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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgacatcagttttttttttggtgttcttaccactcagatctcagtttgtgtttaacaatcggtttttatagGGGTGTGACTGTCTGGGATCTATCAAGTACTTCGATGCCCATTTCACAAATTTCACTGGAGGAGTTGAAACAATTGAGAACTGTGTTTGCTTGCATGAAG

Basic information

species Arabidopsis thaliana
transcript AT2G42490.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G42490.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G147884_T01 (Zea mays), 3'ss of exon 6
---gtttgacatcagttttttttttggtgttcttaccactcagatctcagtttgtgtttaac----------aatcggtttttatagGGGTGTGACTGTCTGGGATCTATCAAGTACTTCGATGCCCATTTCACAAATTTCACTGGAGGAGTTGAAACAATTGAGAACTGTGTTTGCTTGCATGAAG
    ||| |  |||||| ||  | ||      ||  |  ||| |  |    ||   ||| ||          || |  ||| |  |||| || || ||  |||| |  || || || || ||||| ||||||||||| |||||||| || || || |||||||||||||||||||| |||||||| |
gttattttat-tcagttcttgatgtgtatactttgacgttcaaaatttttctttgatttgactatgctctttaacctttttgtgcagGGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAACTTCACTGGTGGTGTGGAGACAATTGAGAACTGTGTTTGTTTGCATGAGG

upper sequence: AT2G42490.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S178_54V6.1 (Physcomitrella patens), 3'ss of exon 7
--------------------------------gtttgacatcagttttttttttggtgttcttaccactcagatctcagtttgtgtttaacaatcggtttttatagGGGTGTGACTGTCTGGGATCTATCAAGTACTTCGATGCCCATTTCACAAATTTCACTGGAGGAGTTGAAACAATTGAGAACTGTGTTTGCTTGCATGAAG
                                  ||||| | |   |||||| ||   |   |     | ||   |   ||     | || |   |     |  |||| ||||| ||||||||    |||||||| || ||||||||||| || ||||||  |||||||||||||||||| || |||||||| ||| |||||||||
agtcaactacacaatattttaaagactagaacagttgacgtgaagattttttatgcaatggat-ttgttgaggagttgattatcactgaaaagatg-----tgcagGGATGTGATTGTCTGGGCCTGATCAAGTATTTTGATGCCCATTTTACCAATTTCCATGGAGGAGTTGAAACAATCGAAAACTGTGTCTGCATGCATGAAG

upper sequence: AT2G42490.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S363_39V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------------gtttgacatcagttttttttttggtgttcttaccactcagatctcagtttgtgtttaacaatcggtt------tttatagGGGTGTGACTGTCTGGGATCTATCAAGTACTTCGATGCCCATTTCACAAATTTCACTGGAGGAGTTGAAACAATTGAGAACTGTGTTTGCTTGCATGAAG
                      ||  | | |  ||  |       ||   |   | | | ||     | |   ||| |  |||  |       | |  |||||||||| ||||| ||    || || ||||| ||||||||||| ||||| ||   ||||||||||||||| || || |||||||| ||| |||||||||
ttagagcagaacactgaagcccttacctttaagttactagaacacgtgagttgaaatgaaatgaacatgttgatttgattatcattcaaaaggtgtgcagGGGTGTGATTGTCTTGGTCTGATTAAATACTTTGATGCCCATTTTACAAACTTTCATGGAGGAGTTGAAACGATCGAAAACTGTGTCTGCATGCATGAAG

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|116380602|gb|EG423194.1|EG423194
EST:     TTGATGCAGGGGAGGATGGTCTCGGGAAAAACGCACATTCGCTTAAGAAG                         GGGTGTGACTGTCTGGGATCTATCAAGTACTTCGATGCCCATTTCACAAAT
genomic: TTGATGCAGGGGAGGATGGTCTCGGGAAAAACGCACATTCGCTTAAGAAGgtttgacatc ... gtttttatagGGGTGTGACTGTCTGGGATCTATCAAGTACTTCGATGCCCATTTCACAAAT
EST: gi|124978997|gb|EL052103.1|EL052103
EST:     TTGATGCAGGGGAGGATGGTCTCGGGAAAAACGCTCATTCGCTTAAGAAG                         GGGTGTGACTGTCTGGGATCTATCAAGTACTTCGATGCCCATTTCACAAAT
genomic: TTGATGCAGGGGAGGATGGTCTCGGGAAAAACGCACATTCGCTTAAGAAGgtttgacatc ... gtttttatagGGGTGTGACTGTCTGGGATCTATCAAGTACTTCGATGCCCATTTCACAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggtgttcttaccactcagatctcagtttgtgtttaacaatcggtttttatagGGGTGTGACTGTCTGGGATCTATCAAGTACTTCGATGCCCATTTCACAAATTTCACTGGAGGAGTTGAAACAATTGAGAACTGTGTTTGCTTGCATGAAG
                                              tttttat  CT-rich tract
                                              tttttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgacatcagttttttttttggtgttcttaccactcagatctcagtttgtgtttaacaatcggtttttatagGGGTGTGACTGTCTGGGATCTATCAAGTACTTCGATGCCCATTTCACAAATTTCACTGGAGGAGTTGAAACAATTGAGAACTGTGTTTGCTTGCATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG