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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatcagcctaattatttctgtttaattttgaagctattatttgtctctctatatacgaccccaattgttttgtctggaatcgtctttccttacctgtttgtttgtgtttttgggaaatagGTATGGCTTTTGGTACTGGAAGTGCAGTTGCACACAGGGCTGTTGATTCTGTGATGGGTCCACGAACCATTCAGCATGAGGCTGTTGAGGCTGCTTCTGC

Basic information

species Arabidopsis thaliana
transcript AT5G64400.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G64400.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g48080.1 (Oryza sativa), 3'ss of exon 3
gtaaatcagcctaattatttctgtttaattttgaagctattattt-gtctctctatatacgaccccaattgttttgt-ctggaatcgtctttccttacctgtttgtttgtgtttttgggaaatagGTATGGCTTTTGGTACTGGAAGTGCAGTTGCACACAGGGCTGTTGATTCTGTGATGGGTCCACGAACCATTCAGCATGAGGCTGTTGAGGCTGCTTCTGC
                                      || |||| |  ||  | ||   ||    ||| |  || |  |   |  |   || || |   ||   | | ||    |   |   ||| ||||||||||||||||| |||||  | ||||| |||||||||||| |||| |||||||| || ||||||||||||||| ||||||   | |   ||||
---------------------------------gtatcatcattttgcttcattttaattgaaatgaatagcattatattaacaatgcagtttctaataagtacttctttgcacatat-atgcagGCATGGCTTTTGGTACTGGTAGTGCCATGGCACATAGGGCTGTTGATGCTGTAATGGGTCCCCGTACCATTCAGCATGAGACTGTTGTCTCCGAGGCTGC

upper sequence: AT5G64400.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G028379_T03 (Zea mays), 3'ss of exon 3
gtaaatcagcctaattatttctgtttaattttgaagctattatttgtctctctatatacgaccccaattgttttgtctggaatcgtctttccttacctgtttgtttgtgtttttgggaaatagGTATGGCTTTTGGTACTGGAAGTGCAGTTGCACACAGGGCTGTTGATTCTGTGATGGGTCCACGAACCATTCAGCATGAGGCTGTTGAGGCTGCTTCTGC
                              | | |   |   ||||||  | | |  |   |  ||  | |      |   ||| |  | | | |  ||  ||    | || ||       ||||||||| ||||| || || |||||  | |||||||||||||||||| ||||  | ||||| || ||||||||||||||| ||||||   | |   ||||
-----------------------------gtggtattcaaagtttgtccttttctggatagcttcagctataaacatt---atcataatccttgaattgaatgaacatattcttt-----cagGTATGGCGTTTGGCACGGGTAGTGCCATGGCACACAGGGCTGTTGATGCTGTATTAGGTCCCCGGACCATTCAGCATGAGACTGTTGCCTCAGAAGCTGC

upper sequence: AT5G64400.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G031501_T01 (Zea mays), 3'ss of exon 3
gtaaatcagcctaattatttctgtttaattttgaagctattatttgtctctctatatacgaccccaattgttttgtctggaatcgtctttccttacctgtttgtttgtgtttttgggaaatagGTATGGCTTTTGGTACTGGAAGTGCAGTTGCACACAGGGCTGTTGATTCTGTGATGGGTCCACGAACCATTCAGCATGAGGCTGTTGAGGCTGCTTCTGC
                         |  | |||||        ||||   | | |  |   |  |   || | |       ||| |  | | | |  ||  ||    | || ||       ||||||||| ||||| || || |||||  | ||||||||||||||||| |||||  | ||||| || ||||| ||||||||| || |||   | |   || |
------------------------gtggtgttgaaa-----gcttgttcttttctggatagcttc---tgctataaacattatcataatccttgaattgaatgaacattttcttt-----cagGTATGGCGTTTGGCACGGGTAGTGCCATGGCACACAGGGCTGTTGACTCTGTATTAGGTCCCCGGACCATCCAGCATGAGACTCTTGCCACAGAAGCTCC

upper sequence: AT5G64400.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G031501_T02 (Zea mays), 3'ss of exon 3
gtaaatcagcctaattatttctgtttaattttgaagctattatttgtctctctatatacgaccccaattgttttgtctggaatcgtctttccttacctgtttgtttgtgtttttgggaaatagGTATGGCTTTTGGTACTGGAAGTGCAGTTGCACACAGGGCTGTTGATTCTGTGATGGGTCCACGAACCATTCAGCATGAGGCTGTTGAGGCTGCTTCTGC
                            | |||||        ||||   | | |  |   |  |   || | |       ||| |  | | | |  ||  ||    | || ||       ||||||||| ||||| || || |||||  | ||||||||||||||||| |||||  | ||||| || ||||| ||||||||| || |||   | |   || |
---------------------------gtgttgaaa-----gcttgttcttttctggatagcttc---tgctataaacattatcataatccttgaattgaatgaacattttcttt-----cagGTATGGCGTTTGGCACGGGTAGTGCCATGGCACACAGGGCTGTTGACTCTGTATTAGGTCCCCGGACCATCCAGCATGAGACTCTTGCCACAGAAGCTCC

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|124981501|gb|EL054366.1|EL054366
EST:     CGGTGGTGGTGGTGGCATGTTCTCAGGCATTGGTTCAACCATTGCTCAGG                         GTATGGCTTTTGGTACTGGAAGTGCAGTTGCACACAG
genomic: CGGTGGTGGTGGTGGCATGTTCTCAGGCATTGGTTCAACCATTGCTCAGGgtaaatcagc ... tgggaaatagGTATGGCTTTTGGTACTGGAAGTGCAGTTGCACACAG
EST: gi|86081614|gb|DR377371.1|DR377371
EST:     CGGTGGTGGTGGTGGCATGTTCTCAGGCATTGGTTCAACCATTGCTCAGG                         GTATGGCTTTTGGTACTGGAAGTGCAGTTGCACACAGGGCTGTTGATTCTG
genomic: CGGTGGTGGTGGTGGCATGTTCTCAGGCATTGGTTCAACCATTGCTCAGGgtaaatcagc ... tgggaaatagGTATGGCTTTTGGTACTGGAAGTGCAGTTGCACACAGGGCTGTTGATTCTG
EST: gi|116439471|gb|EG482063.1|EG482063
EST:     CGGTGGTGGTGGTGGCATGTTTTCAGGCATTGGTTCAACCATTGCTCAGG                         GTATGGCTTTTGGTACTGGAAGTGCAGTTGCACACAGGGCTGTTGGTTTTG
genomic: CGGTGGTGGTGGTGGCATGTTCTCAGGCATTGGTTCAACCATTGCTCAGGgtaaatcagc ... tgggaaatagGTATGGCTTTTGGTACTGGAAGTGCAGTTGCACACAGGGCTGTTGATTCTG
EST: gi|164170071|gb|ES013034.1|ES013034
EST:     CGGTGGTGGTGGTGGCATGTTCTCAGGCATTGGTTCAACCATTGCTCAGG                         GTATGGCTTTTGGTACTGGAAGTGCAGTTGCACACAGGGCT
genomic: CGGTGGTGGTGGTGGCATGTTCTCAGGCATTGGTTCAACCATTGCTCAGGgtaaatcagc ... tgggaaatagGTATGGCTTTTGGTACTGGAAGTGCAGTTGCACACAGGGCT
EST: gi|47829059|gb|CK118743.1|CK118743
EST:     CGGTGGTGGTGGTGGCATGTTCTCAGGCATTGGTTCAACCATTGCTCAGG                         GTATGGCTTTTGGTACTGGAAGTGCAGTTGCACACAGGGCTGTTGATTCTG
genomic: CGGTGGTGGTGGTGGCATGTTCTCAGGCATTGGTTCAACCATTGCTCAGGgtaaatcagc ... tgggaaatagGTATGGCTTTTGGTACTGGAAGTGCAGTTGCACACAGGGCTGTTGATTCTG
EST: gi|124793881|gb|EH883560.1|EH883560
EST:     CGGTGGTGGTGGTGGCATGTTCTCAGGCATTGGTTCAACCATTGCTCAGG                         GTATGGCTTTTGGTACTGGAAG
genomic: CGGTGGTGGTGGTGGCATGTTCTCAGGCATTGGTTCAACCATTGCTCAGGgtaaatcagc ... tgggaaatagGTATGGCTTTTGGTACTGGAAG
EST: gi|125062199|gb|EL130635.1|EL130635
EST:     CATTGGTTCAACCATTGCTCAGG                         GTATGGCTTTTGGTACTGGAAGTGCAGTTGCACACAGGGCTGTTGATTCTG
genomic: CATTGGTTCAACCATTGCTCAGGgtaaatcagc ... tgggaaatagGTATGGCTTTTGGTACTGGAAGTGCAGTTGCACACAGGGCTGTTGATTCTG
EST: gi|125004940|gb|EL077209.1|EL077209
EST:     ATGTTCTCAGGCATTGGTTCAACCACTTGCTCAGG                         GTATGGCTTTTGGTACTGGAAGTGCAGTTGCACACAGGGCTGTTGATTCT
genomic: ATGTTCTCAGGCATTGGTTCAACCA-TTGCTCAGGgtaaatcagc ... tgggaaatagGTATGGCTTTTGGTACTGGAAGTGCAGTTGCACACAGGGCTGTTGATTCT
EST: gi|116462329|gb|EG504921.1|EG504921
EST:     C---GGTGGTGGTGGCGTGTTTTCAGGCATTGGTTCAACCATTGCTCAGG                         GTATGGCTTTTGGTACTGGAAGTGCAGTTGCACACAGGGCTGTTGATTCTG
genomic: CGGTGGTGGTGGTGGCATGTTCTCAGGCATTGGTTCAACCATTGCTCAGGgtaaatcagc ... tgggaaatagGTATGGCTTTTGGTACTGGAAGTGCAGTTGCACACAGGGCTGTTGATTCTG
EST: gi|124881546|gb|EH960448.1|EH960448
EST:     ATTGGTTCAACCATTGCTCAGG                         GTATGGCTTTTGGTACTGGAAGTGCAGTTGCACA
genomic: ATTGGTTCAACCATTGCTCAGGgtaaatcagc ... tgggaaatagGTATGGCTTTTGGTACTGGAAGTGCAGTTGCACA
EST: gi|164102205|gb|ES191306.1|ES191306
EST:     CGGTGGTGGTGGTGGCATGTTCTCAGGCATTGGTTCAACCATTGCTCAGG                         GTATGGCTTTTGGTACTGGAAGTGCAGTTGCACACAGGGCTGTTGATT
genomic: CGGTGGTGGTGGTGGCATGTTCTCAGGCATTGGTTCAACCATTGCTCAGGgtaaatcagc ... tgggaaatagGTATGGCTTTTGGTACTGGAAGTGCAGTTGCACACAGGGCTGTTGATT
EST: gi|301502466|gb|HO208006.1|HO208006
EST:     CGGTGGTGGTGGTGGCATGTTCTCAGGCATTGGTTCAACCATTGCTCAGG                         GTATGGCTTTTGGTACTGGAAGTGCAGTTGCACACAGGGCTGTTGATTCTG
genomic: CGGTGGTGGTGGTGGCATGTTCTCAGGCATTGGTTCAACCATTGCTCAGGgtaaatcagc ... tgggaaatagGTATGGCTTTTGGTACTGGAAGTGCAGTTGCACACAGGGCTGTTGATTCTG
EST: gi|116439469|gb|EG482061.1|EG482061
EST:     CGGTGGTGGTGGTGGCATGTTCTCAGGCATTGGTTCAACCATTGCTCAGG                         GTATGGCTTTTGGTACTGGAAGTGCAGTTGCACACAGGGCTGTTGGTTCTG
genomic: CGGTGGTGGTGGTGGCATGTTCTCAGGCATTGGTTCAACCATTGCTCAGGgtaaatcagc ... tgggaaatagGTATGGCTTTTGGTACTGGAAGTGCAGTTGCACACAGGGCTGTTGATTCTG
EST: gi|125265945|gb|EL280030.1|EL280030
EST:     CATTGGTTCAACCATTGCTCAGG                         GTATGGCTTTTGGTACTGGAAGTGCAGTTGCACACAGGGCTGTTGATTCTG
genomic: CATTGGTTCAACCATTGCTCAGGgtaaatcagc ... tgggaaatagGTATGGCTTTTGGTACTGGAAGTGCAGTTGCACACAGGGCTGTTGATTCTG
EST: gi|152035094|gb|BP844446.2|BP844446
EST:     CGGTGGTGGTGGTGGCATGTTCTCAGGCATTGGTTCAACCATTGCTCAGG                         GTATGGCTTTTGGTACTGGAAGTGCAGTTGCACACAGGGCTGTTGATTCTG
genomic: CGGTGGTGGTGGTGGCATGTTCTCAGGCATTGGTTCAACCATTGCTCAGGgtaaatcagc ... tgggaaatagGTATGGCTTTTGGTACTGGAAGTGCAGTTGCACACAGGGCTGTTGATTCTG
EST: gi|124945501|gb|EL021502.1|EL021502
EST:     CGGTGGTGGTGGTGGCATGTTCTCAGGCATTGGTTCAACCATTGCTCAGG                         GTATGGCTTT-GGTACTGGAAGTGCAGTTGCACACAG
genomic: CGGTGGTGGTGGTGGCATGTTCTCAGGCATTGGTTCAACCATTGCTCAGGgtaaatcagc ... tgggaaatagGTATGGCTTTTGGTACTGGAAGTGCAGTTGCACACAG
EST: gi|125198180|gb|EL213134.1|EL213134
EST:     CATGTTCTCAGGCATTGGTTCAACCATTGCTCAGG                         GTATGGCTTTTGGTACTGGAAGTGCAGTTGCACACAGGGCTGTTGATTCTG
genomic: CATGTTCTCAGGCATTGGTTCAACCATTGCTCAGGgtaaatcagc ... tgggaaatagGTATGGCTTTTGGTACTGGAAGTGCAGTTGCACACAGGGCTGTTGATTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttgtctggaatcgtctttccttacctgtttgtttgtgtttttgggaaatagGTATGGCTTTTGGTACTGGAAGTGCAGTTGCACACAGGGCTGTTGATTCTGTGATGGGTCCACGAACCATTCAGCATGAGGCTGTTGAGGCTGCTTCTGC
                     tccttac  putative branch site (score: 2)
                                       tgttttt  putative PPT
                               tttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatcagcctaattatttctgtttaattttgaagctattatttgtctctctatatacgaccccaattgttttgtctggaatcgtctttccttacctgtttgtttgtgtttttgggaaatagGTATGGCTTTTGGTACTGGAAGTGCAGTTGCACACAGGGCTGTTGATTCTGTGATGGGTCCACGAACCATTCAGCATGAGGCTGTTGAGGCTGCTTCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT