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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattgttcagtgttagaatcttgtaacttaatttgtttcaaatttttggaagaagtcttatgtagcacttgtatgtttctgacaagatgatttagtcccccaaatttctatgtgcattttggaacattaatatgtgattggtgcatctagGTGTTTCACGGGGCTGACAACGATGTTATCTGGCTTCAAAGAGACTTCCATATATATGTTGTTAATATGTTTGATACTGCCAAG

Basic information

species Arabidopsis thaliana
transcript AT2G32415.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G32415.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os07g32890.1 (Oryza sativa), 3'ss of exon 3
gtatattgttcagtgttagaatcttgtaacttaatttgtttcaaatttttggaagaagtcttatgtagcacttgtatgtt--tctgacaagatgattta-gtcccccaaattt-ctatgtgcattttggaacattaatatgtgattggtgcatctagGTGTTTCACGGGGCTGACAACGATGTTATCTGGCTTCAAAGAGACTTCCATATATATGTTGTTAATATGTTTGATACTGCCAAG
                                                        || |  |   |     |||||  |  ||| |  ||| ||| |  ||  |     |||  ||  |||| |||     |          | |  |   || || | || || || |||||||| |||||| | |||||||| |||||||| ||||| |||||||| |||||||||||||||||||||
--------------------------------------------------------agccaaaatcaattgctgtataatcgtctcagcagaagatctgtgttgctttcttttattaaatgcagtttcatttaccttctccctacttatttgtc-agATCTTCCATGGAGCTGACAATGATGTTCTTTGGCTTCAGAGAGACTTTCATATTTATGTTGTGAATATGTTTGATACTGCCAAG

upper sequence: AT2G32415.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G048819_T01 (Zea mays), 3'ss of exon 3
gtatattgttcagtgttagaatcttgtaacttaatttgtttcaaatttttggaagaagtcttatgtagcacttgtatgtttctgacaagatgatttagtcccccaaat-ttctatgtgcattttggaacattaatatgt-gattggtgcatctagGTGTTTCACGGGGCTGACAACGATGTTATCTGGCTTCAAAGAGACTTCCATATATATGTTGTTAATATGTTTGATACTGCCAAG
                                                ||    |   |  ||||   | |   ||     |  | || |  |  ||  |      |  | |||  ||||       |||||  | ||| |  |  ||| | ||| | || || || |||||||| ||| || | ||||||||||| || || ||||| |||||||| ||||||||||||||||| |||
------------------------------------------------ttcattgtgtttatatgccactcaattactcagcccagaataaaagataaactgtgggacgtcctaaatgcac------acatttttctgttgccttatgc-tgtagATCTTCCATGGAGCTGACAATGATATTCTTTGGCTTCAAAGGGATTTTCATATTTATGTTGTGAATATGTTTGATACTGCTAAG

upper sequence: AT2G32415.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G46220.1 (Glycine max), 3'ss of exon 3
gtatattgttcagtgttagaatcttgtaacttaatttgtttcaaatttttggaagaagtcttatgtagcacttgtatgtttctgacaagatgatttagtcccccaaatttctatgt-gca--ttttggaaca-ttaatatgtgattggtgcatctagGTGTTTCACGGGGCTGACAACGATGTTATCTGGCTTCAAAGAGACTTCCATATATATGTTGTTAATATGTTTGATACTGCCAAG
                                             | | | ||| || | || |         || | ||  || ||   || ||| |||  |||| | | | | |  ||  ||||    || | |||     ||| ||| ||  ||||||| || ||||||||||| ||| |  ||||||| || || |||||||||||||| ||||||||| | ||||||||| | |||
---------------------------------------------tctgttgaaaaaatatttta--------gtttattattgtcag--tgtttttgtcatccaattctatttattacagtttttctctcactcaatggaaaatttgtggat--agGTGTTCCATGGGGCTGACAATGATATAGTCTGGCTACAGAGGGACTTCCATATATACGTTGTTAATCTATTTGATACTTCAAAG

upper sequence: AT2G32415.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA12G10530.1 (Glycine max), 3'ss of exon 5
gtatattgttcagtgttagaatcttgtaacttaatttgtttcaaatttttggaagaagtcttatgtagcacttgtatgtttctgacaagatgatttagtcccccaaatttctatgtgcattttggaacattaatatgtgattggtgcatctagGTGTTTCACGGGGCTGACAACGATGTTATCTGGCTTCAAAGAGACTTCCATATATATGTTGTTAATATGTTTGAT--ACTGCCAAG
                                           |  | ||| || ||   || | ||  | |   |   || |  ||      | || |      | ||| |     |    ||||| |||             ||    |||||||| || ||||||||||| ||| |  ||||||| || || |||||||||||||| ||||||| | | ||||||  ||| | |||
----------------------------------------attatctattgaaaaaatatttgtttattattgtcagtgtttttgcatccaagtctatttattacagttttttcccactcaatggaaaatt-------------tgtggatagGTGTTCCATGGGGCTGACAATGATATAGTCTGGCTACAGAGGGACTTCCATATATACGTTGTTAGTCTATTTGATATACTTCAAAG

upper sequence: AT2G32415.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv12s0059g00620.t01 (Vitis vinifera), 3'ss of exon 3
gtatattgttcagtgttagaatcttgtaacttaatttgtttcaaatttttggaagaagtcttatgtagcacttgtatgtttctgacaagatgatttagtcccccaaatttctatgtgcattttggaaca-ttaatatgtgattggtgcatctagGTGTTTCACGGGGCTGACAACGATGTTATCTGGCTTCAAAGAGACTTCCATATATATGTTGTTAATATGTTTGATACTGCCAAG
                                             ||  |   | |||   | | |   | |   ||     |||  ||    |||  |      |||  || |    ||   | || | ||  ||    |||   | ||  ||||||| || || ||||| || |||||| | ||||| || ||||||||||||||||||||||||||  | ||||||||||| |||
---------------------------------------------ttgctaagacaagagctctttcttaataacat-----tgatgag----ttttatttttttaatcactttagtgatgcagtaatagttggtagaatattttcggatgcagGTGTTCCATGGTGCTGATAATGATGTTTTGTGGCTGCAGAGAGACTTCCATATATATGTTGTTAACTTATTTGATACTGCAAAG

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|116401011|gb|EG443603.1|EG443603
EST:     ATGTAATGAGTATTCTTCGTCCTGTTTTCTCTGATCCTAATATTTGTAGG                         GTGTTTCACGGGGCTGACAACGATGTTATCTGGCTTCAAAGAGACTTCCGT
genomic: ATGTAATGAGTATTCTTCGTCCTGTTTTCTCTGATCCTAATATTTGTAAGgtatattgtt ... gtgcatctagGTGTTTCACGGGGCTGACAACGATGTTATCTGGCTTCAAAGAGACTTCCAT
EST: gi|116401007|gb|EG443599.1|EG443599
EST:     ATGTAATGAGTATTCCTCGTCCTGTTTTCTCTGATCCTAATATTTGTAAG                         GTGTTTCACGGGGCTGACAACGATGTTATCTGGCTTCAAAGAGACTTCCAT
genomic: ATGTAATGAGTATTCTTCGTCCTGTTTTCTCTGATCCTAATATTTGTAAGgtatattgtt ... gtgcatctagGTGTTTCACGGGGCTGACAACGATGTTATCTGGCTTCAAAGAGACTTCCAT
EST: gi|116401013|gb|EG443605.1|EG443605
EST:     ATGTAATGAGTATTCTTCGTCCTGTTTTCTCTGATCCTAATATTTGTAAG                         GTGTTTCACGGGGCTGACAACGATGTTATCTGGCTTCAAAGAGACTTCCAT
genomic: ATGTAATGAGTATTCTTCGTCCTGTTTTCTCTGATCCTAATATTTGTAAGgtatattgtt ... gtgcatctagGTGTTTCACGGGGCTGACAACGATGTTATCTGGCTTCAAAGAGACTTCCAT
EST: gi|116401012|gb|EG443604.1|EG443604
EST:     TGTAATGAGTATTCTTCGTCCTGTTTTCTCTGATCCTAATATTTTGTAAG                         GTGTTTCACGGGGCTGACAACGATGTTATCTGGCTTCAA-GAGACTTCCA
genomic: TGTAATGAGTATTCTTCGTCCTGTTTTCTCTGATCCTAATATTT-GTAAGgtatattgtt ... gtgcatctagGTGTTTCACGGGGCTGACAACGATGTTATCTGGCTTCAAAGAGACTTCCA
EST: gi|116401014|gb|EG443606.1|EG443606
EST:     TGTAATGAGTATTCTTCGTCCTGTTTTCTCTGATCCTAATATTTTGTAAG                         GTGTTTCACGGGGCTGACAACGATGTTATCTGGCTTCAAA-AGACTTCCA
genomic: TGTAATGAGTATTCTTCGTCCTGTTTTCTCTGATCCTAATATTT-GTAAGgtatattgtt ... gtgcatctagGTGTTTCACGGGGCTGACAACGATGTTATCTGGCTTCAAAGAGACTTCCA
EST: gi|116401004|gb|EG443596.1|EG443596
EST:     ATGTAATGAGTATTCTTCGTCCTGTTTTCTCTGATCCTAATATTTGTAAG                         GTGTTTCACGGGGCTGACAACGATGTTATCTGGCTTCAAAGAGACTTCCAT
genomic: ATGTAATGAGTATTCTTCGTCCTGTTTTCTCTGATCCTAATATTTGTAAGgtatattgtt ... gtgcatctagGTGTTTCACGGGGCTGACAACGATGTTATCTGGCTTCAAAGAGACTTCCAT
EST: gi|116400762|gb|EG443354.1|EG443354
EST:     ATGTAATGAGTATTCTTCGTCCTGTTTTCTCTGATCCTAATATTTGTAAG                         GTGTTTCACGGGGCTGACAACGATGTTATCTGGCTTCAAAGAGACTTCCAT
genomic: ATGTAATGAGTATTCTTCGTCCTGTTTTCTCTGATCCTAATATTTGTAAGgtatattgtt ... gtgcatctagGTGTTTCACGGGGCTGACAACGATGTTATCTGGCTTCAAAGAGACTTCCAT
EST: gi|116401009|gb|EG443601.1|EG443601
EST:     ATGTAATGAGTATTCTTCGTCCCGTTTTCTCTGATCCTAATATTTGTAAG                         GTGTTTCACGGGGCTGACAACGATGTTATCTGGCTTCAAAGAGACTTCCAT
genomic: ATGTAATGAGTATTCTTCGTCCTGTTTTCTCTGATCCTAATATTTGTAAGgtatattgtt ... gtgcatctagGTGTTTCACGGGGCTGACAACGATGTTATCTGGCTTCAAAGAGACTTCCAT
EST: gi|116401015|gb|EG443607.1|EG443607
EST:     ATGTAATGAGTATTCTTCGTCCTGTTTTCTCTGATCCTAATATTTGTAAG                         GTGTTTCACGGGGCTGACAACGATGTTATCTGGCTTCAAAGAGACTTCCAT
genomic: ATGTAATGAGTATTCTTCGTCCTGTTTTCTCTGATCCTAATATTTGTAAGgtatattgtt ... gtgcatctagGTGTTTCACGGGGCTGACAACGATGTTATCTGGCTTCAAAGAGACTTCCAT
EST: gi|116388634|gb|EG431226.1|EG431226
EST:     ATGTAATGAGTATTCTTCGTCCTGTTTTCTCTGATCCTAATATTTGTAAG                         GTGTTTCACGGGGCTGACAACGATGTTATCTGGCTTCAAAGAGACTTCCAT
genomic: ATGTAATGAGTATTCTTCGTCCTGTTTTCTCTGATCCTAATATTTGTAAGgtatattgtt ... gtgcatctagGTGTTTCACGGGGCTGACAACGATGTTATCTGGCTTCAAAGAGACTTCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcccccaaatttctatgtgcattttggaacattaatatgtgattggtgcatctagGTGTTTCACGGGGCTGACAACGATGTTATCTGGCTTCAAAGAGACTTCCATATATATGTTGTTAATATGTTTGATACTGCCAAG
                             cattaat  putative branch site (score: 3)
                              attaatatgtgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatattgttcagtgttagaatcttgtaacttaatttgtttcaaatttttggaagaagtcttatgtagcacttgtatgtttctgacaagatgatttagtcccccaaatttctatgtgcattttggaacattaatatgtgattggtgcatctagGTGTTTCACGGGGCTGACAACGATGTTATCTGGCTTCAAAGAGACTTCCATATATATGTTGTTAATATGTTTGATACTGCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA