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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgactagtatccttttgctattcatgtaatatatgacattgttacacgtaatgaaaacaaaatgttgacgcagTGCCTAGGCTTTTCACCGCCGATATTGCTGCTTTCTATGAGACTTACTATACAAACAAGGGAGTGAAGATCATTAAAGGAACAGTGGCATCTGGGTTCAC

Basic information

species Arabidopsis thaliana
transcript AT3G52880.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G52880.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os09g39380.1 (Oryza sativa), 3'ss of exon 7
---------------------------------------------------------------------------------------------gtaagt-tgactagtatccttttgctattcatgtaatatatgacattgttacacgtaatgaaaacaaaatgttgacgcagTGCCTAGGCTTTTCACCGCCGATATTGCTGCTTTCTATGAGACTTACTATACAAACAAGGGAGTGAAGATCATTAAAGGAACAGTGGCATCTGGGTTCAC
                                                                                             | |  | |||   | | |    |  || |       |   |||   ||  |  |  |      | || || ||   | ||||||| | || ||||| || ||||| || ||||||||||||| |||||| || ||||| ||||| |||||| | || || ||||| ||   ||| ||   
gtaagtgtcaccactcatattttcgctaaccactgttcaactacctactacgcatcagatgaaaagaatcagttttgcccatacgattgacatgcagttatgatgtgaaacgaacttatagtggaaactttcgtgatgatgggaatctgacattgtaaaatatcttcttgtagTGCCTCGTCTCTTCACTGCTGATATCGCGGCTTTCTATGAGAGTTACTACACTAACAAAGGAGTTAAGATCGTGAAGGGTACAGTAGCTGTTGGTTTTGA

upper sequence: AT3G52880.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G084881_T01 (Zea mays), 3'ss of exon 6
-------------gtaagttgacta-gtatccttttgctattcatgtaatatatgacattgttacacgtaatgaaaacaaaatgttg-------acgcagTGCCTAGGCTTTTCACCGCCGATATTGCTGCTTTCTATGAGACTTACTATACAAACAAGGGAGTGAAGATCATTAAAGGAACAGTGGCATCTGGGTTCAC
               |  ||||  | | |      || ||||   || | |      |||   |||   ||  ||  |    |  ||       | | ||||||| | || ||||| |||||||||||||||||||||||| |||||||||| ||||| || || |||||| | || || ||  | ||   ||| ||   
agcgaaatgtaaatcactttgatcatgcagtgaaatgatattgtagtgacaagaactattcacacaacaaaataactctgcttactgccatttcatgtagTGCCTCGCCTCTTCACTGCCGATATTGCTGCTTTCTATGAGGCTTACTATACTAACAAAGGTGTAAAGATCTTGAAGGGCACGCTAGCTGTTGGTTTTGA
















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|86038365|gb|DR334120.1|DR334120
EST:     AAGGATCAACAATTTAGATGTCACTATGGTTTTCCCTGAACCTTGGTGCA                         TGCCTAGGCTTTTCACCGCCAATATTGCTGCTTTCTATGAGACTTACTATA
genomic: AAGGATCAACAATTTAGATGTCACTATGGTTTTCCCTGAACCTTGGTGCAgtaagttgac ... gttgacgcagTGCCTAGGCTTTTCACCGCCGATATTGCTGCTTTCTATGAGACTTACTATA
EST: gi|124742418|gb|EH833580.1|EH833580
EST:     TGAACCTTGGTGCA                         TGCCTAGGCTTTTCACCGCCGATATTGCTGCTTTCTATGAGACTTACTATA
genomic: TGAACCTTGGTGCAgtaagttgac ... gttgacgcagTGCCTAGGCTTTTCACCGCCGATATTGCTGCTTTCTATGAGACTTACTATA
EST: gi|164091020|gb|ES176555.1|ES176555
EST:     AAGGATCAACAATTTAGATGTCACTATGGTTT-CCCTGAACCTTGGTGCA                         TGCCTAGGCTTT-CACCGCCGATATTGCTGCTTTCTATG
genomic: AAGGATCAACAATTTAGATGTCACTATGGTTTTCCCTGAACCTTGGTGCAgtaagttgac ... gttgacgcagTGCCTAGGCTTTTCACCGCCGATATTGCTGCTTTCTATG
EST: gi|124912711|gb|EH986703.1|EH986703
EST:     ACCTTGGTGCA                         TGCCTAGGCTTTTCACCGCCGATATTGCTGCTTTCTATGAGACTTACTATA
genomic: ACCTTGGTGCAgtaagttgac ... gttgacgcagTGCCTAGGCTTTTCACCGCCGATATTGCTGCTTTCTATGAGACTTACTATA
EST: gi|86038356|gb|DR334111.1|DR334111
EST:     AAGGATCAACAATTTAGATGTCACTATGGTTTTCCCTGAACCTTGGTGAA                         TGCCTAGGCTTTTCACCGCC
genomic: AAGGATCAACAATTTAGATGTCACTATGGTTTTCCCTGAACCTTGGTGCAgtaagttgac ... gttgacgcagTGCCTAGGCTTTTCACCGCC
EST: gi|86038357|gb|DR334112.1|DR334112
EST:     AAGGATCAACAATTTAGAGGTCACTATGGTTTTCCCTGAACCTTGGTGCA                         TGCCTAGGCTTTTCACCGCCAATATTGCTGCTTTCTATGAGACTTAC
genomic: AAGGATCAACAATTTAGATGTCACTATGGTTTTCCCTGAACCTTGGTGCAgtaagttgac ... gttgacgcagTGCCTAGGCTTTTCACCGCCGATATTGCTGCTTTCTATGAGACTTAC
EST: gi|301501396|gb|HO206936.1|HO206936
EST:     AAGGATCAACAATTTAGATGTCACTATGGTTTTCCCTGAACCTTGGTGCA                         TGCCTAGGCTTTTCCCCGCCGATATTGCTGCTTTCTATGAGACTTACTATA
genomic: AAGGATCAACAATTTAGATGTCACTATGGTTTTCCCTGAACCTTGGTGCAgtaagttgac ... gttgacgcagTGCCTAGGCTTTTCACCGCCGATATTGCTGCTTTCTATGAGACTTACTATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattcatgtaatatatgacattgttacacgtaatgaaaacaaaatgttgacgcagTGCCTAGGCTTTTCACCGCCGATATTGCTGCTTTCTATGAGACTTACTATACAAACAAGGGAGTGAAGATCATTAAAGGAACAGTGGCATCTGGGTTCAC
                                            tgttgac  putative branch site (score: 3)
                              taatgaaaacaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgactagtatccttttgctattcatgtaatatatgacattgttacacgtaatgaaaacaaaatgttgacgcagTGCCTAGGCTTTTCACCGCCGATATTGCTGCTTTCTATGAGACTTACTATACAAACAAGGGAGTGAAGATCATTAAAGGAACAGTGGCATCTGGGTTCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA