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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggcaacataataaatcatcttttatgttcaacattgatgagagattaagaaactcaatcaactaaactatcatttgcaacatcaaagttgtctagactaatttgattgtctgatgcgtaacttaacttcttcaatattcttgtttcagGCATATGTTTACTTGGACGAAGCTCACAGCATTGGAGCAATTGGCAAGACAGGAAGAGGTGTTTGTGAACTCCTTGGAGTTGACACTTCTGATGTGGACA

Basic information

species Arabidopsis thaliana
transcript AT3G48780.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G48780.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os01g70370.1 (Oryza sativa), 3'ss of exon 7
------------------------------gtgaggcaacataataaatcatcttttatgttcaacattgatgagagattaagaaactcaatcaactaaactatcatttgcaaca-tcaaagttgtctagactaatttgattgtctgatgcgtaacttaacttcttcaatattcttg--tttc-----agGCATATGTTTACTTGGACGAAGCTCACAGCATTGGAGCAATTGGCAAGACAGGAAGAGGTGTTTGTGAACTCCTTGGAGTTGACACTTCTGATGTGGACA
                               |  |          | |||||     ||||  | | ||  | |   |  |||    | ||||   | | || |||| | ||  | |  || || | |   ||| |   || |    ||   ||       ||    | | | |||   ||||     |||| ||    || || || || || ||||||||||| ||  |||| |||||||| ||||||||||||||| | |||||||| ||| |  | ||||| || |
gttcaagaatttcttacactgacttcttgtatatgttctttcttcagatcattaagcatgtaaatctttttttaatcaa-aagcttgtaaatctgttta-ctgtcatatacattacttcaacttttatcagctattaaaatcgataaatatttactgagttttgactattgtacttaaatttctggacagGCTTACACATATTTAGATGAGGCACACAGCATTGGGGCTGTTGGTAAGACAGGGAGAGGTGTTTGTGAATTACTTGGAGTGGACCCAGCGGATGTTGATA

upper sequence: AT3G48780.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G010202_T01 (Zea mays), 3'ss of exon 7
gtgaggcaacataataaatcatcttttatgttcaacattgatgagagattaagaaactcaatcaactaaactatcatttgcaacatcaaagttgtctagactaatttgattgtctgatgcgtaacttaacttcttcaatattcttgtttcagGCATATGTTTACTTGGACGAAGCTCACAGCATTGGAGCAATTGGCAAGACAGGAAGAGGTGTTTGTGAACTCCTTGGAGTTGACACTTCTGATGTGGACA
                                        ||   || ||| ||  |||| |  |   || |   |||  ||   ||  |       | |||   ||| ||     |  |    | |||  |     | ||        ||||| ||    ||  | |||||||| ||||| ||||||||  |||| || ||||| |||||||||||||| || || ||||| ||  |  ||||||| ||||
--------------------------------------acataccagtttatga--ctcagtttatagaaattagattctcagtttcttaa------aaactgggttgcttcc---aaacagggcctaatatacctcacatatgaa---cagGCCTACACATATCTAGACGAAGCACACAGTATTGGAGCTGTTGGGAAAACAGGGAGAGGTGTTTGTGAGCTGCTCGGAGTGGATCCAGCTGATGTTGACA

upper sequence: AT3G48780.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA16G26210.1 (Glycine max), 3'ss of exon 7
gtgaggcaacataataaatcatcttttatgttcaacattgatgagagattaagaaactcaatcaactaaactatcatttgcaacatcaaagttgtctagactaatttgattgtctgatgcgtaacttaacttcttcaatattcttgtttcagGCATATGTTTACTTGGACGAAGCTCACAGCATTGGAGCAATTGGCAAGACAGGAAGAGGTGTTTGTGAACTCCTTGGAGTTGACACTTCTGATGTGGACA
                                             | ||||||        |  |  ||  | | |||   ||  || |  || || |   || |||| ||   || | | |  ||  | || |||| |  |    ||  |||| |||   || ||||||||||| ||||||||||||||  | |||||||||||||||||||||||||| ||| | || || || ||| ||||||| ||||
---------------------------------------------acattaagggggattttggatgaactttttattataaagttcta--ttttccattttactttggttcattgttacttt-ctgtattttttcattgct----ttatagGCTTATACATATTTGGACGAAGCACACAGCATTGGAGCTGTGGGCAAGACAGGAAGAGGTGTTTGTGAGCTCTTGGGTGTGGATACTGCTGATGTTGACA

upper sequence: AT3G48780.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA02G07250.1 (Glycine max), 3'ss of exon 7
gtgaggcaacataataaatcatcttttatgttcaacattgatgagagattaagaaactcaatcaactaaactatcatttgcaacatcaaagttgtctagactaatttgattgtctgatgcgtaacttaacttcttcaatattcttgtttcagGCATATGTTTACTTGGACGAAGCTCACAGCATTGGAGCAATTGGCAAGACAGGAAGAGGTGTTTGTGAACTCCTTGGAGTTGACACTTCTGATGTGGACA
                                               ||||||        |  | |||||| |   ||   |  |   | || || |   || |||| ||   || | | |    ||  || | || |  |    ||  |||| |||   || ||||||||||| ||||||||||||||  | |||||| ||||||||||||||||||| ||| | || || || ||| ||||||| ||||
----------------------------------------------cattaagggggatttttga-taaactttttattatgaagttttattt-tccattttactttggttcattgttactttgtgtattttttccattgct----ttatagGCTTATACATATTTGGACGAAGCACACAGCATTGGAGCTGTGGGCAAGTCAGGAAGAGGTGTTTGTGAGCTCTTGGGTGTGGATACTGCTGATGTTGACA

upper sequence: AT3G48780.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 8
gtgaggcaacataataaatcatcttttatgttcaacattgatgagagattaagaaactcaatcaactaaactatcatttgcaacatcaaagttgtctagactaatttgattgtctgatgcgtaacttaacttcttcaatattcttgtttcagGCATATGTTTACTTGGACGAAGCTCACAGCATTGGAGCAATTGGCAAGACAGGAAGAGGTGTTTGTGAACTCCTTGGAGTTGACACTTCTGATGTGGACA
                                             || |       |||  |    |  |   | | ||    | || |   | |  |   |   |  ||  | |  |  || | ||  ||   |   |||  ||| |  ||||||||||||||||||| || || ||||| ||||||||| |||| || |||||||||||||| ||||| ||| | || || || ||  |||||||||| |
---------------------------------------------agctctgttttctc--tttgatgcatcttaacttagggcctcta---ttttcatttttcataaatatttttgtttgtcatttttctatctttctat--ttggtgtagGCATATGTTTACTTGGATGAGGCACACAGTATTGGAGCAGTTGGGAAAACAGGAAGAGGTGTCTGTGAGCTCTTAGGTGTGGATACCGCTGATGTGGATA

upper sequence: AT3G48780.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 7
gtgaggcaacataataaatcatcttttatgttcaacattgatgagagattaagaaactcaatcaactaaactatcatttgcaacatcaaagttgtctagactaatttgattgtctgatgcgtaacttaacttcttcaatattcttgtttcagGCATATGTTTACTTGGACGAAGCTCACAGCATTGGAGCAATTGGCAAGACAGGAAGAGGTGTTTGTGAACTCCTTGGAGTTGACACTTCTGATGTGGACA
                                                ||  |   ||   || |    | ||    |       ||     | ||  | |         | |||  || | |  || ||| | |    |  | ||||  ||||||||   || ||||| || || |||||||| || ||| |||| || |||||||||||||||||||| ||| | ||||| ||  || |||||||||| |
-----------------------------------------------ttttcgttgctttttctatgtgaatagttctctttgtctctttcctttcc-gccccccccccctctcttttgagca--ttcactacatt--caaccctgttgtagGCATATTCCTATTTGGATGAGGCCCACAGCATAGGTGCAGTTGGGAAAACAGGAAGAGGTGTTTGTGAGCTCTTAGGAGTGGATCCTGCTGATGTGGATA

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|116478473|gb|EG521065.1|EG521065
EST:     GGGAAATTTGTCATCTGCCCGAGATTGTTTCAATATGCAAGAAGTATAAG                         GCATATGTTTACTTGGACGAAGCTCACAGCATTGGAGCAATTGGCAAGACA
genomic: GGGAAATTTGTCATCTGCCCGAGATTGTTTCAATATGCAAGAAGTATAAGgtgaggcaac ... cttgtttcagGCATATGTTTACTTGGACGAAGCTCACAGCATTGGAGCAATTGGCAAGACA
EST: gi|116478474|gb|EG521066.1|EG521066
EST:     GGGAAATTTGTCATCTGCCCGAGATTGTTTCAATATGCAAGAAGTATAAG                         GCATATGTTTACTTGGACGAAGCTCACAGCATTGGAGCAATTGGCAAGACA
genomic: GGGAAATTTGTCATCTGCCCGAGATTGTTTCAATATGCAAGAAGTATAAGgtgaggcaac ... cttgtttcagGCATATGTTTACTTGGACGAAGCTCACAGCATTGGAGCAATTGGCAAGACA
EST: gi|19878645|gb|AU239476.1|AU239476
EST:     GGGAAATTTGTCATCTGCCCGAGATTGTTTCAATATGCAAGAAGTATAAG                         GCATATGTTTACTTGGACGAAGCTCACAGCATTGGAGCAATTGGCAAGACA
genomic: GGGAAATTTGTCATCTGCCCGAGATTGTTTCAATATGCAAGAAGTATAAGgtgaggcaac ... cttgtttcagGCATATGTTTACTTGGACGAAGCTCACAGCATTGGAGCAATTGGCAAGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agactaatttgattgtctgatgcgtaacttaacttcttcaatattcttgtttcagGCATATGTTTACTTGGACGAAGCTCACAGCATTGGAGCAATTGGCAAGACAGGAAGAGGTGTTTGTGAACTCCTTGGAGTTGACACTTCTGATGTGGACA
                                           ttcttgtttc  CT-rich tract
     aatttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggcaacataataaatcatcttttatgttcaacattgatgagagattaagaaactcaatcaactaaactatcatttgcaacatcaaagttgtctagactaatttgattgtctgatgcgtaacttaacttcttcaatattcttgtttcagGCATATGTTTACTTGGACGAAGCTCACAGCATTGGAGCAATTGGCAAGACAGGAAGAGGTGTTTGTGAACTCCTTGGAGTTGACACTTCTGATGTGGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG