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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttggttttgcatagctttttaaaactctcatcaacgtctgctgactattatgttggctagaaaagggaatgtgatatatttatgcttgttgttatcacagGTGATTGATTATAAAACTCAGCAGAACAGGCTATTTCCTCTGCTAGCATCTGCATATGCATTTCGATTTGTTGGAGAGTGGCTAAAATGGCTGTACACGG

Basic information

species Arabidopsis thaliana
transcript AT4G16760.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G16760.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os06g01390.1 (Oryza sativa), 3'ss of exon 7
---ttggttttgcatagctt-tttaaaactctcatcaacgtctgctgactattatgttggctagaaaagggaatgtgatatatttatgcttgttgttatcacagGTGATTGATTATAAAACTCAGCAGAACAGGCTATTTCCTCTGCTAGCATCTGCATATGCATTTCGATTTGTTGGAGAGTGGCTAAAATGGCTGTACACGG
    |  || | | | | |  | |||||   | |      |   |    |    | || ||||  || |  || |||    ||    |  | |  |  | ||||||  |  |||| || |||||||| | ||| || |||||| |||| || || || ||||||||| | ||||| || |||||||| || |||||||||||||
ttaatatttgtactttgttcatctaaaagaattaaattgataaacgagtttaactttttgctaccaatgacaa-gtggctaatg---gtctataatggttacagGTCCTCAATTACAAGACTCAGCAAAGCAGACTCTTTCCTTTGCTGGCTTCAGCTTATGCATTTAGGTTTGTGGGTGAGTGGCTGAAGTGGCTGTACACGG

upper sequence: AT4G16760.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv00s0389g00020.t01 (Vitis vinifera), 3'ss of exon 5
ttggttttgcatagctttttaaaactc-tcatcaacgtctgctgactattatgttggctagaaaagggaatgtgatatattta-tgcttgttgttatcacagGTGATTGATTATAAAACTCAGCAGAACAGGCTATTTCCTCTGCTAGCATCTGCATATGCATTTCGATTTGTTGGAGAGTGGCTAAAATGGCTGTACACGG
   | | |  |  | ||| |  |     |  ||||  |    | |||  |  | |    |||| | | ||| | ||  ||||  || ||  |        ||||||||||||| ||||||||||| |  ||||| |||||| |||| || ||||| ||||| ||  ||||||||||  ||||| | |||||||| || | ||
-gagatatctagggttttctgcagtggattttcaaaattaaatcacttcttagctctaaagaagatgtaat-taatggattttctgtttacttggtctttagGTGATTGATTACAAAACTCAGCAAAGTAGGCTCTTTCCTTTGCTGGCTTCTGCCTATGCTTTCAGATTTGTTGGTCAGTGGTTGAAATGGCTATATATGG
















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|152033860|gb|BP817910.2|BP817910
EST:     GTGCAGTGGGGAGGCAATTTGGCGCACATAATGGTGGCATTGAGACACAG                         GTGATTGATTATAAAACTCAGCAGAACAGGCTATT-CCTCTGCTAGTATCT
genomic: GTGCAGTGCGGAGGCAATTTGGCGCACATAATGGTGGCATTGAGACACAGgtacttattc ... gttatcacagGTGATTGATTATAAAACTCAGCAGAACAGGCTATTTCCTCTGCTAGCATCT
EST: gi|116424738|gb|EG467330.1|EG467330
EST:     GTGCAGTGCGGAGGCAATTTGGCGCACATAATGGTGGCATTGAGACACAG                         GTGATTGATTATAAAACTCAGCAGAACAGGCTATTTCCTCTGCTAGCATCT
genomic: GTGCAGTGCGGAGGCAATTTGGCGCACATAATGGTGGCATTGAGACACAGgtacttattc ... gttatcacagGTGATTGATTATAAAACTCAGCAGAACAGGCTATTTCCTCTGCTAGCATCT
EST: gi|116448274|gb|EG490866.1|EG490866
EST:     CAATTTGGCGCACATAATGGTGGCATTGAGACACAG                         GTGATTGATTATAAAACTCAGCAGAACAGGCTATTTCCTCTGCTAGCATCT
genomic: CAATTTGGCGCACATAATGGTGGCATTGAGACACAGgtacttattc ... gttatcacagGTGATTGATTATAAAACTCAGCAGAACAGGCTATTTCCTCTGCTAGCATCT
EST: gi|116441440|gb|EG484032.1|EG484032
EST:     GTGCAGTGCGGAGGCAATTTGGCGCACATAATGGTGGCATTGAGACACAG                         GTGATTGATTATAAAACTCAGCAGAACAGGCTATTTCCTCTGCTAGCATCT
genomic: GTGCAGTGCGGAGGCAATTTGGCGCACATAATGGTGGCATTGAGACACAGgtacttattc ... gttatcacagGTGATTGATTATAAAACTCAGCAGAACAGGCTATTTCCTCTGCTAGCATCT
EST: gi|116448277|gb|EG490869.1|EG490869
EST:     CAATTTGGCGCACATAATGGTGGCATTGAGACACAG                         GTGATTGATTATAAAACTCAGCAGAACAGGCTATTTCCTCTGCTAGCATCT
genomic: CAATTTGGCGCACATAATGGTGGCATTGAGACACAGgtacttattc ... gttatcacagGTGATTGATTATAAAACTCAGCAGAACAGGCTATTTCCTCTGCTAGCATCT
EST: gi|301501186|gb|HO206726.1|HO206726
EST:     GTGCAGTGCGGAGGCAATTTGGCGCACATAATGGTGGCATTGAGACACAG                         GTGATTGATTATAAAACTCAGCAGAACAGGCTATTTCCTCTGCTAGCATCT
genomic: GTGCAGTGCGGAGGCAATTTGGCGCACATAATGGTGGCATTGAGACACAGgtacttattc ... gttatcacagGTGATTGATTATAAAACTCAGCAGAACAGGCTATTTCCTCTGCTAGCATCT
EST: gi|116424736|gb|EG467328.1|EG467328
EST:     GTGCAGTGCGGAGGCAATTTGGCGCACATAATGGTGGCATTGAGACACAG                         GTGATTGATTATAAAACTCAGCAGAACAGGCTATTTCCTCTGCTAGCATCT
genomic: GTGCAGTGCGGAGGCAATTTGGCGCACATAATGGTGGCATTGAGACACAGgtacttattc ... gttatcacagGTGATTGATTATAAAACTCAGCAGAACAGGCTATTTCCTCTGCTAGCATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattatgttggctagaaaagggaatgtgatatatttatgcttgttgttatcacagGTGATTGATTATAAAACTCAGCAGAACAGGCTATTTCCTCTGCTAGCATCTGCATATGCATTTCGATTTGTTGGAGAGTGGCTAAAATGGCTGTACACGG
                      aatgtgatatatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttggttttgcatagctttttaaaactctcatcaacgtctgctgactattatgttggctagaaaagggaatgtgatatatttatgcttgttgttatcacagGTGATTGATTATAAAACTCAGCAGAACAGGCTATTTCCTCTGCTAGCATCTGCATATGCATTTCGATTTGTTGGAGAGTGGCTAAAATGGCTGTACACGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA