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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatacctgatcttactgagcacaaaagtttccccttacaggttttagatttcaattgtgtatgctttatagcccaatgtatctcatttatttcctggttaatcttttggtgcttaatagGTGGATGACCTGGAAGAAGTCAGCGAGTACTACCAGAACAGAGGGTGCTTCAATGAATTAATCTCACTTATGGAGAGTGGACTTGGGCTTGAACGTGCTC

Basic information

species Arabidopsis thaliana
transcript AT3G08530.1
intron # 24
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 24
gtgaatacctgatcttactgagcacaaaagtttccccttacaggttttagatttcaattgtgtatgctttatagcccaatgtatctcatttatttcctggttaatcttttggtgcttaatagGTGGATGACCTGGAAGAAGTCAGCGAGTACTACCAGAACAGAGGGTGCTTCAATGAATTAATCTCACTTATGGAGAGTGGACTTGGGCTTGAACGTGCTC
               || |    |||  ||   ||  ||| |     || |    | ||  |||    |  |  |      |||||   || ||| ||        |||| ||     |||||| |||||  |||| ||||| || || ||||||||||||||||| || ||||||||| | || || || ||||| ||||| || || || || |||||||
--------------gta-tatatacaggagcaacctgttagaa---ctaaaacatatttcagtacaagtcttttct-----tatctagatt-ttttctaacacccttttttgt-----atagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 24
gtgaatacctgatcttactgagcacaaaagtttccccttacaggttttagatttcaattgtgtatgctttatagcccaatgtatctcatttatttcctggttaat-cttttggtgcttaatagGTGGATGACCTGGAAGAAGTCAGCGAGTACTACCAGAACAGAGGGTGCTTCAATGAATTAATCTCACTTATGGAGAGTGGACTTGGGCTTGAACGTGCTC
                  |    | | | |     |||        |||||  | ||      ||  || |   |      | ||| || ||  |  |   |||  |  ||  |  |  |||||| |||||  |||| ||||| || || ||||||||||||||||| || ||||||||| | || || || ||||| ||||| || || || || |||||||
-----------------gtatatatacaggaccaacctg-------ttagaactaaa----acatatttcagtacaagtcttttcttatctagattttttctaacacccttttttttgtatagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 22
gtgaatacctgatcttactgagcacaaaagtttccccttacaggttttagatttcaattgtgtatgctttatagcccaatgtatctcatttatttcctggttaatcttttggtgcttaatagGTGGATGACCTGGAAGAAGTCAGCGAGTACTACCAGAACAGAGGGTGCTTCAATGAATTAATCTCACTTATGGAGAGTGGACTTGGGCTTGAACGTGCTC
||  | |  |       |  |    |  | ||| ||||     || || | |||  ||||   |   | |||      || ||| || ||| |  | |   |  ||||||  |  ||  ||||| || ||||||||||||||||| |||||||||||||||||||| ||||||| |||| | ||  | || ||||||||||| ||||| ||||||||||| |
gtatacaagtaggagggcatacttgatgatttttccct----agtctttgtttt--attgcaaagtttctatg-----atatatttc-tttctgacatacctgctcttttttttgtt--tagGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: GRMZM2G395549_T01 (Zea mays), 3'ss of exon 9
-----------------------------------------gtgaatacctgatcttactg--agcacaaaagtttcccctta------caggttttagatttcaattgtgtatgctttatagcccaatgtatctcatttatttc---ctggttaatcttttggtgcttaat--agGTGGATGACCTGGAAGAAGTCAGCGAGTACTACCAGAACAGAGGGTGCTTCAATGAATTAATCTCACTTATGGAGAGTGGACTTGGGCTTGAACGTGCTC
                                            ||||  || ||| | |   |      |  | | |   ||      ||   || |  ||||  |  | | || ||||| ||  | | | | | || ||||||   |||    | ||  |  |  ||  |  |||| |||||||| ||||||||||| |||||||||||||||||||| ||||||| |||| | ||  | || ||||||||||| ||||| ||||||||||| |
gtctgctttgcttgtgttgacgtggaggagttccgtcttgcacaaatatgtggtctcaatattattgttcagatatacaagtaggagggcatacttgatttttccctattctttgttttattgcaaagtttctatgatatatttctttctgacatagctgctctttttttgtttagGTTGATGACCTCGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 1
gtgaatacctgatcttactgagcacaaaagtttccccttacaggttttagatttcaattgtgtatgctttatagcccaatgtatctcatttatttcctggttaatcttttggtgcttaatagGTGGATGACCTGGAAGAAGTCAGCGAGTACTACCAGAACAGAGGGTGCTTCAATGAATTAATCTCACTTATGGAGAGTGGACTTGGGCTTGAACGTGCTC
||  | |  |      ||  |    | || |||    ||  ||  | |   ||  |   | |  |   | |  |    || ||| |  ||| | || |   |  | || |  |  |   ||||| |||||| ||||||||||||| ||||||||||| || ||||| |||||||||||| | ||  | || ||||||||||| ||||| ||||||||||| |
gtatacaagtaggagcacatacttgataatttt----ttgtagtatctgctttatagcagagcttctatcactgt--gatctatttttttt-tctcatatctgcttttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 1
gtgaatacctgatcttactgagcacaaaagtttccccttacaggttttagatttcaattgtgtatgctttatagcccaatgtatctcatttatttcc--------tggttaatcttttggtgcttaatagGTGGATGACCTGGAAGAAGTCAGCGAGTACTACCAGAACAGAGGGTGCTTCAATGAATTAATCTCACTTATGGAGAGTGGACTTGGGCTTGAACGTGCTC
                     | | | ||||     |  |||   || | | ||   |   || || |||||| |  |   | | | || ||||||         ||  | || || |  |  |   ||||| |||||| ||||||||||||| |||||||||||||| ||||| ||||||| |||| | ||  | || ||||||||||| ||||| ||||||||||| |
---------------------gtatacaagtaggagc--acatacttgataattttttctagtctgttttataacagagcttctatgatctatttctgtctgacatgtctgattttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAGAATAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: GRMZM2G325285_T01 (Zea mays), 3'ss of exon 14
gtgaatacctgatcttactgagcacaaaagtttccccttacaggttttagatttcaattgtgtatgctttatagcccaatgtatctcatttatttcctggttaatcttttggtgcttaatagGTGGATGACCTGGAAGAAGTCAGCGAGTACTACCAGAACAGAGGGTGCTTCAATGAATTAATCTCACTTATGGAGAGTGGACTTGGGCTTGAACGTGCTC
||  | |  |      ||  | |  || | |||    ||  ||  | |   ||  |   | |      || || | | |||       ||| | || |   |  | || |  |  |   ||||| |||||| ||||||||||||| ||||||||||| || ||||| |||||||||||| | ||  | || ||||||||||| ||||| || |||||||| |
gtatacaagtaggagcacata-cttaataattttt--ttgtagtatctgctttatagcagagc-----ttctatcactatgatctatttttttctcatatctgcttttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTAGAACGTGCAC

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 24
gtgaatacctgatcttactgagcacaaaagtttccccttacaggttttagatttcaattgtgtatgctttatagcccaatgtatctcatttatttcctg-gttaatcttttggt--gcttaatagGTGGATGACCTGGAAGAAGTCAGCGAGTACTACCAGAACAGAGGGTGCTTCAATGAATTAATCTCACTTATGGAGAGTGGACTTGGGCTTGAACGTGCTC
                   | |         | |   ||| | |   |  || |  |||   ||    | ||  |  | || || ||   |  ||  || || | | ||||  |    || ||||||||||||| ||||||||||||| || || ||||| |||||||| |||||||||||  | || || || |||||||||||  | ||| | ||||| || |
-------------------gggtgttg----tgcttgttatatgaacttaatgttgatttgctactagtgat--cttattgaatttctaatgcttattgcgtcattttttttattaatttcatagGTGGATGACTTGGAAGAAGTCAGTGAATATTACCAAAACAGAGGTTGCTTCAATGAGCTCATATCTCTCATGGAGAGTGGTTTAGGGTTAGAACGGGCAC

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 23
gtgaatacctgatcttactgagcacaaaagtttccccttacaggttttagatttcaattgtgtatgctttatagcccaatgtatctcatttatttcctggttaatcttttggtgcttaatagGTGGATGACCTGGAAGAAGTCAGCGAGTACTACCAGAACAGAGGGTGCTTCAATGAATTAATCTCACTTATGGAGAGTGGACTTGGGCTTGAACGTGCTC
                   ||| | ||||  | |      ||    ||| || |  | | ||| | | |||||| |      ||     |||||   |   |  || ||  |   ||  |||||||||||| ||||||| ||||| || || ||||| || ||||| |||||||||||  |||| || ||||||||||||||  | ||  | ||||| || |
------------------agagaaaaaaaaatgctgtgagcattacttaaatctgcagtttgt-taccttatagtctttccaat---gcttattatgtcaattttcattgtgaatttggtagGTGGATGACTTGGAAGAGGTCAGTGAATATTACCAAAATAGAGGTTGCTTCAATGAGCTAATATCGCTTATGGAGAGTGGTTTAGGATTAGAACGGGCAC

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 24
gtgaatacctgatcttactgagcacaaaagtttccccttacaggttttagatttcaattgtgtatgctttatag----cccaatgtatctcatttatttcctg-gttaatcttttggt--gcttaatagGTGGATGACCTGGAAGAAGTCAGCGAGTACTACCAGAACAGAGGGTGCTTCAATGAATTAATCTCACTTATGGAGAGTGGACTTGGGCTTGAACGTGCTC
                             ||||  | |    ||| || ||  | |||  ||      |  |||    |  | || || ||   |  ||  || || | | ||||  |    || | ||||||||||| ||||||||||||| || || ||||| || ||||| |||||||||||  |||| || || |||||||||||  | ||| | ||||| || |
-------------------------gggtgttttgctt----ggtatttgaacttaatgctgatctgctggtagtgatcttattgaatttctaatgcttattgcgtcatttttttaattaattttaaagGTGGATGACTTGGAAGAAGTCAGTGAATATTACCAAAATAGAGGTTGCTTCAATGAGCTAATATCTCTGATGGAGAGTGGTTTAGGGTTAGAACGGGCAC

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 23
gtgaatacctgatcttactgagcacaaaagtttccccttacaggttttagatttcaattgtgtatgctttatagcccaatgtatctcatttatttcctggttaatcttttggtgcttaatagGTGGATGACCTGGAAGAAGTCAGCGAGTACTACCAGAACAGAGGGTGCTTCAATGAATTAATCTCACTTATGGAGAGTGGACTTGGGCTTGAACGTGCTC
                     |   ||||  | |      ||    ||  || |  | | ||| | | |||||| |      ||     |||||   |   |  || ||  |   ||  |||||||||||| ||||||| ||||| || || ||||| || ||||| |||||||||||  |||| || || |||||||||||  | ||  | ||||| || |
-------------------aggagaaaaaaatgctgtgagcattacttgaatctgcagtttgtttaccttatagtctttccaat---gcttattatgtcaattttcattgtgaatttggtagGTGGATGACTTGGAAGAGGTCAGTGAATATTACCAAAATAGAGGTTGCTTCAATGAGCTAATATCCCTCATGGAGAGTGGTTTAGGATTAGAACGGGCAC

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 24
---------------gtgaatacctgatcttactg-agcacaaaagtttccccttacaggttttagatttcaat-tgtgtatgctttatagcccaatgtat---ctcatttatttcctggt-taatcttttggtgc------------ttaatagGTGGATGACCTGGAAGAAGTCAGCGAGTACTACCAGAACAGAGGGTGCTTCAATGAATTAATCTCACTTATGGAGAGTGGACTTGGGCTTGAACGTGCTC
                | |      | |   |    | ||  | |        ||   | ||  | |||||  | ||| |  ||||   |||| ||||| |   ||  ||||||  | ||| |||| |  | |||             ||  ||||| |||||  |||| || ||||| || || |||||||| ||||| |||||||||||  |||| ||||| ||||||||||| || ||  | || ||||| |
gtaatgtattgttttttaagggtagggtgggatgataacatcataaaaatggattgttgtttcaaaatttccttctgtatgagcttccaagcctaatgttttcgcttttttattatcaggtctaatttcctagtgtattgatttgaattttgtagGTCGATGATTTGGAGGAGGTCAGTGATTATTACCAGAATAGAGGATGCTTCAATGAGCTAATATCACTCATGGAGAGTGGTCTGGGCTTGGAGCGTGCAC

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|116468290|gb|EG510882.1|EG510882
EST:     CTGAGGAATTCCGGTTGGCTCAAATATGTGGTCTTAACATTATCATTCAG                         GTGGATGACCTGGAAGAAGTCAGCGAGTACTACCAGAACAGAGGGTGCTTC
genomic: CTGAGGAATTCCGGTTGGCTCAAATATGTGGTCTTAACATTATCATTCAGgtgaatacct ... tgcttaatagGTGGATGACCTGGAAGAAGTCAGCGAGTACTACCAGAACAGAGGGTGCTTC
EST: gi|116435883|gb|EG478475.1|EG478475
EST:     CTGAGGAATTCCGGTTGGCTCAAATATGTGGTCTTAACATTATCATTCAG                         GTGGATGACCTGGAAGAAGTCAGCGAGTACTACCAGAACAGAGGGTGCTTC
genomic: CTGAGGAATTCCGGTTGGCTCAAATATGTGGTCTTAACATTATCATTCAGgtgaatacct ... tgcttaatagGTGGATGACCTGGAAGAAGTCAGCGAGTACTACCAGAACAGAGGGTGCTTC
EST: gi|116431737|gb|EG474329.1|EG474329
EST:     CTGAGGAATTCCGGTTGGCTCAAATATGTGGTCTTAACATTATCATTCAG                         GTGGATGACCTGGAAGAAGTCAGCGAGTACTACCAGAACAGAGGGTGCTTC
genomic: CTGAGGAATTCCGGTTGGCTCAAATATGTGGTCTTAACATTATCATTCAGgtgaatacct ... tgcttaatagGTGGATGACCTGGAAGAAGTCAGCGAGTACTACCAGAACAGAGGGTGCTTC
EST: gi|86058163|gb|DR353920.1|DR353920
EST:     CTGAGGAATTCCGGTTGGCTCAAATATGTGGTCTTAACATTATCATTCAG                         GTGGATGACCTGGAAGAAGTCAGCGAGTACTACCAGAACAGAGGGTGCTTC
genomic: CTGAGGAATTCCGGTTGGCTCAAATATGTGGTCTTAACATTATCATTCAGgtgaatacct ... tgcttaatagGTGGATGACCTGGAAGAAGTCAGCGAGTACTACCAGAACAGAGGGTGCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatagcccaatgtatctcatttatttcctggttaatcttttggtgcttaatagGTGGATGACCTGGAAGAAGTCAGCGAGTACTACCAGAACAGAGGGTGCTTCAATGAATTAATCTCACTTATGGAGAGTGGACTTGGGCTTGAACGTGCTC
                               ggttaat  putative branch site (score: 4)
              tatctcatttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaatacctgatcttactgagcacaaaagtttccccttacaggttttagatttcaattgtgtatgctttatagcccaatgtatctcatttatttcctggttaatcttttggtgcttaatagGTGGATGACCTGGAAGAAGTCAGCGAGTACTACCAGAACAGAGGGTGCTTCAATGAATTAATCTCACTTATGGAGAGTGGACTTGGGCTTGAACGTGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA