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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatttcatgtttcactatctgcttctagtcagatttgcttggttcaagtagacaatagctcaagaggaaaagttctgaagatctcataggtaatgaatgtctctgttttggtttttcagGTATACCGGGGAAGATGGGTTTGAGATTTCGGTTCCAGATGAGCATGCTGTGGATCTAGCAAAAGCAATCTTGGAGAAGTCCGAGGGTAAGGTAAGGCTT

Basic information

species Arabidopsis thaliana
transcript AT1G11860.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G11860.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G01550.1 (Glycine max), 3'ss of exon 3
gtaaaatttcatgttt-cactatctgcttctagtcagatttgcttggttcaagtagacaatagctcaagaggaaaagttctgaagatctcataggtaatgaatgtctct-gttttggtttttcagGTATACCGGGGAAGATGGGTTTGAGATTTCGGTTCCAGATGAGCATGCTGTGGATCTAGCAAAAGCAATCTTGGAGAAGTCCGAGGGTAAGGTAAGGCTT
       | |||||||    |||  |||      |||| || ||     || | | || ||  ||       ||      |||   |  ||    |||| |   | ||| | || ||  |||||||||||| ||||||||||| |||||||| || |||||    |||||||  || ||||| || ||||||||  |||| || || || || ||||||||  | 
-------tgcatgtttgtgttattagct------cagagtttct-----cagggacaccatgcct-------aatctcattgattgtaccaagcataataaccttttcttgattgggactttcagGTATACTGGGGAAGATGGATTTGAGATCTCAGTTCCTTCAGAGCATGGAGTAGATCTTGCCAAAGCAATACTGGAAAAATCTGAAGGGAAGGTAAGATTG

upper sequence: AT1G11860.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv10s0116g01540.t01 (Vitis vinifera), 3'ss of exon 2
gtaaaatttcatgtttcactatctgcttctagtcagatttgcttggttcaagtagacaatagctcaagaggaaaagttctgaagatctcataggtaatgaatgtctctgttttggtttttcagGTATACCGGGGAAGATGGGTTTGAGATTTCGGTTCCAGATGAGCATGCTGTGGATCTAGCAAAAGCAATCTTGGAGAAGTCCGAGGGTAAGGTAAGGCTT
               | |  || |  |   | ||  | |||       |||   ||  |  |    |    | ||   |   | |    | |  | ||   |   |          |||||||||| || || |||||||| ||||| ||||| |||||    ||| |||| || ||||| || ||||||||||||||||| || || || ||||||||| | 
---------------taatgatttagtcacaatccaaattg-------caatatgatgactgtctgaatcaacaaaccccaca-acaagacacttgatattttctttacacgaaaattttcagGTACACAGGTGAAGATGGATTTGAAATTTCAGTTCCTTCCGAGAATGCAGTAGATCTTGCCAAAGCAATCTTGGAGAAATCTGAAGGGAAGGTAAGGTTA
















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|124900235|gb|EH974853.1|EH974853
EST:     TTCCAGATTCTGGACATTAATGGTTCCACATGTTTCCTTACCAGGACTGG                         GTATACCGGGGAAGATGGGTTTGAGATTTCGGTTCCAGA
genomic: TTCCAGATTCTGGACATTAATGGTTCCACATGTTTCCTTACCAGGACTGGgtaaaatttc ... ggtttttcagGTATACCGGGGAAGATGGGTTTGAGATTTCGGTTCCAGA
EST: gi|124805673|gb|EH892936.1|EH892936
EST:     TGTTTCCTTACCAGGACTGG                         GTATACCGGGGAAGATGGGTTTGAGATTTCGGTTCCAGATGAGCATGCTGT
genomic: TGTTTCCTTACCAGGACTGGgtaaaatttc ... ggtttttcagGTATACCGGGGAAGATGGGTTTGAGATTTCGGTTCCAGATGAGCATGCTGT
EST: gi|125287201|gb|EL301286.1|EL301286
EST:     TTCCAGATTCTGGACATTAATGGTTCCACATGTTTCCTTACCAGGACTGG                         GTATACCGGGGAAGATGGGTTTGAGATTTCGGTTC
genomic: TTCCAGATTCTGGACATTAATGGTTCCACATGTTTCCTTACCAGGACTGGgtaaaatttc ... ggtttttcagGTATACCGGGGAAGATGGGTTTGAGATTTCGGTTC
EST: gi|125081495|gb|EL142699.1|EL142699
EST:     ATTAATGGTTCCACATGTTTCCTTACCAGGACTGG                         GTATACCGGGGAAGATGG-TT-GAGATTTCGGTTCCAGATGAGCATGCTGT
genomic: ATTAATGGTTCCACATGTTTCCTTACCAGGACTGGgtaaaatttc ... ggtttttcagGTATACCGGGGAAGATGGGTTTGAGATTTCGGTTCCAGATGAGCATGCTGT
EST: gi|125294859|gb|EL308944.1|EL308944
EST:     TTCCAGATTCTGGACATTAATGGTTCCACATGTTTCCTTACCAGGACTGG                         GTATACCGGGGAAGATGGGTTTGAGATTTCGGTT
genomic: TTCCAGATTCTGGACATTAATGGTTCCACATGTTTCCTTACCAGGACTGGgtaaaatttc ... ggtttttcagGTATACCGGGGAAGATGGGTTTGAGATTTCGGTT
EST: gi|125221815|gb|EL235900.1|EL235900
EST:     TGGTTCCACATGTTTCCTTACCAGGACTGG                         GTATACC-GGGAAGATGGGTTTGAGATTTCGGTTCCAGATGAGCATGCTGT
genomic: TGGTTCCACATGTTTCCTTACCAGGACTGGgtaaaatttc ... ggtttttcagGTATACCGGGGAAGATGGGTTTGAGATTTCGGTTCCAGATGAGCATGCTGT
EST: gi|125231677|gb|EL245762.1|EL245762
EST:     TACCAGGACTGG                         GTATACCGGGGAAGATGGGTTTGAGATTTCGGTTCCAGATGAGCATGCTGT
genomic: TACCAGGACTGGgtaaaatttc ... ggtttttcagGTATACCGGGGAAGATGGGTTTGAGATTTCGGTTCCAGATGAGCATGCTGT
EST: gi|125014384|gb|EL086653.1|EL086653
EST:     TCCAGATTTCTGGACATTAATGGTTCCACATGTTTCCTTACCAGGACTGG                         GTATACCGGGGAAGATGGGTTTGAGATTTCGGTTCCAGA
genomic: TCCAGA-TTCTGGACATTAATGGTTCCACATGTTTCCTTACCAGGACTGGgtaaaatttc ... ggtttttcagGTATACCGGGGAAGATGGGTTTGAGATTTCGGTTCCAGA
EST: gi|125063254|gb|EL131299.1|EL131299
EST:     TTCCAGATTCTGGACATTAATGGTTCCACATGTTTCCTTACCAGGACTGG                         GTATACCGGGGAAGATGGGTTTGAGATTTCGG
genomic: TTCCAGATTCTGGACATTAATGGTTCCACATGTTTCCTTACCAGGACTGGgtaaaatttc ... ggtttttcagGTATACCGGGGAAGATGGGTTTGAGATTTCGG
EST: gi|125010791|gb|EL083060.1|EL083060
EST:     TTCCAGATTCTGGACATTAATGGTTCCACATGTTTCCTTACCAGGACTGG                         GTATACCGGGGAAGATGGGTTTGAGATTTCGGTTCCAGATGAGCATGCTGT
genomic: TTCCAGATTCTGGACATTAATGGTTCCACATGTTTCCTTACCAGGACTGGgtaaaatttc ... ggtttttcagGTATACCGGGGAAGATGGGTTTGAGATTTCGGTTCCAGATGAGCATGCTGT
EST: gi|125003052|gb|EL075321.1|EL075321
EST:     TTCCAGATTCTGGACATTAATGGTTCCACATGTTTCCTTACCAGGACTGG                         GTATACCGGGGAAGATGGGTTTGAGA
genomic: TTCCAGATTCTGGACATTAATGGTTCCACATGTTTCCTTACCAGGACTGGgtaaaatttc ... ggtttttcagGTATACCGGGGAAGATGGGTTTGAGA
EST: gi|124745307|gb|EH836267.1|EH836267
EST:     TTCTGGACATTAATGGTTCCACATGTTTCCTTACCAGGACTGG                         GTATACCGGGGAAGATGGGTTTGAGATTTCGGTTCCAGATGAAGCATGCTG
genomic: TTCTGGACATTAATGGTTCCACATGTTTCCTTACCAGGACTGGgtaaaatttc ... ggtttttcagGTATACCGGGGAAGATGGGTTTGAGATTTCGGTTCCAGATGA-GCATGCTG
EST: gi|124970399|gb|EL044232.1|EL044232
EST:     TTAATGGTTCCACATGTTTCCTTACCAGGACTGG                         GTATACCGGGGAAGATGGGTTTGAGATTTCGGTTCCAGATGAGCATGCTGT
genomic: TTAATGGTTCCACATGTTTCCTTACCAGGACTGGgtaaaatttc ... ggtttttcagGTATACCGGGGAAGATGGGTTTGAGATTTCGGTTCCAGATGAGCATGCTGT
EST: gi|125105432|gb|EL159197.1|EL159197
EST:     CAGATTCTGGACATTAATGGTTCCACATGTTTCCTTACCAGGACTGG                         GTATACCGGGGAAGATGGGTTTGAGATTTCGGTTCCAGATGAGCATGCTGT
genomic: CAGATTCTGGACATTAATGGTTCCACATGTTTCCTTACCAGGACTGGgtaaaatttc ... ggtttttcagGTATACCGGGGAAGATGGGTTTGAGATTTCGGTTCCAGATGAGCATGCTGT
EST: gi|47832124|gb|CK121808.1|CK121808
EST:     TTCCAGATTCTGGACATTAATGGTTCCACATGTTTCCTTACCAGGACTGG                         GTATACCGGGGAAGATGGGTTTTGAGATTTCGGTTCCAGATGAGCATGCTG
genomic: TTCCAGATTCTGGACATTAATGGTTCCACATGTTTCCTTACCAGGACTGGgtaaaatttc ... ggtttttcagGTATACCGGGGAAGATGGGTTT-GAGATTTCGGTTCCAGATGAGCATGCTG
EST: gi|125063788|gb|EL131643.1|EL131643
EST:     TTCCAGATTCTGGACATTAATGGTTCCACATGTTTCCTTACCAGGACTGG                         GTATACCGGGGAAGATGGGTTTGAGATTTCGGTT
genomic: TTCCAGATTCTGGACATTAATGGTTCCACATGTTTCCTTACCAGGACTGGgtaaaatttc ... ggtttttcagGTATACCGGGGAAGATGGGTTTGAGATTTCGGTT
EST: gi|125215586|gb|EL229670.1|EL229670
EST:     TGTTTCCTTACCAGGACTGG                         GTATACCGGGGAAGATGGGTTTGAGATTTCGGTTCCAGATGAGCATGCTGT
genomic: TGTTTCCTTACCAGGACTGGgtaaaatttc ... ggtttttcagGTATACCGGGGAAGATGGGTTTGAGATTTCGGTTCCAGATGAGCATGCTGT
EST: gi|124756859|gb|EH846989.1|EH846989
EST:     TGTTTCCTTACCAGGACTGG                         GTATACCGGGGAAGATGGGTTTGAGATTTCGGTTCCAGATGAGCATGCTGT
genomic: TGTTTCCTTACCAGGACTGGgtaaaatttc ... ggtttttcagGTATACCGGGGAAGATGGGTTTGAGATTTCGGTTCCAGATGAGCATGCTGT
EST: gi|125240059|gb|EL254144.1|EL254144
EST:     TCCAGATTCTGGACATTAATGGTTCCACATTGTTTCCTTACCAGGACTGG                         GTATACCGGGGAAGATTGGGTTTGA
genomic: TCCAGATTCTGGACATTAATGGTTCCACAT-GTTTCCTTACCAGGACTGGgtaaaatttc ... ggtttttcagGTATACCGGGGAAGAT-GGGTTTGA
EST: gi|116483791|gb|EG526383.1|EG526383
EST:     TTCCAGATTCTGGACATTAATGGTTCCACATGTTTCCTTACCAGGACTGG                         GTATACCGGGGAAGATGGGTTTGA
genomic: TTCCAGATTCTGGACATTAATGGTTCCACATGTTTCCTTACCAGGACTGGgtaaaatttc ... ggtttttcagGTATACCGGGGAAGATGGGTTTGA
EST: gi|125202929|gb|EL217883.1|EL217883
EST:     TTCCAGATTCTGGACATTAATGGTTCCACATGTTTCCTTACCAGGACTGG                         GTATACCGGGGAAGATTGGGTTTGA
genomic: TTCCAGATTCTGGACATTAATGGTTCCACATGTTTCCTTACCAGGACTGGgtaaaatttc ... ggtttttcagGTATACCGGGGAAGAT-GGGTTTGA
EST: gi|125132367|gb|EL174483.1|EL174483
EST:     TTCCACATGTTTCCTTACCAGGACTGG                         GTATACCGGGGAAGATGGGTTTGAGATTTCGGTTCCAGATGAGCATGCTGT
genomic: TTCCACATGTTTCCTTACCAGGACTGGgtaaaatttc ... ggtttttcagGTATACCGGGGAAGATGGGTTTGAGATTTCGGTTCCAGATGAGCATGCTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggaaaagttctgaagatctcataggtaatgaatgtctctgttttggtttttcagGTATACCGGGGAAGATGGGTTTGAGATTTCGGTTCCAGATGAGCATGCTGTGGATCTAGCAAAAGCAATCTTGGAGAAGTCCGAGGGTAAGGTAAGGCTT
                                               tttttc  CT-rich tract
                          taatgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaatttcatgtttcactatctgcttctagtcagatttgcttggttcaagtagacaatagctcaagaggaaaagttctgaagatctcataggtaatgaatgtctctgttttggtttttcagGTATACCGGGGAAGATGGGTTTGAGATTTCGGTTCCAGATGAGCATGCTGTGGATCTAGCAAAAGCAATCTTGGAGAAGTCCGAGGGTAAGGTAAGGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT