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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgatcattttcggtttatgttttaccaatttagtcaacataatgtgattgttgatgttcatatagtagtttctctgtatattggtagATGTTCACGTCTATGATAAAGAACATGAACCCTGAGATGATGGCTAGCATGAGCGAACAATTTGGAATGAAGCTTTCTCAAGAAGACGCTGCAAAAGCTC

Basic information

species Arabidopsis thaliana
transcript AT5G21990.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G21990.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM5G878044_T01 (Zea mays), 3'ss of exon 1
--------------------gtttgatcattttcggtttatgttttacc----aatttagtcaacataatgtgattgttgatgttcatatagtagtttctctgtatattggtagATGTTCACGTCTATGATAAAGAACATGAACCCTGAGATGATGGCTAGCATGAGCGAACAATTTGGAATGAAGCTTTCTCAAGAAGACGCTGCAAAAGCTC
                         || || ||    | ||   || |     |  |||  | |   ||  ||| |  | |  ||| | | |  |||| | | |   ||   ||||| | || || ||||| |||||||||| ||| ||||||||||| |  |||||||| || ||||||||||| || ||  | || || || ||||||||||
gtaagaaaatgctcagccaaaggaaattatatttaaatcattgcttcctgtgaacgttatgccaggcaacttgagttctaac-ttcttttgg--gtttttttat---ttaacagATGCTTACATCCATGATGAAGAACATGAGCCCCGAGATGATGGCAAATATGAGCGAGCAGTTTGGAATGAAACTGTCAAAGGAGGATGCCGCAAAAGCTC

upper sequence: AT5G21990.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA12G10270.2 (Glycine max), 3'ss of exon 9
------gtttgatcatt--ttcgg----tttatgttttaccaatttagtcaacataatgtgattgttgatgttcatatagtagtttctctgtatattggtagATGTTCACGTCTATGATAAAGAACATGAACCCTGAGATGATGGCTAGCATGAGCGAACAATTTGGAATGAAGCTTTCTCAAGAAGACGCTGCAAAAGCTC
       ||||   | |  | | |    | ||| ||  | || | | |||      || |   |||   | |||   || |  |||     | | |||| |||||||||| || ||| | || || |||| ||| || |||||||||| |||| | |||||||||||  | |||||||| | |||||| |||||||||||||
attttcttttggcaagtagtacagattctctatcttgaaacattcttgtctttggcatttatatgt--gtattcccgtaattttttaatgttgttttggcagATGTTCACATCCATGGTTAAAAATATGAGCCCGGAAATGATGGCTAACATGGGTGAACAATTTGGTGTTAAGCTTTCACCAGAAGAAGCTGCAAAAGCTC
















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|116411509|gb|EG454101.1|EG454101
EST:     ACTTACAGGAACAGATGAGAAACCAAATGAAAGATCCAGCGATGCGACAG                         ATGTTCACGTCTATGATAAAGAACATGAACCCTGAGATGATGGCTAGCATG
genomic: ACTTACAGGAACAGATGAGAAACCAAATGAAAGATCCAGCGATGCGACAGgtttgatcat ... atattggtagATGTTCACGTCTATGATAAAGAACATGAACCCTGAGATGATGGCTAGCATG
EST: gi|86083802|gb|DR379561.1|DR379561
EST:     ACTTACAGGANCAGATGAGAAACC-AATGAAAGATCCAGCGATGCGACAG                         ATGTTCACGTCTATGATAAAGAACATGAACCCTGAGATGATGGCTAGCATG
genomic: ACTTACAGGAACAGATGAGAAACCAAATGAAAGATCCAGCGATGCGACAGgtttgatcat ... atattggtagATGTTCACGTCTATGATAAAGAACATGAACCCTGAGATGATGGCTAGCATG
EST: gi|116419435|gb|EG462027.1|EG462027
EST:     ACTTACAGGAACAGATGAGAAACCAAATGAAAGATCCAGCGATGCGACAG                         ATGTTCACGTCTATGATAAAGAACATGAACCCTGAGATGATGGCTAGCATG
genomic: ACTTACAGGAACAGATGAGAAACCAAATGAAAGATCCAGCGATGCGACAGgtttgatcat ... atattggtagATGTTCACGTCTATGATAAAGAACATGAACCCTGAGATGATGGCTAGCATG
EST: gi|116411508|gb|EG454100.1|EG454100
EST:     ACTTACAGGAACAGATGAGAAACCAAATGAAAGATCCAGCGATGCGACAG                         ATGTTCACGTTTATGATAAAGAACATGAACCCTGAGATGATGGCTAGCATG
genomic: ACTTACAGGAACAGATGAGAAACCAAATGAAAGATCCAGCGATGCGACAGgtttgatcat ... atattggtagATGTTCACGTCTATGATAAAGAACATGAACCCTGAGATGATGGCTAGCATG
EST: gi|116419434|gb|EG462026.1|EG462026
EST:     ACTTACAGGAACAGATGAGAAACCAAATGAAAGATCCAGCGATGCGACAG                         ATGTTCACGTCTATGATAAAGAACATGAACCCTGAGATGATGGCTAGCATG
genomic: ACTTACAGGAACAGATGAGAAACCAAATGAAAGATCCAGCGATGCGACAGgtttgatcat ... atattggtagATGTTCACGTCTATGATAAAGAACATGAACCCTGAGATGATGGCTAGCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcaacataatgtgattgttgatgttcatatagtagtttctctgtatattggtagATGTTCACGTCTATGATAAAGAACATGAACCCTGAGATGATGGCTAGCATGAGCGAACAATTTGGAATGAAGCTTTCTCAAGAAGACGCTGCAAAAGCTC
                tgttgat  putative branch site (score: 4)
                        ttcatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgatcattttcggtttatgttttaccaatttagtcaacataatgtgattgttgatgttcatatagtagtttctctgtatattggtagATGTTCACGTCTATGATAAAGAACATGAACCCTGAGATGATGGCTAGCATGAGCGAACAATTTGGAATGAAGCTTTCTCAAGAAGACGCTGCAAAAGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG