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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccttttgcacttagctttttgtcaatgtcactaactcgttcttcttcacaaatagtcatggtggaactttcatatgttaattaatcaatgatgttaaacaagaaggaaaaaccctgccttatagtagatattattatgttttcctatatacaatattagATGTTGCTAAGTTGCAGAATGAAGATGGATCCTTCTCAGGAGATATGTGGGGAGAAATAGATACGAG

Basic information

species Arabidopsis thaliana
transcript AT5G12210.2
intron # 4
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G12210.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G11710.1 (Glycine max), 3'ss of exon 4
gtatccttttgcacttagctttttgtcaatgtcactaactcgttcttcttcacaaatagtcatggtggaactttcatatgttaattaatcaatgatgttaaacaagaaggaaaaaccctgccttatagtagatattattatgttttcctatatacaatattagATGTTGCTAAGTTGCAGAATGAAGATGGATCCTTCTCAGGAGATATGTGGGGAGAAATAGATACGAG
                                                           |     |   | |    | || || | || | || ||  |||| |   |  | ||||       |||| | ||| || |  | | || |||| ||   | | |||  |||  |   |||| ||||||||||||||||| ||||| ||||||||||| ||| | |||||| |
-----------------------------------------------------------tgtaaattttagtacagtttgatactaaaactataatagtaaa-atttataataaactagaaaatatactggatcttgtgttttcttactattta---tgtcagACATTGTCAGCCTGCAAAATGAAGATGGATCCTTTTCAGGGGATATGTGGGGTGAAGTTGATACGCG

upper sequence: AT5G12210.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G28630.1 (Glycine max), 3'ss of exon 3
gtatccttttgcacttagctttttgtcaatgtcactaactcgttcttcttcacaaatagtcatggtggaactttcatatgttaattaatcaatgatgttaaacaagaaggaaaaaccctgccttatagtagatattattatgttttcctatatacaatattagATGTTGCTAAGTTGCAGAATGAAGATGGATCCTTCTCAGGAGATATGTGGGGAGAAATAGATACGAG
                                                             | |   ||| |||  ||  || ||      |  |   ||   ||     | ||||   |   ||||   ||| || |  | | || |||| ||   | | |||| |||  |   |||| ||||||||||||||||| ||||| ||||||||||| ||| | |||||  |
-----------------------------------------------------------gaaagaaagaattttagtagtttgatactaagactacaatagtaaaatttaataaactaggaagtataccggatcttgt-gtttcttactattta---tctcagATATTGTCAGCCTGCAAAATGAAGATGGATCCTTTTCAGGGGATATGTGGGGTGAAGTTGATACACG

upper sequence: AT5G12210.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv15s0024g00080.t01 (Vitis vinifera), 3'ss of exon 4
gtatccttttgcacttagctttttgtcaatgtcactaactcgttcttcttcacaaatagtcatggtggaactttcatatgttaattaa-tcaatgatgttaaacaagaaggaaaaaccctgccttatagtagatattattatgttttcctatatacaatattagATGTTGCTAAGTTGCAGAATGAAGATGGATCCTTCTCAGGAGATATGTGGGGAGAAATAGATACGAG
                                                          |||    |   |  || |||||||  | || |  |  || ||       || | |||||   |   | |     || || || |  ||  |  |  |     |||||| ||||   | |||||||||||||||| || || ||||| || |||||||| ||||| |||||| |
--------------------------------------------------------aggtc----taagaaatttatatgttggtaaaattgaaaattttggtttgcaatgtaaaacagggtaatttcagtcattttgttgttcttgacccttga----gttagATATTGCGGGGCTGCAGAATGAAGATGGGTCATTTTCAGGTGACATGTGGGGCGAAATTGATACGCG

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|19874896|gb|AU235727.1|AU235727
EST:     GGCCCTATTTGACAAAATCAACATTCTTGACATTGGGAAAGTGTCAAGTT                         ATGTTGCTAAGTTGCAGAATGAAGATGGATCCTTCTNAGGAGATATGTGGG
genomic: GGCCCTATTTGACAAAATCAACATTCTTGACATTGGGAAAGTGTCAAGTTgtatcctttt ... acaatattagATGTTGCTAAGTTGCAGAATGAAGATGGATCCTTCTCAGGAGATATGTGGG
EST: gi|124859584|gb|EH944021.1|EH944021
EST:     GGCCCTATTTGACAAAATCAACATTCTTGACATTGGGAAAGTGTCAAGTT                         ATGTTGCTAAGTTG
genomic: GGCCCTATTTGACAAAATCAACATTCTTGACATTGGGAAAGTGTCAAGTTgtatcctttt ... acaatattagATGTTGCTAAGTTG
EST: gi|125103648|gb|EL157982.1|EL157982
EST:     AATCAACATTCTTGACATTGGGAAAGTGTCAAGTT                         ATGTTGCTAAGTTGCAGAATGAAGATGGATCCTTCTCAGGAGATATGTGGG
genomic: AATCAACATTCTTGACATTGGGAAAGTGTCAAGTTgtatcctttt ... acaatattagATGTTGCTAAGTTGCAGAATGAAGATGGATCCTTCTCAGGAGATATGTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaaaaaccctgccttatagtagatattattatgttttcctatatacaatattagATGTTGCTAAGTTGCAGAATGAAGATGGATCCTTCTCAGGAGATATGTGGGGAGAAATAGATACGAG
 ttcctatat  putative branch site 
                    tagatattattatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatccttttgcacttagctttttgtcaatgtcactaactcgttcttcttcacaaatagtcatggtggaactttcatatgttaattaatcaatgatgttaaacaagaaggaaaaaccctgccttatagtagatattattatgttttcctatatacaatattagATGTTGCTAAGTTGCAGAATGAAGATGGATCCTTCTCAGGAGATATGTGGGGAGAAATAGATACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA