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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgttgatgcaaatatatttgaactccattatcgttcctgctatacacttcgtataactctgaatttttcagtcgggtttttttttggataataatgtttcatgtttttacagGTTGTCTTTTGGAAGTGGATTACACCAAAGATGTTGGGGCTGGTCACACAGAATTCCGTCTATCATTGGTCAATTGAAG

Basic information

species Arabidopsis thaliana
transcript AT3G08530.1
intron # 3
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 3
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 3
gtgagtgttgatgcaaatatatttgaactccattatcgttcctgctatacacttcgtataactctgaatttttcagtcgggtttttttttggataataatgtttcatgttt----ttacagGTTGTCTTTTGGAAGTGGATTACACCAAAGATGTTGGGGCTGGTCACACAGAATTCCGTCTATCATTGGTCAATTGAAG
            | | | |  ||  |  |     |  ||    |  |  ||||| || ||| |   |   | | |      | | || || |   ||  | |||  | ||     | ||||||||| |||||||| ||||| || |||||| |||||||  |||| ||||| |  || || ||||| ||||||||||| |
------------gtacaaaatttgaagttttgccaaagtatgcgtaac-cactttgtttaaattgtatcctataatcttaatgtattctttgcatattttattttcttttcacaatcacagGTTGTGTTTTGGAAATGGATCACCCCAAAGTTGTTGGGTTTGGTAACACAAACATCAGTTTATCACTGGTCAATTGAGG

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 3
gtgagtgttgatgcaaatatatttgaactccattatcgttcctgctatacacttcgtataactctgaatttttcagtcgggtttttttttggataataatgtttcatgtttttacagGTTGTCTTTTGGAAGTGGATTACACCAAAGATGTTGGGGCTGGTCACACAGAATTCCGTCTATCATTGGTCAATTGAAG
|| | |||| |||||    |||   ||| | ||||        || ||       |  | |   ||||   |  | |     |     | | ||  |    ||||||||     ||||| |||||||||||||||||||| || ||| ||||||| || || |||||||  || || || ||||||||||||||||
gtaactgtt-atgcacgagtatacaaacactattaa-------gcgat-------ggttgatgatgaaaactctattaa---tccacgtggaatgctctaatttcatgt----gcagGTGGTCTTTTGGAAGTGGATTACCCCCAAGTTGTTGGGTCTTGTAACACAGACCTCTGTATACCATTGGTCAATTGAAG

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 3
gtgagtgttgatgcaaatatatttgaactccattatcgttcctgctatacacttcgtataactctgaatttttcagtcgggtttttttttggataataatgtttcatgtttttacagGTTGTCTTTTGGAAGTGGATTACACCAAAGATGTTGGGGCTGGTCACACAGAATTCCGTCTATCATTGGTCAATTGAAG
|| | |||| ||||     | |   ||| | ||||    |  || |  ||| |    | ||||||     |    || |  |  | |       |||    ||||||||     ||||| |||||||||||||||||||| || ||| |||||||  | || |||||||  || || || ||||||||||||||||
gtaactgtt-atgctcgagtgtacaaacactatta--agtgatggttgacaatg---aaaactctattaatccttgtggaatgctct-------aat----tttcatgt----gcagGTGGTCTTTTGGAAGTGGATTACCCCCAAGTTGTTGGGTATTGTAACACAGACCTCTGTATACCATTGGTCAATTGAAG

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 3
gtgagtgttgatgcaaatatatttgaactccattatcgttcctgctatacacttcgtataactctgaatttttcagtcgggtttttttttggataataatgtttcatgtttttacagGTTGTCTTTTGGAAGTGGATTACACCAAAGATGTTGGGGCTGGTCACACAGAATTCCGTCTATCATTGGTCAATTGAAG
                                     ||  ||  ||| |||   |    |             |||  |||    | | | |  |||   | | |    |  | |||| |||||||||||||||||||  || ||||||||||| || || |||||||  || || || || |||||||||||||
-------------------------------------gtaactattatgcacaaggacacatatattgcaacatagt-aggtccaatatggtaacatatattgttaatcatgcatagGTAGTCTTTTGGAAGTGGATTAGCCCCAAGATGTTGGGTCTCGTAACACAGACCTCTGTATACCACTGGTCAATTGAAG

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 3
gtgagtg-ttgatgcaaatatatttgaactccattatcgttcctgctatacacttcgtataactctgaatttttcagtcgggtttttttttggataataatgtttcatgttttta--cagGTTGTCTTTTGGAAGTGGATTACACCAAAGATGTTGGGGCTGGTCACACAGAATTCCGTCTATCATTGGTCAATTGAAG
|||||   ||  | |      ||||    | ||||       ||  | |  || || || |    | |  ||   | |   |||   ||      ||  |||  |  |  ||| |   || |||| || |||||||||||||| ||||||||| |||| |||||||| ||||  || || |||||||||||||| ||||
gtgagaactttgttctttagcatttctgttacatttcttgagctattttg-acatcctacattgttaacattgctattacagttagctt------aactatgccttgttgtttaaaatagATTGTTTTCTGGAAGTGGATTACCCCAAAGATGCTGGGCCTGGTCACGCAGACCTCAGTATATCATTGGTCAATCGAAG

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|116431736|gb|EG474328.1|EG474328
EST:     TTAACATTGAAGCCAAAGCAAAGTTGAAATCACATCAGATGCCTGAGCAG                         GTTGTCTTTTGGAAGTGGATTACACCAAAGATGTTGGGGCTGGTCACACAG
genomic: TTAACATTGAAGCCAAAGCAAAGTTGAAATCACATCAGATGCCTGAGCAGgtgagtgttg ... gtttttacagGTTGTCTTTTGGAAGTGGATTACACCAAAGATGTTGGGGCTGGTCACACAG
EST: gi|116430170|gb|EG472762.1|EG472762
EST:     TTAACATTGAAGCCAAAGCAAAGTTGAAATCACATCAGATGCCTGAGCAG                         GTTGTCTTTTGGAAGTGGATTACACCAAAGATGTTGGGGCTGGTCACACAG
genomic: TTAACATTGAAGCCAAAGCAAAGTTGAAATCACATCAGATGCCTGAGCAGgtgagtgttg ... gtttttacagGTTGTCTTTTGGAAGTGGATTACACCAAAGATGTTGGGGCTGGTCACACAG
EST: gi|116379678|gb|EG422270.1|EG422270
EST:     TTAACATTGAAGCCAAAGCAAAGTTGAAATCACATCAGATGCCTGAGCAG                         GTTGTCTTTTGGAAGTGGATTACACCAAAGATGTTGGGGCTGGTCACACAG
genomic: TTAACATTGAAGCCAAAGCAAAGTTGAAATCACATCAGATGCCTGAGCAGgtgagtgttg ... gtttttacagGTTGTCTTTTGGAAGTGGATTACACCAAAGATGTTGGGGCTGGTCACACAG
EST: gi|116430172|gb|EG472764.1|EG472764
EST:     TTAACATTGAAGCCAAAGCAAAGTTGAAATCACATCAGATGTCTGAGCAG                         GTTGTCTTTTGGAAGTGGATTACACCAAAGATGTTGGGGCTGGTCACACAG
genomic: TTAACATTGAAGCCAAAGCAAAGTTGAAATCACATCAGATGCCTGAGCAGgtgagtgttg ... gtttttacagGTTGTCTTTTGGAAGTGGATTACACCAAAGATGTTGGGGCTGGTCACACAG
EST: gi|116435872|gb|EG478464.1|EG478464
EST:     TTAACATTGAAGCCAAAGCAAAGTTGAAATCACATCAGATGCCTGAGCAG                         GTTGTCTTTTGGAAGTGGATTACACCAAAGATGTTGGGGCTGGTCACACAG
genomic: TTAACATTGAAGCCAAAGCAAAGTTGAAATCACATCAGATGCCTGAGCAGgtgagtgttg ... gtttttacagGTTGTCTTTTGGAAGTGGATTACACCAAAGATGTTGGGGCTGGTCACACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgaatttttcagtcgggtttttttttggataataatgtttcatgtttttacagGTTGTCTTTTGGAAGTGGATTACACCAAAGATGTTGGGGCTGGTCACACAGAATTCCGTCTATCATTGGTCAATTGAAG
                                            tgttttt  CT-rich tract
                   tttttttttggataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgttgatgcaaatatatttgaactccattatcgttcctgctatacacttcgtataactctgaatttttcagtcgggtttttttttggataataatgtttcatgtttttacagGTTGTCTTTTGGAAGTGGATTACACCAAAGATGTTGGGGCTGGTCACACAGAATTCCGTCTATCATTGGTCAATTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG