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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctctgccatgttggatttaagttggtttgttttgaatacacctgctttaactgtggtgggtgatctcttactgattttatcttaataatttttgcacagAGGGTGATGGATCAAAAATATTTGTCAGTTGCATTGCATTTCGGGATCGAGTCTGTGAGGATATTATTGAAGCTTATCGCTTACCGCCGAATACATACGC

Basic information

species Arabidopsis thaliana
transcript AT1G49040.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G49040.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os01g39380.1 (Oryza sativa), 3'ss of exon 2
--------------------------------------------------------tctctgccatgttggatttaagttggtttgttttgaatacacctgct-ttaactgtggtgggt-gatctcttactgattttatcttaataatttttgcacagAGGGTGATGGATCAAAAATATTTGTCAGTTGCATTGCATTTCGGGATCGAGTCTGTGAGGATATTATTGAAGCTTATCGCTTACCGCCGAATACATACGC
                                                        ||     | | |||    |  |||   || || |   || | ||| | ||   |   ||   | |||  ||  || |  || | ||   | || ||| |  ||||| ||||| |||||||| | ||| ||||| |||||||||||||||| | | ||||| |||||| |||||||||| |   | ||| | ||  | |  ||
gtgcatgcaacggttgttcagattgatgatcctgtcgaaggcttgaagctgatatttcctaaaccttttgagact--gtttcattcttctagttaaaactgttattggttactgtatatagattgctcccttacctt-tgttctcacttcttgta--gAGGGAGATGGCTCAAAAATTTATGTTAGTTGTATTGCATTTCGGGATCCAATTTGTGAAGATATTCTTGAAGCTTACCAAATTCCGGCAAACTCTTTTGC

upper sequence: AT1G49040.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G074572_T01 (Zea mays), 3'ss of exon 2
-------tctctgccatgttggatttaagttggtttgttttgaatacacctgctttaactgtggtgggtgatctcttactgattttatcttaataatttttgcacagAGGGTGATGGATCAAAAATATTTGTCAGTTGCATTGCATTTCGGGATCGAGTCTGTGAGGATATTATTGAAGCTTATCGCTTACCGCCGAATACATACGC
           |  | |    |  |||   ||  | |  | |||   |  | |      | |    ||| |||  ||  | | | | |  | ||  || ||| |  ||||| ||||| |||||||| | ||||||||| ||||||||||||||||   | ||||| || || ||||| ||||| |   | ||| ||||| | |  ||
atcgaggggcatttcctagccgtcttagaatgagtggcatcgaacgaattttcccgttgtata-caggtcatccttt--taactatgttgtgat--ttcttgta--gAGGGAGATGGCTCAAAAATTTATGTCAGTTGTATTGCATTTCGGGATCCTATTTGTGAAGACATAATTGAGGCTTACCAAATTCCGGCGAATTCGTTTGC

upper sequence: AT1G49040.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G04510.1 (Glycine max), 3'ss of exon 2
--tctctgccatgttggatttaagttggtttgttttgaatacacctgctttaactgtggtgggtgatctcttactgattttatcttaat----aatttttgcacagAGGGTGATGGATCAAAAATATTTGTCAGTTGCATTGCATTTCGGGATCGAGTCTGTGAGGATATTATTGAAGCTTATCGCTTACCGCCGAATACATACGC
  | ||    |  ||| || |   || | ||| ||  |  |    | | |   ||||  |||||| | | || |||||   || ||||     || |||   ||||||||||||||||||||||| | |||||| |||||| | || ||||||| ||| ||||||||||||   || || || ||  | | | | ||| |||| ||
tatttcaattactttgtatat---tttggttgcttgcatcatttttacctct-ctgta-tgggtgttatttt-ctgataccatattaacttaaaaatttgatacagAGGGTGATGGATCAAAAATTTATGTCAGCTGCATTTCTTTCCGGGATCCAGTTTGTGAGGATATTGCAGAGGCCTACCGGATTCAGGCAAATTCATATGC

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|19875217|gb|AU236048.1|AU236048
EST:     TTCCAGTGACCCTGCAAGTTTNCCACGGAGCTATCCCATAGTCTTGACGG                         AGGGTGATGGATCAAAAATATTTTGTCAGTTTGCATTGCATTTNCGGGATC
genomic: TTCCAGTGACCCTGCAAGTTTCCCACGGAGCTATCCCATAGTCTTGACGGgtatgtgatt ... ttttgcacagAGGGTGATGGATCAAAAATATTT-GTCAGTT-GCATTGCATTT-CGGGATC
EST: gi|124973174|gb|EL046825.1|EL046825
EST:     TTCCAGTGACCCTGCAAGTATCCCACGGAGCTATCCCATAGTCTTGACGG                         AGGGTGATGGATCAAAAATATTTGTCAGTTGCATTGC
genomic: TTCCAGTGACCCTGCAAGTTTCCCACGGAGCTATCCCATAGTCTTGACGGgtatgtgatt ... ttttgcacagAGGGTGATGGATCAAAAATATTTGTCAGTTGCATTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttaactgtggtgggtgatctcttactgattttatcttaataatttttgcacagAGGGTGATGGATCAAAAATATTTGTCAGTTGCATTGCATTTCGGGATCGAGTCTGTGAGGATATTATTGAAGCTTATCGCTTACCGCCGAATACATACGC
                                            tttttgc  CT-rich tract
                     tcttactgattttatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctctgccatgttggatttaagttggtttgttttgaatacacctgctttaactgtggtgggtgatctcttactgattttatcttaataatttttgcacagAGGGTGATGGATCAAAAATATTTGTCAGTTGCATTGCATTTCGGGATCGAGTCTGTGAGGATATTATTGAAGCTTATCGCTTACCGCCGAATACATACGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC