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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGATCCCCTCACCCATCAGTGTAAGCTCTGTGATTTTGGAAGTGCAAAAGTACTGgtaagaggtttagacttttatttaccccatttgttgtttgtcttttccactgtgcttgtgtctttgcatgcagtagttaaaaactccaattaagtgaatattatgcaagtaatttacataagtatggatgcagtttcagatatttctctgttagcctgatatttgcaacatttggctttttatattag

Basic information

species Arabidopsis thaliana
transcript AT2G30980.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G30980.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G045330_T02 (Zea mays), 5'ss of exon 6
GTTGATCCCCTCACCCATCAGTGTAAGCTCTGTGATTTTGGAAGTGCAAAAGTACTGgtaagaggtttagacttttatttaccccatttgttgtttgtcttttccactgtgcttgtgtctttgcatgcagtagttaaaaactccaattaagtgaatattatgcaagtaatttacataagtatggatgcagtttcagatatttctctgttagcctgatatttgcaacatttggctttttatattag
|||||||| |||||||| |||   ||||||||||| ||||| ||||||||||| |||||| |  ||||    ||          |  | ||    |  |||||    | ||||  | | |    ||   ||  | |||   |  ||| | ||| |  |||                                                                                     
GTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGTGCAAAAGTTCTGgtatgttgtttttctttcctcgaggatctgtagtcacat-ccttttgttttatgctcttttttaaaaatattgttatcaaaggttt-aatcatgtgca-gtta-------------------------------------------------------------------------------------

upper sequence: AT2G30980.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G045330_T01 (Zea mays), 5'ss of exon 5
-------------------------------------------GTTGATCCCCTCACCCATCAGTGTAAGCTCTGTGATTTTGGAAGTGCAAAAGTACTGgtaagaggtttagacttttatttaccccatttgttgtttgtcttttccactgtgcttgtgtctttgcatgcagtagttaaaaactccaattaagtgaatattatgcaagtaatttacataagtatggatgcagtttcagatatttctctgttagcctgatatttgcaacatttggctttttatattag
                                           |||||||| |||||||| |||   ||||||||||| ||||| ||||||||||| |||||| |  ||||    ||          |  | ||    |  |||||    | ||||  | | |    ||   ||  | |||   |  ||| | ||| |  |||                                                                                     
AATTAGTTCTGAATTGGTCTCGTCGTCTCTCTTTGATGTACAGGTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGTGCAAAAGTTCTGgtatgttgtttttctttcctcgaggatctgtagtcacat-ccttttgttttatgctcttttttaaaaatattgttatcaaaggttt-aatcatgtgca-gtta-------------------------------------------------------------------------------------

upper sequence: AT2G30980.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA12G33950.1 (Glycine max), 5'ss of exon 6
GTTGATCCCCTCACCCATCAGTGTAAGCTCTGTGATTTTGGAAGTGCAAAAGTACTGgtaagaggtttagacttttatttaccccatttgttgtttgtcttttccactgtgcttgtgtctttgcatgcagtagttaaaaactccaattaagtgaatattatgcaagtaatttacataagtatggatgcagtttcagatatttctctgttagcctgatatttgcaacatttggctttttatattag
|||||||  ||||| || ||    ||||||||||||||||| ||||||||||| |||||| |          || ||||   ||  |   || |   |  |||  ||  ||  ||   |  ||    |||| |      |||   |||||    ||||  | |   ||    |                                                                        
GTTGATCGACTCACACACCAAGTCAAGCTCTGTGATTTTGGGAGTGCAAAAGTTCTGgtatg---------tttgtattcttccagtgcatt-tcactactttatac-atgtatgctaccatgttaacagtggacgtggact---attaatgtcatatgctacc--tacccca------------------------------------------------------------------------

upper sequence: AT2G30980.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA13G36570.1 (Glycine max), 5'ss of exon 5
GTTGATCCCCTCACCCATCAGTGTAAGCTCTGTGATTTTGGAAGTGCAAAAGTACTGgtaagaggtttagacttttatttaccccatttgttgtttgtcttttccactgtgcttgtgtctttgcatgcagtagttaaaaactccaattaagtgaatattatgcaagtaatttacataagtatggatgcagtttcagatatttctctgttagcctgatatttgcaacatttggctttttatattag
|||||||| ||||| || ||    ||||||||||||||||| ||||||||||| |||||| |    || |  || |   |   |  ||   |  ||   | | |   | ||||    | ||  || |  |  ||  || | |   || |  ||     ||  |                                                                                  
GTTGATCCACTCACACACCAAGTCAAGCTCTGTGATTTTGGGAGTGCAAAAGTTCTGgtatg----ttggtattcttcctgtgcatttcactactt---tatacatgtatgctaccatgttaaca-gtggacgtggaatattaatatcatatgctacctaccccg--------------------------------------------------------------------------------

upper sequence: AT2G30980.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv12s0028g01810.t01 (Vitis vinifera), 5'ss of exon 6
GTTGATCCCCTCACCCATCAGTGTAAGCTCTGTGATTTTGGAAGTGCAAAAGTACTGgtaagaggtttagacttttatttaccccatttgttgtttgtcttttccactgtgcttgtgtctttgcatgcagtagttaaaaactccaattaagtgaatattatgcaagtaatttacataagtatggatgcagtttcagatatttctctgttagcctgatatttgcaacatttggctttttatattag
|||||||| ||||||||||||  |||||| |||||||||||||||||||| || |||||||| | |  ||||  |   |   ||   || || ||||     |   |  |  |  | ||  ||  |       |      ||  | ||    |  |                                                                                         
GTTGATCCTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTGgtaagtgttgaagaccatgtgtgctccttcttcttttttgatgcgtgttccttcttcttatccctgtctctttctctctctctctttattttttgggctc----------------------------------------------------------------------------------------

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|164213230|gb|ES085181.1|ES085181
EST:     CCCTCACCCATCAGTGTAAGCTCTGTGATTTTGGAAGTGCAAAAGTACTG                         GTGAAAGGTGAAGCAAACATATCATATATCTGCTCTCGGTA
genomic: CCCTCACCCATCAGTGTAAGCTCTGTGATTTTGGAAGTGCAAAAGTACTGgtaagaggtt ... tttatattagGTGAAAGGTGAAGCAAACATATCATATATCTGCTCTCGGTA
EST: gi|164161409|gb|ES102541.1|ES102541
EST:     CCCTCACCCATCAGTGTAAGCTCTGTGATTTTGGAAGTGCAAAAGTACTG                         GTGAAAGGTGAAGCAAACATATCATATAT
genomic: CCCTCACCCATCAGTGTAAGCTCTGTGATTTTGGAAGTGCAAAAGTACTGgtaagaggtt ... tttatattagGTGAAAGGTGAAGCAAACATATCATATAT
EST: gi|164230800|gb|EL995165.1|EL995165
EST:     ACCCATCAGTGTAAGCTCTGTGATTTTGGAAGTGCAAAAGTACTG                         GTGAAAGGTGAAGCAAACATATCATATATCTGCTCTCGGTATTACCGAGCT
genomic: ACCCATCAGTGTAAGCTCTGTGATTTTGGAAGTGCAAAAGTACTGgtaagaggtt ... tttatattagGTGAAAGGTGAAGCAAACATATCATATATCTGCTCTCGGTATTACCGAGCT
EST: gi|124897022|gb|EH973236.1|EH973236
EST:     CCCTCACCCATCAGTGTAAGCTCTGTGATTTTGGAAGTGCAAAAGTACTG                         GTGAAAGGTGAAGCAAAACATATCATATAT
genomic: CCCTCACCCATCAGTGTAAGCTCTGTGATTTTGGAAGTGCAAAAGTACTGgtaagaggtt ... tttatattagGTGAAAGGTGAAGCAAA-CATATCATATAT
EST: gi|125115303|gb|EL165353.1|EL165353
EST:     CTGTGATTTTGGAAGTGCAAAAGTACTG                         GTGAAAGGTGAAGCAAACATATCATATATCTGCTCTCGGTATTAACCGAGC
genomic: CTGTGATTTTGGAAGTGCAAAAGTACTGgtaagaggtt ... tttatattagGTGAAAGGTGAAGCAAACATATCATATATCTGCTCTCGGTATTA-CCGAGC
EST: gi|125289930|gb|EL304015.1|EL304015
EST:     CCCTCACCCATCAGTGTAAGCTCTGTGATTTTGGAAGTGCAAAAGTACTG                         GTGAAAGGTGAAGCAAACATATCATATATCTGCTCTCGGTAT
genomic: CCCTCACCCATCAGTGTAAGCTCTGTGATTTTGGAAGTGCAAAAGTACTGgtaagaggtt ... tttatattagGTGAAAGGTGAAGCAAACATATCATATATCTGCTCTCGGTAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGATCCCCTCACCCATCAGTGTAAGCTCTGTGATTTTGGAAGTGCAAAAGTACTGgtaagaggtttagacttttatttaccccatttgttgtttgtcttttccactgtgcttgtgtctttgcatgcagtagttaaaaactccaattaagtgaatattatgcaagtaatttacataagtatggatgcagtttcagatatttctctgttagcctgatatttgcaacatttggctttttatattag

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