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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgccatcactcttttgacttttacttatccgaaatttataatggaattaacattgtataccatataatgcacataaactgtttactttgagattggttatgttatagacaatgtaagactaactcttaacttgtcctatgattgatgcagAGAGCTCTACAAAAACAACATCCAAGGAACTATACCTTCCGAACTTGGAAATCTGAAGAATCTCATCAGCTTGGATCTGTACAACAACAATCTTACAGGG

Basic information

species Arabidopsis thaliana
transcript AT5G21090.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G21090.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os01g17250.1 (Oryza sativa), 3'ss of exon 2
gtatgccatcactcttttgacttttacttatccgaaatttataatggaattaacattgtataccatataatgcacataaactgtttactttgagattggttatgttatagacaatgtaagactaactcttaacttgtcctatgattgatgcagAGAGCTCTACAAAAACAACATCCAAGGAACTATACCTTCCGAACTTGGAAATCTGAAGAATCTCATCAGCTTGGATCTGTACAACAACAATCTTACAGGG
                                               |||   | |||   | | | ||||   |  |  || |||    ||  ||||    ||  ||  |   |      ||||||    | || |   |  |||| | ||||||||| ||||||||||| || || || ||||| ||  | || || || | ||||||||| || || |||||||||||||| ||||||||  |||| || 
----------------------------------------------aaatatgctttggtcatcct-taatttccg-atgctattt-tactgcaattgagcttgacattcatgttagtgctctaact----agtttttgaaaaattgttacagAGAGCTGTACAAAAACAATATTCAGGGCACTATCCCAGCTGAGCTCGGGAGTCTGAAGAACCTTATTAGCTTGGATCTGTATAACAACAACATTACTGGA

upper sequence: AT5G21090.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA14G04520.1 (Glycine max), 3'ss of exon 2
gtatgccatcactcttttgacttttacttatccgaaatttataatggaattaacattgtataccatataatgcacataaactgtttact-ttgagattggttatgttatagacaatgtaagactaactcttaacttgtcctatgattgatgcagAGAGCTCTACAAAAACAACATCCAAGGAACTATACCTTCCGAACTTGGAAATCTGAAGAATCTCATCAGCTTGGATCTGTACAACAACAATCTTACAGGG
                                                      ||||         || |     |       ||| | ||| ||    |    || || ||    ||    | | | |    || |  |    | |||| || ||| | |||||||||||||| ||||||||||| ||| | ||||||||||| ||||||| |||| | ||||||||  |||||||||||||  |  |||| 
-----------------------------------------------------gattgatcgattggtattttctgtggctctcttattgttgtgaactatagaattttatacctgttagtgtttaatgtggttttctttt-cattggatgtagTGAGTTGTACAAAAACAACATTCAAGGAACTATTCCTCCAGAACTTGGAAACCTGAAGAGTCTCGTTAGCTTGGACTTGTACAACAACAACATATCAGGC

upper sequence: AT5G21090.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G44250.2 (Glycine max), 3'ss of exon 2
gtatgccatcactcttttgacttttacttatccgaaatttataatggaattaacattgtataccatataatgcacataaactgtttactttgagattggttatgttatagacaatgtaagactaactcttaacttgtcctatgattg-atgcagAGAGCTCTACAAAAACAACATCCAAGGAACTATACCTTCCGAACTTGGAAATCTGAAGAATCTCATCAGCTTGGATCTGTACAACAACAATCTTACAGGG
                                            |   | |||  | ||||    | |    | | ||      ||  | |||  |     || | |||     |    |  |||   | |  || || | | |||| ||| || ||| | |||||||||||||| ||||||||||| ||| | ||||||||||| ||||||| |||  | ||||||||  |||||||||||||  |  |||| 
--------------------------------------------tattactaaattggtatttgctgtggctctctta------ttgttgtgaactatagcatttcatacctgtta-gtgtttaa---tgaggttttctttttattggatgtagTGAGTTGTACAAAAACAACATTCAAGGAACTATTCCTCCGGAACTTGGAAACCTGAAGAGTCTAGTTAGCTTGGACTTGTACAACAACAACATATCAGGC

upper sequence: AT5G21090.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0040g00520.t01 (Vitis vinifera), 3'ss of exon 2
------gtatgccatcactcttttgacttttacttatccgaaatttataa--tggaattaacattgtataccatataat-gcacataaactgtttactt--tgagattg-gttatgttatagac----aatgtaagacta----actcttaacttgtcctatgat----tgatgcagAGAGCTCTACAAAAACAACATCCAAGGAACTATACCTTCCGAACTTGGAAATCTGAAGAATCTCATCAGCTTGGATCTGTACAACAACAATCTTACAGGG
      || |   |     || || |  ||| |  ||    | |   |    |||  | ||   |       || |||  |  |   | |||   | ||  |||  |   || |||||     |    |||  ||  | |        | || ||    || | |    | |||||||||||| ||||| |||||||| ||||| || || |||   || ||||||||  | ||||| || |||||||||||| |||||||||||||  |  | |||
gtaagtgtcttttaatttgctgttaaaatttgccaataacgagtgcgttgcttggtgtcaaatgttagctttatgtaagagttctctatctgaacaattgttgatgtcatgtgatgtttggagcttataattcaaagccacagggaaatgaaattaaattaagttcttctcatgcagAGAGCTTTACAAGAACAACATTCAAGGGACAATCCCTGTTGAGCTTGGAAACTTAAAGAACCTAATCAGCTTGGATTTGTACAACAACAACATCTCGGGG

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|164193656|gb|EL973864.1|EL973864
EST:     TTTACAGTATCT                         AGAGCTCTACAAAAACAACATCCGAGGAACTATACCTTCCGAACTTGGAAA
genomic: TTTACAGTATCTgtatgccatc ... attgatgcagAGAGCTCTACAAAAACAACATCCAAGGAACTATACCTTCCGAACTTGGAAA
EST: gi|125082634|gb|EL143469.1|EL143469
EST:     TGAGCTTGGGAAGCTTGAACATTTACAGTATCT                         AGAGCTCTACAAAA-CAACATCCAAGGAACTATACCTTCCGAACTTGGAAA
genomic: TGAGCTTGGGAAGCTTGAACATTTACAGTATCTgtatgccatc ... attgatgcagAGAGCTCTACAAAAACAACATCCAAGGAACTATACCTTCCGAACTTGGAAA
EST: gi|116443563|gb|EG486155.1|EG486155
EST:     TCTGGACATCTTGCGCCTGAGCTTGGGAAGCTTGAACATTTACAGTATCT                         AGAGCTCTACAAAAACAACATCCAAGGAACTATACCTTCCGAACTTGGAAA
genomic: TCTGGACATCTTGCGCCTGAGCTTGGGAAGCTTGAACATTTACAGTATCTgtatgccatc ... attgatgcagAGAGCTCTACAAAAACAACATCCAAGGAACTATACCTTCCGAACTTGGAAA
EST: gi|124798199|gb|EH887878.1|EH887878
EST:     TCTGGACATCTTGCGCCTGAGCTTGGGAAGCTTGAACATTTACAGTATCT                         AGAGCTCTACAAAAACAACATCCAAGGAACTATACCTTCCGAACT
genomic: TCTGGACATCTTGCGCCTGAGCTTGGGAAGCTTGAACATTTACAGTATCTgtatgccatc ... attgatgcagAGAGCTCTACAAAAACAACATCCAAGGAACTATACCTTCCGAACT
EST: gi|125047199|gb|EL119468.1|EL119468
EST:     TCTGGACATCTTGCGCCTGAGCTTGGGAAGCTTGAACATTTACAGTATCT                         AGAGCTCTACAAAAACAACATCCAAGGAACTATACCTTCCG
genomic: TCTGGACATCTTGCGCCTGAGCTTGGGAAGCTTGAACATTTACAGTATCTgtatgccatc ... attgatgcagAGAGCTCTACAAAAACAACATCCAAGGAACTATACCTTCCG
EST: gi|124706483|gb|EH797885.1|EH797885
EST:     TTTACAGTATCT                         AGAGCTCTACAAAAACAACATCCAAGGAACTATACCTTCCGAACTTGGAAA
genomic: TTTACAGTATCTgtatgccatc ... attgatgcagAGAGCTCTACAAAAACAACATCCAAGGAACTATACCTTCCGAACTTGGAAA
EST: gi|116456652|gb|EG499244.1|EG499244
EST:     TCTGGACATCTTGCGCCTGAGCTTGGGAAGCTTGAACATTTACAGTATCT                         AGAGCTCTACAAAAACAACATCCAAGGAACTATACCTTCCGAACTTGGAAA
genomic: TCTGGACATCTTGCGCCTGAGCTTGGGAAGCTTGAACATTTACAGTATCTgtatgccatc ... attgatgcagAGAGCTCTACAAAAACAACATCCAAGGAACTATACCTTCCGAACTTGGAAA
EST: gi|301501628|gb|HO207168.1|HO207168
EST:     TCTGGACATCTTGCGCCTGAGCTTGGGAAGCTTGAACATTTACAGTATCT                         AGAGCTCTACAAAAACAACATCCAAGGAACTATACCTTCCGAACTTGGAAA
genomic: TCTGGACATCTTGCGCCTGAGCTTGGGAAGCTTGAACATTTACAGTATCTgtatgccatc ... attgatgcagAGAGCTCTACAAAAACAACATCCAAGGAACTATACCTTCCGAACTTGGAAA
EST: gi|124988432|gb|EL060818.1|EL060818
EST:     ACATTTACAGTATCT                         AGAGCTCTACAAAAACAACATCCAAGGAACTATACCTTCCGAACTTGGAAA
genomic: ACATTTACAGTATCTgtatgccatc ... attgatgcagAGAGCTCTACAAAAACAACATCCAAGGAACTATACCTTCCGAACTTGGAAA
EST: gi|125245819|gb|EL259904.1|EL259904
EST:     TCTGGACATCTTGCGCCTGAGCTTGGGAAGCTTGAACATTTACAGTATCT                         AGAGCTCTAACAAAAAACAACATCCAAGGAACTATACCTTCCGAACTTGG
genomic: TCTGGACATCTTGCGCCTGAGCTTGGGAAGCTTGAACATTTACAGTATCTgtatgccatc ... attgatgcagAGAGCTCTA-CAAAAA-CAACATCCAAGGAACTATACCTTCCGAACTTGG
EST: gi|125325224|gb|EL339304.1|EL339304
EST:     GAAGCTTGAACATTTTACAGTATCT                         AGAGCTCTACAAAAACAACATCCAAGGAACTATACCTTCCGAACTTGGAAA
genomic: GAAGCTTGAACA-TTTACAGTATCTgtatgccatc ... attgatgcagAGAGCTCTACAAAAACAACATCCAAGGAACTATACCTTCCGAACTTGGAAA
EST: gi|116456643|gb|EG499235.1|EG499235
EST:     TCTGGACATCTTGCGCCCGAGCTTGGGAAGCTTGAACATTTACAGTATCT                         AGAGCTCTACAAAAACAACATCCAAGGAACTATACCTTCCGAACTTGGAAA
genomic: TCTGGACATCTTGCGCCTGAGCTTGGGAAGCTTGAACATTTACAGTATCTgtatgccatc ... attgatgcagAGAGCTCTACAAAAACAACATCCAAGGAACTATACCTTCCGAACTTGGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttatgttatagacaatgtaagactaactcttaacttgtcctatgattgatgcagAGAGCTCTACAAAAACAACATCCAAGGAACTATACCTTCCGAACTTGGAAATCTGAAGAATCTCATCAGCTTGGATCTGTACAACAACAATCTTACAGGG
      ttataga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgccatcactcttttgacttttacttatccgaaatttataatggaattaacattgtataccatataatgcacataaactgtttactttgagattggttatgttatagacaatgtaagactaactcttaacttgtcctatgattgatgcagAGAGCTCTACAAAAACAACATCCAAGGAACTATACCTTCCGAACTTGGAAATCTGAAGAATCTCATCAGCTTGGATCTGTACAACAACAATCTTACAGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT