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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttgatctattgtgggttttgtctttggtaaccttgactagattgtaatcttattctctgtatgttctgtagGTTGATCCCCTCACCCATCAGTGTAAGCTCTGTGATTTTGGAAGTGCAAAAGTACTG

Basic information

species Arabidopsis thaliana
transcript AT2G30980.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G30980.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G045330_T02 (Zea mays), 3'ss of exon 5
-------------gtacgttgatctattgtgggttttgtctttggtaaccttgactagattgtaatcttattctctgtatgttctgtagGTTGATCCCCTCACCCATCAGTGTAAGCTCTGTGATTTTGGAAGTGCAAAAGTACTG
             | ||   ||| | || |   |||  |  |||||||      ||  ||||   || |  ||||| | || | |  |||||||||| |||||||| |||   ||||||||||| ||||| ||||||||||| |||
gtatgtgtcatgtggacaaggatttgttcttcctttgat--ttggtaattagttctgaattggtctcgtcgtctctctttgatgtacagGTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGTGCAAAAGTTCTG

upper sequence: AT2G30980.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G36570.1 (Glycine max), 3'ss of exon 4
gtacgttgatctattgtgggttttgtctttggtaaccttgacta--gattgtaatcttattctctgtatgttctgtagGTTGATCCCCTCACCCATCAGTGTAAGCTCTGTGATTTTGGAAGTGCAAAAGTACTG
||| ||| ||  |||     ||||  ||   | |        ||   ||| ||| | |||| ||  | |||||||||||||||||| ||||| || ||    ||||||||||||||||| ||||||||||| |||
gtaagtt-attaatttgctatttttcctcaaggagttgcatttatttattataaacctattgtccatttgttctgtagGTTGATCCACTCACACACCAAGTCAAGCTCTGTGATTTTGGGAGTGCAAAAGTTCTG

upper sequence: AT2G30980.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA12G33950.1 (Glycine max), 3'ss of exon 5
gtacgttgatctattgtgggttttgtctttgg--taaccttgactagattgtaatcttattctctgtatgttctgtagGTTGATCCCCTCACCCATCAGTGTAAGCTCTGTGATTTTGGAAGTGCAAAAGTACTG
||| |||  |   |||    |||| |    ||  || | || | |  ||| ||| | |||| ||  | |||||||||||||||||  ||||| || ||    ||||||||||||||||| ||||||||||| |||
gtaagttattagtttgctatttttcttcaaggaatagcatttattt-attctaaacctattttccatttgttctgtagGTTGATCGACTCACACACCAAGTCAAGCTCTGTGATTTTGGGAGTGCAAAAGTTCTG

upper sequence: AT2G30980.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 5
-----------------------gtacgttgatctattgtgggttttgtctttggtaaccttgactagattg---taatcttattctctgtatgtt-ctgtagGTTGATCCCCTCACCCATCAGTGTAAGCTCTGTGATTTTGGAAGTGCAAAAGTACTG
                         |   ||   |  ||       |  | ||     | ||   |  | ||   |   ||  |||| || |  |   || |||||||||| ||||||||||||  |||||| |||||||||||||||||||| || |||
gtatattgttcattttttgataaagattatggcatgctgaatcccctccccttcccccctttcctttaaatgacttggactgtttctttgaacataattgcagGTTGATCCTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTG

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|124977065|gb|EL050435.1|EL050435
EST:     ATGTGAAACCACAAAATCTTTTG                         GTTTGATCCCCTCACCCATCAGTGTAAGCTCTGT
genomic: ATGTGAAACCACAAAATCTTTTGgtacgttgat ... tgttctgtagG-TTGATCCCCTCACCCATCAGTGTAAGCTCTGT
EST: gi|164161409|gb|ES102541.1|ES102541
EST:     AAACCACAAAATCTTTTG                         GTTGATCCCCTCACCCATCAGTGTAAGCTCTGTGATTTTGGAAGTGCAAAA
genomic: AAACCACAAAATCTTTTGgtacgttgat ... tgttctgtagGTTGATCCCCTCACCCATCAGTGTAAGCTCTGTGATTTTGGAAGTGCAAAA
EST: gi|86048167|gb|DR343922.1|DR343922
EST:     ATACTGCTCCTGGTGTCTGCCACAGAGATGTGAAAC-ACAAAATCTTTTG                         GGTGATCCCNNCACCCATCAGTGTAAGCTCTGTGATTTTG-AAGTGCAAAA
genomic: ATACTGCTCCTGGTGTCTGCCACAGAGATGTGAAACCACAAAATCTTTTGgtacgttgat ... tgttctgtagGTTGATCCCCTCACCCATCAGTGTAAGCTCTGTGATTTTGGAAGTGCAAAA
EST: gi|124897022|gb|EH973236.1|EH973236
EST:     CAAAATCTTTTG                         GTTGATCCCCTCACCCATCAGTGTAAGCTCTGTGATTTTGGAAGTGCAAAA
genomic: CAAAATCTTTTGgtacgttgat ... tgttctgtagGTTGATCCCCTCACCCATCAGTGTAAGCTCTGTGATTTTGGAAGTGCAAAA
EST: gi|124799220|gb|EH888899.1|EH888899
EST:     ATACTGCTCCTGGTGTCTGCCACAGAGATGTGAAACCACAAAATCTTTTG                         GTTGATCCCCTCACCCATCAGTGTAAGCTCTGT
genomic: ATACTGCTCCTGGTGTCTGCCACAGAGATGTGAAACCACAAAATCTTTTGgtacgttgat ... tgttctgtagGTTGATCCCCTCACCCATCAGTGTAAGCTCTGT
EST: gi|86048156|gb|DR343911.1|DR343911
EST:     TACTGGCTCCTGGTGTCTGCCACAGAGATGTGAAACCACAAAATCTTTTG                         GTTGATCCCCTCACCCATCAGTGTAAGCTCTGTGATTTTGGAAGTGCAAAA
genomic: TACTG-CTCCTGGTGTCTGCCACAGAGATGTGAAACCACAAAATCTTTTGgtacgttgat ... tgttctgtagGTTGATCCCCTCACCCATCAGTGTAAGCTCTGTGATTTTGGAAGTGCAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtctttggtaaccttgactagattgtaatcttattctctgtatgttctgtagGTTGATCCCCTCACCCATCAGTGTAAGCTCTGTGATTTTGGAAGTGCAAAAGTACTG
                        attgtaatcttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgttgatctattgtgggttttgtctttggtaaccttgactagattgtaatcttattctctgtatgttctgtagGTTGATCCCCTCACCCATCAGTGTAAGCTCTGTGATTTTGGAAGTGCAAAAGTACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG