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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaagtaaagtttagacctttatggatatgttgttgatgaatagaagtaaagcagctcacactcacctttattgtgactctagGGTCCTGAGTTTGCAACCATTGTGAACTCAGTCACGTCGAAGAAAGTTGCTGCTTGATTGAGAACTATCAGTAACGGAAATCGCTAGTCTCCATGGAACA

Basic information

species Arabidopsis thaliana
transcript AT2G21170.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA19G36990.1 (Glycine max), 3'ss of exon 8
-------gtaaaagtaaagttta---gacctttatggatatgtt----gttgatgaatagaagtaa--agcagctcacact---cacctttattgtgac----tctagGGTCCTGAGTTTGCAACCATTGTGAACTCAGTCACGTCGAAGAAAGTTGCTGCTTGA--TTGAGAACTATCAGTAACGGAAATCGCTAGTCTCCATGGAACA
       ||      ||| |||    ||||    ||   |        ||| | |||   | || |  ||   |  | |||   ||  || ||  ||      |  |||||||||||||||| |||||||| || |||||||| || ||||||||||| ||||||  ||||  ||     || |           ||    |||  |   
gtacatggtttcttcaaaatttgtttgaccaaagtgagcaaagcatgagttaaggaactcaggttattagttacatatacttgacaagttgatcttgttgaggtgcagGGTCCTGAGTTTGCTACCATTGTCAATTCAGTCACATCCAAGAAAGTTGCGGCTTGAACTTGATTACATATTGTGATTTTGGCAATAAGAGAGCATTAAG--

upper sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA03G34300.1 (Glycine max), 3'ss of exon 8
-------------------------gtaaaagtaaagtttagacctttatggatatgttgttga---tgaatagaagtaaagcagctcacac-tcacctttattgtgactctagGGTCCTGAGTTTGCAACCATTGTGAACTCAGTCACGTCGAAGAAAGTTGCTGCTTGATTGAGAACTATCAGTAACGGAAATCGCTAGTCTCCATGGAACA
                          |   |  |||||  ||      ||| ||  |||   ||       |     |  ||   || |||  |     || ||| |   | |||||||||||||||| |||||||| || |||||||| || ||||||||||| |||| |||    | | | | |   | ||   |  ||  |  | |  | |
gtacacatagtttcttcaaaaatttcttttaccaaagtg-agcaaaccatgcatgagttaaggaactcaggttattatgtagttacttacaagttgatcttgttgaggtgc-agGGTCCTGAGTTTGCTACCATTGTCAATTCAGTCACATCCAAGAAAGTTGCGGCTTAATTACTTATTGTGATTTTGGCAATATGAGAGCATTAAGGATAAA

upper sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA13G20930.1 (Glycine max), 3'ss of exon 8
gtaaaagtaaagtttagac-------ctttatggatatgttgttgatgaatagaa---gtaaagcagctcacactcacctttattg------tgactct---------agGGTCCTGAGTTTGCAACCATTGTGAACTCAGTCACGTCGAAGAAAGTTGCTGCTTGATTGAGAACTATCAGTAACGGAAATCGCTAGTCTCCATGGAACA-
||| |   |  |||||  |       ||||    | ||||  || ||   ||||    |||||  | |||  |      ||||||       ||| | |         |||||||||||||||| |||||| | || |||||||| || ||||||||||| |||| |||    | |||   |       | ||| | |    ||    || 
gtacacacacggtttattcaaagtttctttgaccagatgtgtttcattcctagagtttgtaaatgaactcgaatgattgtttattaatgtgttgattttttgctgtacagGGTCCTGAGTTTGCTACCATTATCAATTCAGTCACTTCCAAGAAAGTTGCGGCTTAATTACTTATTATGTTTTTTTAGGAGCGC-ATTAAAAATATGGCAA

upper sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA10G06740.1 (Glycine max), 3'ss of exon 8
----------------------gtaaaagtaaagtttagacctttatggatatgttgttgatgaatagaagtaaagcagctcacactcacctttattgtgac-tctagGGTCCTGAGTTTGCAACCATTGTGAACTCAGTCACGTCGAAGAAAGTTGCTGCTTGATTGAGAACTATCAGTAACGGAAATCGCTAGTCTCCATGGAACA--
                       |   | || | | |    | ||       | ||||  ||||| |  | | ||      |  |   |    | || ||   |  ||||||| |||||||| |||||| | || |||||||| || ||||||||||| |||| |||    | |||  ||     | | ||| | |    |||   ||  
gtacacgatttattcacaacttctttgactagaatgtgcttcattcctagagt-ttgtaaatgaacacgaatgaatgtttactgatgtattgattttttgctgtacagGGTCCGGAGTTTGCTACCATTATCAATTCAGTCACATCCAAGAAAGTTGCGGCTTAATTACTTATTAT-GGTTTTCAAGAGCGC-ATTAAAAATGTGGCAAT

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|116400904|gb|EG443496.1|EG443496
EST:     CCAAAGAAGGAGACATTGATGGATTTCTTGTTGGTGGTGCCTCCTTGAAG                         GGTCCTGAGTTTGCAACCATTGTGAACTCAGTCAC
genomic: CCAAAGAAGAAGACATTGATGGATTTCTTGTTGGTGGTGCCTCCTTGAAGgtaaaagtaa ... gtgactctagGGTCCTGAGTTTGCAACCATTGTGAACTCAGTCAC
EST: gi|124815306|gb|EH900172.1|EH900172
EST:     GTGCCTCCTTGAAG                         GGTCCTGAGTTTGCAACCATTGTGAACTCAGTCACGTCGAAGAAAGTTGCT
genomic: GTGCCTCCTTGAAGgtaaaagtaa ... gtgactctagGGTCCTGAGTTTGCAACCATTGTGAACTCAGTCACGTCGAAGAAAGTTGCT
EST: gi|124879326|gb|EH958763.1|EH958763
EST:     CCAAAGAAGAAGACATTGATGGATTTCTTGTTGGTGGTGCCTCCTTGAAG                         GGTCCTGAGTTTG
genomic: CCAAAGAAGAAGACATTGATGGATTTCTTGTTGGTGGTGCCTCCTTGAAGgtaaaagtaa ... gtgactctagGGTCCTGAGTTTG
EST: gi|124826583|gb|EH911449.1|EH911449
EST:     GATGGATTTCTTGTTGGTGGTGCCTCCTTGAAG                         GGTCCTGAGTTTGCAACCATTGTGAACTCAGTCACGTCGAAAGAAAGTTGC
genomic: GATGGATTTCTTGTTGGTGGTGCCTCCTTGAAGgtaaaagtaa ... gtgactctagGGTCCTGAGTTTGCAACCATTGTGAACTCAGTCACGTCGAA-GAAAGTTGC
EST: gi|124954442|gb|EL029535.1|EL029535
EST:     ATTTCTTGTTGGTGGTGCCTCCTTGAAG                         GGTCCTTGAGTTTGCAACCATTGTGAACTCAGTCACGTCGAAGAAAGTTGC
genomic: ATTTCTTGTTGGTGGTGCCTCCTTGAAGgtaaaagtaa ... gtgactctagGGTCC-TGAGTTTGCAACCATTGTGAACTCAGTCACGTCGAAGAAAGTTGC
EST: gi|124947475|gb|EL023311.1|EL023311
EST:     CCAAAGAAGAAGACATTGATGGATTTCTTGTTGGTGGTGCCTCCTTGAAG                         GGTCCTGAGTTTGCAACCATTGTGAACTCAGTCACGTCGAAGAAAGTTG
genomic: CCAAAGAAGAAGACATTGATGGATTTCTTGTTGGTGGTGCCTCCTTGAAGgtaaaagtaa ... gtgactctagGGTCCTGAGTTTGCAACCATTGTGAACTCAGTCACGTCGAAGAAAGTTG
EST: gi|125038901|gb|EL111170.1|EL111170
EST:     GACATTGATGGATTTCTTTGTTGGTGGTGCCTCCTTGAAG                         GGTCCTGAGTTTGCAACCATTGTGAACTCAGTCACGTCGAAGAAAGTTGCT
genomic: GACATTGATGGATTTC-TTGTTGGTGGTGCCTCCTTGAAGgtaaaagtaa ... gtgactctagGGTCCTGAGTTTGCAACCATTGTGAACTCAGTCACGTCGAAGAAAGTTGCT
EST: gi|47828644|gb|CK118328.1|CK118328
EST:     CCAAAGAAGAAGACATTGATGGATTTCTTGTTGGTGGTGCCTCCTTGAAG                         GGTCCTGAGTTTGCAACCATTGTGAACTCAGTCACGTCGAAGAAAGTTGCT
genomic: CCAAAGAAGAAGACATTGATGGATTTCTTGTTGGTGGTGCCTCCTTGAAGgtaaaagtaa ... gtgactctagGGTCCTGAGTTTGCAACCATTGTGAACTCAGTCACGTCGAAGAAAGTTGCT
EST: gi|116463095|gb|EG505687.1|EG505687
EST:     CCAAAGAAGAAGACATTGATGGATTTCTTGTTGGTGGTGCCTCCTTGAAG                         GGTCCTGAGTTTGCAACCATTGTGAACTCAGTCACGTCGAAGAAAGTTGCT
genomic: CCAAAGAAGAAGACATTGATGGATTTCTTGTTGGTGGTGCCTCCTTGAAGgtaaaagtaa ... gtgactctagGGTCCTGAGTTTGCAACCATTGTGAACTCAGTCACGTCGAAGAAAGTTGCT
EST: gi|116454376|gb|EG496968.1|EG496968
EST:     CCAAAGAAGAAGACATTGATGGATTTCTTGTTGGTGGTGCCTCCTTGAAG                         GGTCCTGAGTTTGCAACCATTGTGAACTCAGTCACGTCGAAGAAAGTTGCT
genomic: CCAAAGAAGAAGACATTGATGGATTTCTTGTTGGTGGTGCCTCCTTGAAGgtaaaagtaa ... gtgactctagGGTCCTGAGTTTGCAACCATTGTGAACTCAGTCACGTCGAAGAAAGTTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgttgatgaatagaagtaaagcagctcacactcacctttattgtgactctagGGTCCTGAGTTTGCAACCATTGTGAACTCAGTCACGTCGAAGAAAGTTGCTGCTTGATTGAGAACTATCAGTAACGGAAATCGCTAGTCTCCATGGAACA
                               cactcac  putative branch site (score: 2)
                                       tttattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaagtaaagtttagacctttatggatatgttgttgatgaatagaagtaaagcagctcacactcacctttattgtgactctagGGTCCTGAGTTTGCAACCATTGTGAACTCAGTCACGTCGAAGAAAGTTGCTGCTTGATTGAGAACTATCAGTAACGGAAATCGCTAGTCTCCATGGAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA