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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggataaataacagatcctagttcccgagaaagttttttagttataattgggtttcaatttcaattttgtatgcctttttgtaatatttttgtgctttaatagGTGGATGACCTGGAAGAAGTAAGCGAGTACTACCAGAACAGAGGATGCTTCAATGAATTGATCTCCCTTATGGAGAGTGGACTTGGTCTGGAACGTGCTC

Basic information

species Arabidopsis thaliana
transcript AT3G11130.1
intron # 24
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 24
gtggataaataacagatcctagttcccgagaaagttttttagttataattgggtttcaatttcaattttgtatgcctttttgtaatatttttgtgctttaatagGTGGATGACCTGGAAGAAGTAAGCGAGTACTACCAGAACAGAGGATGCTTCAATGAATTGATCTCCCTTATGGAGAGTGGACTTGGTCTGGAACGTGCTC
||  ||| | |  ||   |  |||    ||||      | |   ||| ||  ||   | | |    ||     |  ||||| ||| |   || |  ||  |||||| |||||  |||| |||||||| || |||||||||||||||||||| ||||||||| | || ||||| ||||| ||||| || || ||||| |||||||
gtatatatacaggagcaacctgtt----agaa-----ctaaaacatatttcagtacaagtcttttcttatctagattttttctaacaccctttt--ttgtatagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 24
gtggataaataacagatcctagttcccgagaaagttttttagttataattgggtttcaatttcaattttgtatgcctttttgtaatatttttgtgctttaatagGTGGATGACCTGGAAGAAGTAAGCGAGTACTACCAGAACAGAGGATGCTTCAATGAATTGATCTCCCTTATGGAGAGTGGACTTGGTCTGGAACGTGCTC
  | ||| ||| |||  || |  |      |       | |   ||| ||  ||   | | |    ||     |  ||||| ||| |   || |  ||  |||||| |||||  |||| |||||||| || |||||||||||||||||||| ||||||||| | || ||||| ||||| ||||| || || ||||| |||||||
--gtatatata-caggaccaacctgttagaa------ctaaaacatatttcagtacaagtcttttcttatctagattttttctaacacccttttttttgtatagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 22
gtggataaataacagatcctagttcccgagaaagttttttagttataattgggtttcaa--tttcaattttgtatgcctttttgtaata----tttttgtgctttaatagGTGGATGACCTGGAAGAAGTAAGCGAGTACTACCAGAACAGAGGATGCTTCAATGAATTGATCTCCCTTATGGAGAGTGGACTTGGTCTGGAACGTGCTC
||  | || ||  ||  | || ||   ||     ||   ||||  |  ||   || |||  |||| ||  | |||  |||| ||  |||     | || |  ||   ||||| || |||||||||||||| || |||||||||||||||||||||||||||| |||| | ||  | || ||||||||||| ||||| || |||||||| |
gtatacaagtaggagggcatacttgatgattt--ttccctagtctttgttttattgcaaagtttctatgatatatttctttctgacatacctgctcttttttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: GRMZM2G395549_T01 (Zea mays), 3'ss of exon 9
------------------------------------------------------------------------gtggataaataacagatcctagttcccgagaaagttttttagttataattgggtttcaa--tttcaattttgtatgcctttttg---taatatttttgtgctttaatagGTGGATGACCTGGAAGAAGTAAGCGAGTACTACCAGAACAGAGGATGCTTCAATGAATTGATCTCCCTTATGGAGAGTGGACTTGGTCTGGAACGTGCTC
                                                                         |  | || ||  ||  | || ||     ||   ||   || |  |  ||   || |||  |||| ||  | |||  |||| ||   ||     | | |  ||   ||||| |||||||| |||||||| || |||||||||||||||||||||||||||| |||| | ||  | || ||||||||||| ||||| || |||||||| |
gtctgctttgcttgtgttgacgtggaggagttccgtcttgcacaaatatgtggtctcaatattattgttcagatatacaagtaggagggcatactt-----gatttttccctattctttgttttattgcaaagtttctatgatatatttctttctgacatagctgctctttttttgtttagGTTGATGACCTCGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 1
gtggataaataacagatcctagttcccgag-----aaagttttttagttataattgggtttcaatttcaattttgtatgcctttttgtaatat----ttttgtgctttaat--agGTGGATGACCTGGAAGAAGTAAGCGAGTACTACCAGAACAGAGGATGCTTCAATGAATTGATCTCCCTTATGGAGAGTGGACTTGGTCTGGAACGTGCTC
||  | || ||  ||  | || ||    |        ||| | |   |||||   | | ||| ||  |  |  | |||   ||||| | ||||    ||||||  |||  |  |||| |||||| |||||||||| || ||||||||||| || |||||||||||||||||| | ||  | || ||||||||||| ||||| || |||||||| |
gtatacaagtaggagcacatacttgataattttttgtagtatctgctttatagcagagcttctatcactgtgatctatttttttttctcatatctgcttttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 1
gtggataaataacagatcctagttcccgagaaagttttttagttataattgggtttcaatttcaattttgtatgcctttttgtaatat----ttttgtgctttaat--agGTGGATGACCTGGAAGAAGTAAGCGAGTACTACCAGAACAGAGGATGCTTCAATGAATTGATCTCCCTTATGGAGAGTGGACTTGGTCTGGAACGTGCTC
||  | || ||  ||  | || ||   || ||  |||| ||||     ||       |  ||| ||  | |||  || | ||  || |    ||||||  |||  |  |||| |||||| |||||||||| || |||||||||||||| ||||||||||||| |||| | ||  | || ||||||||||| ||||| || |||||||| |
gtatacaagtaggagcacatactt---gataattttttctagtctgttttataacagagcttctatgatctatttctgtctgacatgtctgattttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAGAATAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: GRMZM2G325285_T01 (Zea mays), 3'ss of exon 14
gtggataaataacagatcctagttcccgag------aaagttttttagttataattgggtttcaatttcaattttgtatgcctttttgtaa--tatttttgtgctttaat--agGTGGATGACCTGGAAGAAGTAAGCGAGTACTACCAGAACAGAGGATGCTTCAATGAATTGATCTCCCTTATGGAGAGTGGACTTGGTCTGGAACGTGCTC
||  | || ||  ||  | || ||    |         ||| | |   |||||   | | ||| ||  | ||  | |||   ||| |   |  |  ||||||  |||  |  |||| |||||| |||||||||| || ||||||||||| || |||||||||||||||||| | ||  | || ||||||||||| ||||| || |||||||| |
gtatacaagtaggagcacatacttaataatttttttgtagtatctgctttatagcagagcttctatcactatgatctatttttttctcatatctgcttttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTAGAACGTGCAC

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 24
gtggataaataacagatcctagttcccgagaaagttttttagttataattgggtttcaatttcaattttgtatgcct-ttttgtaatatttttg--tgctttaatagGTGGATGACCTGGAAGAAGTAAGCGAGTACTACCAGAACAGAGGATGCTTCAATGAATTGATCTCCCTTATGGAGAGTGGACTTGGTCTGGAACGTGCTC
              |  | |  |    ||      | || | ||   | | |   ||   || |||||   |||| | ||  || || |||||   |  ||| ||||||||||||| |||||||||| || || || ||||| |||||||| |||||||||||  | || || || |||||||||||  | ||  | ||||| || |
-------gggtgttgtgcttgttatatgaacttaatgttgatttgctactagtgatcttattgaatttctaatgcttattgcgtcattttttttattaatttcatagGTGGATGACTTGGAAGAAGTCAGTGAATATTACCAAAACAGAGGTTGCTTCAATGAGCTCATATCTCTCATGGAGAGTGGTTTAGGGTTAGAACGGGCAC

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 23
gtggataaataacagatcctagttcccgagaaagttttttagttataattgggtttcaatttcaattttgtatgcctttttgtaatattttt----gtgc-tttaatagGTGGATGACCTGGAAGAAGTAAGCGAGTACTACCAGAACAGAGGATGCTTCAATGAATTGATCTCCCTTATGGAGAGTGGACTTGGTCTGGAACGTGCTC
    |  |  || | || ||       ||| |    ||  |  |  | || | || |  | |    |||  |   ||| || |   | ||||    |||  |||  |||||||||||| ||||||| || || || || ||||| || ||||| |||||||||||  | || ||||| |||||||||||  | ||  | ||||| || |
----aggagaaaaaaatgctg-----tgagcattacttgaatctgcagtttgtttaccttatagtctttccaatgcttattatgtcaattttcattgtgaatttggtagGTGGATGACTTGGAAGAGGTCAGTGAATATTACCAAAATAGAGGTTGCTTCAATGAGCTAATATCCCTCATGGAGAGTGGTTTAGGATTAGAACGGGCAC

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 23
gtggataaataacagatcctagttcccgagaaagttttttagttataattgggtttcaatttcaattttgtatgcct-ttttgtaatattt--ttgtgc-tttaatagGTGGATGACCTGGAAGAAGTAAGCGAGTACTACCAGAACAGAGGATGCTTCAATGAATTGATCTCCCTTATGGAGAGTGGACTTGGTCTGGAACGTGCTC
   || ||| || | || ||       ||| |    ||  |  |  | || | |  |   |    |||   |||| | || ||| |  |||  |||||  |||  |||||||||||| ||||||| || || || || ||||| || ||||| |||||||||||  | || || ||||||||||||||  | ||  | ||||| || |
--agagaaaaaa-aaatgctg-----tgagcattacttaaatctgcagtttgttaccttatagtctttccaatgcttattatgtcaattttcattgtgaatttggtagGTGGATGACTTGGAAGAGGTCAGTGAATATTACCAAAATAGAGGTTGCTTCAATGAGCTAATATCGCTTATGGAGAGTGGTTTAGGATTAGAACGGGCAC

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 24
gtggataaataacagatcctagttcccgagaaagttttttagttataattgggtttcaatttcaattttgtatgcct-ttttgtaatatttttg--tgctttaatagGTGGATGACCTGGAAGAAGTAAGCGAGTACTACCAGAACAGAGGATGCTTCAATGAATTGATCTCCCTTATGGAGAGTGGACTTGGTCTGGAACGTGCTC
  || |   |  |      | ||    ||      |  | |  |     | |   ||   || |||||   |||| | ||  || || |||||   |  ||| | ||||||||||| |||||||||| || || || ||||| || ||||| |||||||||||  | || || || |||||||||||  | ||  | ||||| || |
--gggtgttttgc-----ttggtatttgaacttaatgctgatctgctggtagtgatcttattgaatttctaatgcttattgcgtcatttttttaattaattttaaagGTGGATGACTTGGAAGAAGTCAGTGAATATTACCAAAATAGAGGTTGCTTCAATGAGCTAATATCTCTGATGGAGAGTGGTTTAGGGTTAGAACGGGCAC

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|125210974|gb|EL225928.1|EL225928
EST:     GAATTCCGACTGGCTCAAATCTGTGGACTTAACATTATCATACAG                         GTGGATGACCTGGAAGAAGTAAGCGAGTACTACCAGAACAGAGGATGC
genomic: GAATTCCGACTGGCTCAAATCTGTGGACTTAACATTATCATACAGgtggataaat ... gctttaatagGTGGATGACCTGGAAGAAGTAAGCGAGTACTACCAGAACAGAGGATGC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgggtttcaatttcaattttgtatgcctttttgtaatatttttgtgctttaatagGTGGATGACCTGGAAGAAGTAAGCGAGTACTACCAGAACAGAGGATGCTTCAATGAATTGATCTCCCTTATGGAGAGTGGACTTGGTCTGGAACGTGCTC
                           tttttgtaatattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggataaataacagatcctagttcccgagaaagttttttagttataattgggtttcaatttcaattttgtatgcctttttgtaatatttttgtgctttaatagGTGGATGACCTGGAAGAAGTAAGCGAGTACTACCAGAACAGAGGATGCTTCAATGAATTGATCTCCCTTATGGAGAGTGGACTTGGTCTGGAACGTGCTC

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