAACCCTTAGAAATGACTATGCTA

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv18s0041g00680.t01 (Vitis vinifera), 3'ss of exon 6
--ataattattcttccaagaatctaccaaagttctatattccatctcttcaagatttctgttcaagctttataagccttctgag--agtttgttctttttgcagATCCACTGGTTCTCCATCTTTAACTCGTTCATGATGGTTATTTTCCTCACCGGTTTGGTCTCAATGATATTGATGAGGACTCTCAGAAATGATTATGCGA
   ||       |||||  |||     ||| ||  ||  | | ||  ||  | |||  | ||  |      |     |||| ||  || ||   |||  |||||||||| |||||||| ||||| || || ||||||||||||||||||||||| || ||||| || |||||||| ||| | |||||  ||||||||||||| |
tgctaggaggaattccattaatga---aaaatttcatgctacttca-tttgatattgtttttgtattccagtgctttttctaagcaagctttaacttggtgcagATCCATTGGTTCTCAATCTTCAATTCATTCATGATGGTTATTTTCCTCACTGGATTGGTGTCTATGATATTAATGCGAACTCTTCGAAATGATTATGCCA

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S438_26V6.1 (Physcomitrella patens), 3'ss of exon 6
------------------------------------------------------------------------------------------------------ataattattcttccaagaatctaccaaagttctatattccatctcttcaagatttctgttcaagctttataagccttctgagagtttgttctttttgcagATCCACTGGTTCTCCATCTTTAACTCGTTCATGATGGTTATTTTCCTCACCGGTTTGGTCTCAATGATATTGATGAGGACTCTCAGAAATGATTATGCGA
                                                                                                      |   | ||        ||||    | | ||      ||  |  | |    |  ||  |||   | || ||        || | |   |      |  ||||| || |||||||| ||||| ||||||||||||||||| || || || || ||  |||| || |||||  ||||| | || ||| | || ||||||||||
gtgggtgtgaggagggagcggagggctgagttgcaagatttgtgtagcgagtgtgggtggagacgggagcttgaagctacatgcgagttagtggtgtgttggaggttcatgggatggtgaatgggacga-gtcgcgagtttgacgtgtgggggtgtttggtttgtggttgatg------ttgggtggcggccgcgatgacagATACATTGGTTCTCTATCTTCAACTCGTTCATGATGGTGATATTTCTGACGGGGCTGGTATCGATGATTCTGATGCGCACCCTCCGCAACGATTATGCGA

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|124744897|gb|EH836059.1|EH836059
EST:     TTATCCGTTCTTTGAACACCAG                         ATCCACTGGTTCTCCATCTTTAACTCGTTCATGATGGTTATTTTCCTCACC
genomic: TTATCCGTTCTTTGAACACCAGgtaactttta ... ctttttgcagATCCACTGGTTCTCCATCTTTAACTCGTTCATGATGGTTATTTTCCTCACC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaagatttctgttcaagctttataagccttctgagagtttgttctttttgcagATCCACTGGTTCTCCATCTTTAACTCGTTCATGATGGTTATTTTCCTCACCGGTTTGGTCTCAATGATATTGATGAGGACTCTCAGAAATGATTATGCGA
                                       tttgttctttttgc  CT-rich tract
                    tttataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataattattcttccaagaatctaccaaagttctatattccatctcttcaagatttctgttcaagctttataagccttctgagagtttgttctttttgcagATCCACTGGTTCTCCATCTTTAACTCGTTCATGATGGTTATTTTCCTCACCGGTTTGGTCTCAATGATATTGATGAGGACTCTCAGAAATGATTATGCGA

- - - - - - -caagaat
- - - - - - - - - - -taccaaa
- - - - - - - - - - - - - - - - - - - -catctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agtttgt