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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaagttttagactcttatatcaccgttagagagattttcagaactagtggggaacaaactctgactactagtgtagtgtttgtataatgatctcatgggttaattatacttttcagACCATCTTCCTCCCTGTTGTTGGACTTGTTGATCCAGATACATTGAAGCCTGGGGACTTAGTTGGAGTTAACAAAGATAGTTACTTGATTCTGGATACTT

Basic information

species Arabidopsis thaliana
transcript AT1G09100.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 3
gtgaagttttagactcttatatcaccgttagagagattttcagaactagtggggaacaaactctgactactagtgtagtgtttgtataatgatctcatgggttaattatacttttcagACCATCTTCCTCCCTGTTGTTGGACTTGTTGATCCAGATACATTGAAGCCTGGGGACTTAGTTGGAGTTAACAAAGATAGTTACTTGATTCTGGATACTT
      ||  | ||   | |||    |||  | |   |||        |  |        || | |  |  |||  || |||  | |  | ||    |||||||| |        |||||||| ||||| |||||  ||||  | ||||| || ||||   | |||||||| || |||||||||||||||||||| || |||||||| || ||||| |
------ttcaatacaactttatt-tagttccacattcttttttgttccgccgatcttgtgcttt-atgaagagttcag-gttcat-tgttcattgt-tgggttaactg-------cagACCATATTCCTTCCTGTAATTGGGTTAGTTGACCCCGATAAGCTAAAGCCTGGCGATTTAGTTGGAGTTAACAAAGACAGCTACTTGATACTAGATACAT

upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 3
gtgaagttt-tagactcttatat-caccgttagagagattttcagaactagtggggaacaaactctgactactagtgtagtgtttgtataatgatctcatgggttaattatacttttcagACCATCTTCCTCCCTGTTGTTGGACTTGTTGATCCAGATACATTGAAGCCTGGGGACTTAGTTGGAGTTAACAAAGATAGTTACTTGATTCTGGATACTT
|| |  | | |  ||  | | || | | |  || ||  |||||   ||  |||     |||  | ||| |   | |    |  |  |  | |||  ||||   ||  || |  | | ||||| |||||| | ||||| ||||| || || ||||||||||  |||||||| || || || |||||||| ||||| || || ||| |||||||||||||  
gtaagttatatccacattgagattctctggcagtgacgttttc--cacatgtgactgtcaa--tatgaatttaatttatatcatgttgcactgacatcat---ttttttgtg-tgtacagACGATCTTCTTGCCTGTAGTTGGTCTAGTCGATCCAGATAGTTTGAAGCCCGGTGATTTGGTTGGAGTAAACAAGGACAGCTACCTGATTCTGGATACAC
















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|164181409|gb|ES098973.1|ES098973
EST:     ACTCTCAGAGGAAGGGAAAGTGTATCGTTCTAAAAACATCAACTCGTCAG                         ACCATCTTCCTCCCTGTTGTTGGACTTGTTGATCCAGATACATTG
genomic: ACTCTCAGAGGAAGGGAAAGTGTGTCGTTCTAAAAACATCAACTCGTCAGgtgaagtttt ... tacttttcagACCATCTTCCTCCCTGTTGTTGGACTTGTTGATCCAGATACATTG
EST: gi|86061010|gb|DR356767.1|DR356767
EST:     ACTCTCAGAGGAAGGGAAAGTGTGTCGTTCTAAAAACATCAACTCGTCAG                         ACCATCTTCCTCCCTGTTGTTGGACTTGTTGATCCAGATACATTGAAGCCT
genomic: ACTCTCAGAGGAAGGGAAAGTGTGTCGTTCTAAAAACATCAACTCGTCAGgtgaagtttt ... tacttttcagACCATCTTCCTCCCTGTTGTTGGACTTGTTGATCCAGATACATTGAAGCCT
EST: gi|164235359|gb|ES079543.1|ES079543
EST:     CTCTCAGAGGAAGGGAAAGTGTATCGTTCTAAAAAACATCAACTCGTCAG                         ACCATCTTCCTCCCTGTTGTTGGACTTGTTGATCCAGATACATTG
genomic: CTCTCAGAGGAAGGGAAAGTGTGTCGTTCT-AAAAACATCAACTCGTCAGgtgaagtttt ... tacttttcagACCATCTTCCTCCCTGTTGTTGGACTTGTTGATCCAGATACATTG
EST: gi|125197943|gb|EL212897.1|EL212897
EST:     CATCAACTCGTCAG                         ACCATCTTCCTCCCTGTTGTTGGAC-TGTTGATCCAGATACATTGAAGCCT
genomic: CATCAACTCGTCAGgtgaagtttt ... tacttttcagACCATCTTCCTCCCTGTTGTTGGACTTGTTGATCCAGATACATTGAAGCCT
EST: gi|86061012|gb|DR356769.1|DR356769
EST:     ACTCTCAGAGGAAGGGAAAGTGTGTCGTTCTAAAAACATCAACTCGTCAG                         ACCATCTTCCTCCCTGTTGTTGGACTTGTTGATCCAGATACATTGAAGCCT
genomic: ACTCTCAGAGGAAGGGAAAGTGTGTCGTTCTAAAAACATCAACTCGTCAGgtgaagtttt ... tacttttcagACCATCTTCCTCCCTGTTGTTGGACTTGTTGATCCAGATACATTGAAGCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgactactagtgtagtgtttgtataatgatctcatgggttaattatacttttcagACCATCTTCCTCCCTGTTGTTGGACTTGTTGATCCAGATACATTGAAGCCTGGGGACTTAGTTGGAGTTAACAAAGATAGTTACTTGATTCTGGATACTT
                                             tacttttc  CT-rich tract
                                      ttaattatacttttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaagttttagactcttatatcaccgttagagagattttcagaactagtggggaacaaactctgactactagtgtagtgtttgtataatgatctcatgggttaattatacttttcagACCATCTTCCTCCCTGTTGTTGGACTTGTTGATCCAGATACATTGAAGCCTGGGGACTTAGTTGGAGTTAACAAAGATAGTTACTTGATTCTGGATACTT

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