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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataacctgtctttgtttactcttttgattgctcttccttctgttttcttctactctcatactctgtttctgtttttgcatctaatgtagGCGTTTGTGAACCTTGTTATTACATTATGTGATGCTGGTGATTCGGTTGTCATGTTTGAGCCATACTACTTCAACTCCTACATGGCCTTTCAGATGACAG

Basic information

species Arabidopsis thaliana
transcript AT1G80360.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G80360.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g08270.1 (Oryza sativa), 3'ss of exon 5
-----------gtataacctgtctttgtttactcttttgattgctcttccttctgttttcttctactctcatactctgtttctgtttttgcatctaatgtagGCGTTTGTGAACCTTGTTATTACATTATGTGATGCTGGTGATTCGGTTGTCATGTTTGAGCCATACTACTTCAACTCCTACATGGCCTTTCAGATGACAG
           |||| ||    |||    ||  | ||   |  |   |   |  |     |   | ||  |||   || |    | | |  |  |   | |||| ||||| ||  | ||  | ||  | ||||||||||| ||| | |||||||||||||  ||||| |||||||| ||||||||| | || ||||||||||
cttacttttctgtatgactg--cttcacctaaaccttgtttaccaactaggttagccaaataaaagtcaaataaagtgatgtcttctatcaaattttggcagGCCTTTGTAAATGTGGTCCTCACCCTTTGTGATGCTGGGGATGCAGTTGTCATGTTTGCACCATATTACTTCAATTCCTACATGTCATTCCAGATGACAG

upper sequence: AT1G80360.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G029135_T01 (Zea mays), 3'ss of exon 4
---gtataacctgtctttgtttactcttttgattgc---tcttccttctg--ttttcttctactctcatactctgtttctgtttttgcatctaatgt--agGCGTTTGTGAACCTTGTTATTACATTATGTGATGCTGGTGATTCGGTTGTCATGTTTGAGCCATACTACTTCAACTCCTACATGGCCTTTCAGATGACAG
     || || | | |  |   || || ||  || |   | || || |||    ||  |||  ||| ||  |||| |  | || || |||  | | |  |||| ||||||||| | ||  | ||  | |||||||| |||||||| |||||||||||||  ||||| || |||||  |||||||| | || ||||||||||
tgttgattacttctttgggggcacactcttcctttcctgttttactcctgaaccttgatcttgtcttattatctggtctt-ttcttacattgatttttcagGCTTTTGTGAACTTGGTCCTCACTCTTTGTGATGCCGGTGATTCTGTTGTCATGTTTGCACCATATTATTTCAATGCCTACATGTCATTCCAGATGACAG

upper sequence: AT1G80360.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G107639_T01 (Zea mays), 3'ss of exon 4
----------------------------------------------------------------gtataacctgtctttgtt---tactcttttgattgctcttccttctgttttcttctactctcatactctgtttctgtttttgcatctaatgt--------------------agGCGTTTGTGAACCTTGTTATTACATTATGTGATGCTGGTGATTCGGTTGTCATGTTTGAGCCATACTACTTCAACTCCTACATGGCCTTTCAGATGACAG
                                                                    ||  |   | ||||   ||||  ||||   || |   ||||| |  | ||  |||   | ||  || |  ||| ||   ||||  | |                    |||| ||||||||| | ||  | ||  | ||||||||||||||||| |||||||||||||  || || || |||||  |||||||| | || ||||||||||
gtaagttctgcctgcatttactacctattttgccttgtagtgttttccaaatgggccttatgtttcccaatttacttctgttaattacttctttgggggcacactcttctttcctgtttcactgctagaccttgatcttgtcttataatctggtcttttctaacattgattttttcagGCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTCATGTTTGCACCGTATTATTTCAATGCCTACATGTCATTCCAGATGACAG

upper sequence: AT1G80360.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv09s0002g05250.t01 (Vitis vinifera), 3'ss of exon 4
------gtataacctgtctttgtttactcttttgattgct--cttccttctgttttcttctactctcatactctgtttctgtttttgcatctaatg-tagGCGTTTGTGAACCTTGTTATTACATTATGTGATGCTGGTGATTCGGTTGTCATGTTTGAGCCATACTACTTCAACTCCTACATGGCCTTTCAGATGACAG
        |    ||||  ||| |          | || |  ||||| ||  ||||  |  |||   | |   |  |    || ||  |  | |||  |||| |||||||| || ||| ||||||||||||||||||| |||| |||||| |||||||  ||||||||||||||  | |||||| |||| ||||||||||
tatagaacagtttctgttcttgctattagccaaaagtgttagcttccatccatttttctagacttctaaagcattgtctacttattttacttgatggcagGCATTTGTGAATCTCGTTCTTACATTATGTGATGCTGGAGATTTGGTTGTTATGTTTGCACCATACTACTTCAATGCATACATGTCCTTCCAGATGACAG

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|86063484|gb|DR359241.1|DR359241
EST:     AAAACAAGCTAACCAATTCACAAGTGATGGTTACTGCAGGTGCCAATCAG                         GCGTTTGTGAACCTTGTTATKACATTATGTGATGCTGGTGATACGGTTGTC
genomic: AAAACAAGCTAACCAATTCACAAGTGATGGTTACTGCAGGTGCCAATCAGgtataacctg ... tctaatgtagGCGTTTGTGAACCTTGTTATTACATTATGTGATGCTGGTGATTCGGTTGTC
EST: gi|86063488|gb|DR359245.1|DR359245
EST:     AAAACAAGCTAACCAATTCACAAGTGATGGTTACTGCAGGTGCCAATCAG                         GCGTTTGTGAACCTTGTTATTN-ATTATGTGATGSTGGTGATTCGGTTGTC
genomic: AAAACAAGCTAACCAATTCACAAGTGATGGTTACTGCAGGTGCCAATCAGgtataacctg ... tctaatgtagGCGTTTGTGAACCTTGTTATTACATTATGTGATGCTGGTGATTCGGTTGTC
EST: gi|86063487|gb|DR359244.1|DR359244
EST:     AAAACAAGSTAASCAATTCACAAGTGATGGTTACTGCAGGTGCCAATCAG                         GCGTTTGTGAACCTTGTTATTACATTATGTGATGCTGGTGATTCGGTTGTC
genomic: AAAACAAGCTAACCAATTCACAAGTGATGGTTACTGCAGGTGCCAATCAGgtataacctg ... tctaatgtagGCGTTTGTGAACCTTGTTATTACATTATGTGATGCTGGTGATTCGGTTGTC
EST: gi|125041877|gb|EL114146.1|EL114146
EST:     CAATTCACAAGTGATGGTTACTGCAGGTGCCAATCAG                         GCGTTTGTGAACCTTGTTATTACATTATGTGATGCTGGTGATTCGGTTGTC
genomic: CAATTCACAAGTGATGGTTACTGCAGGTGCCAATCAGgtataacctg ... tctaatgtagGCGTTTGTGAACCTTGTTATTACATTATGTGATGCTGGTGATTCGGTTGTC
EST: gi|124885316|gb|EH964218.1|EH964218
EST:     CAATTCACAAGTGATGGTTACTGCTAGGTGCCAATCAG                         GCGTTTGTGAACCTTGTTATTACATTATGTGATGCTGGTGATTCGGTTGTC
genomic: CAATTCACAAGTGATGGTTACTGC-AGGTGCCAATCAGgtataacctg ... tctaatgtagGCGTTTGTGAACCTTGTTATTACATTATGTGATGCTGGTGATTCGGTTGTC
EST: gi|86063483|gb|DR359240.1|DR359240
EST:     AAAACAAGCTAACCAATTCACAAGTGATGGTTACTGCAGGTGCCAATCAG                         GCGTTTGTGAACCTTGTTATTACATTATGTGATGCTGGTGATTCGGTTGTC
genomic: AAAACAAGCTAACCAATTCACAAGTGATGGTTACTGCAGGTGCCAATCAGgtataacctg ... tctaatgtagGCGTTTGTGAACCTTGTTATTACATTATGTGATGCTGGTGATTCGGTTGTC
EST: gi|86063485|gb|DR359242.1|DR359242
EST:     AAAACAAGCTAACCAATTCACAAGTGATGGTTACTGCAGGTGCCAATCAG                         GCGTTTGTGAACCTTGTTATTACATTATGTGATGCTGGTGATTCGGTTGTC
genomic: AAAACAAGCTAACCAATTCACAAGTGATGGTTACTGCAGGTGCCAATCAGgtataacctg ... tctaatgtagGCGTTTGTGAACCTTGTTATTACATTATGTGATGCTGGTGATTCGGTTGTC
EST: gi|86063482|gb|DR359239.1|DR359239
EST:     AAAACAAGCTAACCAATTCACAAGTGATGGTTACTGCAGGTGCCAATCAG                         GCGTTTGTGAACCTTGTTATTACATTATGTGATGCTGGTGATTCGGTTGTC
genomic: AAAACAAGCTAACCAATTCACAAGTGATGGTTACTGCAGGTGCCAATCAGgtataacctg ... tctaatgtagGCGTTTGTGAACCTTGTTATTACATTATGTGATGCTGGTGATTCGGTTGTC
EST: gi|86063486|gb|DR359243.1|DR359243
EST:     AAAACAAGCTAACCAATTCACAAGTGATGGTTACTGCAGGTGCCAATCAG                         GCGTTTGTGAACCTTGTTATTACATTATGTGATGCTGGTGATTCGGTTGTC
genomic: AAAACAAGCTAACCAATTCACAAGTGATGGTTACTGCAGGTGCCAATCAGgtataacctg ... tctaatgtagGCGTTTGTGAACCTTGTTATTACATTATGTGATGCTGGTGATTCGGTTGTC
EST: gi|124716466|gb|EH807868.1|EH807868
EST:     AAAACAAGCTAACCAATTCACAAGTGATGGTTACTGCAGGTGCCAATCAG                         GCGTTTGTGAACCTTGTTATTACATTATGTGAT
genomic: AAAACAAGCTAACCAATTCACAAGTGATGGTTACTGCAGGTGCCAATCAGgtataacctg ... tctaatgtagGCGTTTGTGAACCTTGTTATTACATTATGTGAT
EST: gi|47830762|gb|CK120446.1|CK120446
EST:     AAAACAAGCTAACCAATTCACAAGTGATGGTTACTGCAGGTGCCAATCAG                         GCGTTTGTGAACCTTGTTATTACATTATGTGATGCTGGTGATTCGGTTGTC
genomic: AAAACAAGCTAACCAATTCACAAGTGATGGTTACTGCAGGTGCCAATCAGgtataacctg ... tctaatgtagGCGTTTGTGAACCTTGTTATTACATTATGTGATGCTGGTGATTCGGTTGTC
EST: gi|86063489|gb|DR359246.1|DR359246
EST:     AAAACAAGCTAACCAATTCACAAGTGATGGTTACTGCAGGTGCCAATCAG                         GCGTTTGTGAACCTTGTTATTACATTATGTGATGCTGGTGATTCGGTTGTC
genomic: AAAACAAGCTAACCAATTCACAAGTGATGGTTACTGCAGGTGCCAATCAGgtataacctg ... tctaatgtagGCGTTTGTGAACCTTGTTATTACATTATGTGATGCTGGTGATTCGGTTGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccttctgttttcttctactctcatactctgtttctgtttttgcatctaatgtagGCGTTTGTGAACCTTGTTATTACATTATGTGATGCTGGTGATTCGGTTGTCATGTTTGAGCCATACTACTTCAACTCCTACATGGCCTTTCAGATGACAG
                                            atctaat  putative branch site (score: 3)
        ttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataacctgtctttgtttactcttttgattgctcttccttctgttttcttctactctcatactctgtttctgtttttgcatctaatgtagGCGTTTGTGAACCTTGTTATTACATTATGTGATGCTGGTGATTCGGTTGTCATGTTTGAGCCATACTACTTCAACTCCTACATGGCCTTTCAGATGACAG

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