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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccattttcactcccattacttgaaagacttcgtctaaactttattctgtttctaattcactaatcaatttttgtatgggttcttttttcttgcagTCACCATGTCCTAGATGAGGCTGAAAGATCACTCCATGATGCCTTATGTGTACTCTCTCAAACAGTGAATGATACTAGAGTTTTGCTTGGAGGTGGATGG

Basic information

species Arabidopsis thaliana
transcript AT5G20890.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G20890.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA11G19220.1 (Glycine max), 3'ss of exon 10
-------gtatccattttcactcccattacttgaaagacttcgtctaaactttattctgtttctaattcactaatcaatttttgtatgggttcttttttcttgcagTCACCATGTCCTAGATGAGGCTGAAAGATCACTCCATGATGCCTTATGTGTACTCTCTCAAACAGTGAATGATACTAGAGTTTTGCTTGGAGGTGGATGG
        |       |  ||  |  ||  || ||  |  | |  | ||  || ||    || | |||  ||  | || | |   ||   | ||||| | |  ||| |||||||| || |||||||||||||| ||| | ||||||||||| || || || ||||| || || ||||| | |||||| |||||||||||||| |||
gctttctttgcatgggtagacatcttttttttcaacaaactggaatgaatgttttt----ttttcatttgctctttaagtatgacatatctacttttgttt--cagCCACCATGTTCTTGATGAGGCTGAAAGGTCATTGCATGATGCCTTGTGCGTGCTATCTCAGACTGTCAATGACAGTAGAGTGTTGCTTGGAGGTGGGTGG

upper sequence: AT5G20890.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA12G09250.1 (Glycine max), 3'ss of exon 10
gtatccattttcactcccattacttgaaagacttcgtctaaactttattctgtttctaattcactaatcaatttttgtatgg---gttcttttttcttgcagTCACCATGTCCTAGATGAGGCTGAAAGATCACTCCATGATGCCTTATGTGTACTCTCTCAAACAGTGAATGATACTAGAGTTTTGCTTGGAGGTGGATGG
 | || ||          |   |||       ||     |||||| | |   | | |  |||| |   || | |  |||||    ||    |||| |||||| |||||||| || ||||||||||| || ||| | ||||||||||| ||||| || ||||| || || ||||| |  || || |||||||||||||| |||
-tttctatgcatgaatagacatcttttttttttttcaacaaacttgaatgaatgtttttttcatttg-cactctaagtatgatatgtctacttttgttgcagCCACCATGTTCTTGATGAGGCTGAGAGGTCATTGCATGATGCCTTGTGTGTGCTATCTCAGACTGTCAATGACAGCAGGGTGTTGCTTGGAGGTGGGTGG

upper sequence: AT5G20890.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 10
-gtatccattttcactcccattacttgaaagacttcgtctaaactttattctgtttctaattc-actaatcaattt---ttgtatgggttcttttttcttgcagTCACCATGTCCTAGATGAGGCTGAAAGATCACTCCATGATGCCTTATGTGTACTCTCTCAAACAGTGAATGATACTAGAGTTTTGCTTGGAGGTGGATGG
  |||   ||   || |     |||    || || |  ||    || | |||| ||||||  | ||  ||   |||   |  | ||   ||| |||| | ||||    |||||  | |||||||| ||||| || || ||||||||||| ||||| || ||||| ||||||| ||| |   ||||||||||||||||||| |||
aatatttgttaggac-cttgaaact---gaggctgccactcttattcactctggttctaaagctacatatttttttgggtgatgtgctatctattttttggcagCTTTCATGTGTTGGATGAGGCAGAAAGGTCTCTGCATGATGCCTTGTGTGTGCTTTCTCAGACAGTGATTGACAGCCGAGTTTTGCTTGGAGGTGGTTGG

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|125270105|gb|EL284190.1|EL284190
EST:     CTTGTTCAATTGTCCTAAGAGGGGCCAG                         TCACCATGTCCTAGATGAGGCTGAAAGATCACTCCATGATGCCTTATGTGT
genomic: CTTGTTCAATTGTCCTAAGAGGGGCCAGgtatccattt ... tttcttgcagTCACCATGTCCTAGATGAGGCTGAAAGATCACTCCATGATGCCTTATGTGT
EST: gi|164187850|gb|ES023524.1|ES023524
EST:     TCCTAAGAGGGGCCAG                         TCACCATGTCCTAGATGAGGCTGAAAGATCACTCCATGATGCCTTA
genomic: TCCTAAGAGGGGCCAGgtatccattt ... tttcttgcagTCACCATGTCCTAGATGAGGCTGAAAGATCACTCCATGATGCCTTA
EST: gi|47828867|gb|CK118551.1|CK118551
EST:     TCTGGTTGTGAAATGGGCCAGGCTTGNTCAATTGTCCTAAGAGGGGCCAG                         TCACCATGTCCTAGATGAGGCTGAAAGATCACTCCATGATG
genomic: TCTGGTTGTGAAATGGGCCAGGCTTGTTCAATTGTCCTAAGAGGGGCCAGgtatccattt ... tttcttgcagTCACCATGTCCTAGATGAGGCTGAAAGATCACTCCATGATG
EST: gi|164186624|gb|ES076911.1|ES076911
EST:     TTGTCCTAAGAGGGGCCAG                         TCACCATGTCCTAGATGAGGCTGAAAGATCACTCCATGATGCCTTATGTGT
genomic: TTGTCCTAAGAGGGGCCAGgtatccattt ... tttcttgcagTCACCATGTCCTAGATGAGGCTGAAAGATCACTCCATGATGCCTTATGTGT
EST: gi|163996144|gb|ES112788.1|ES112788
EST:     TCTGGTTGTGAAATGGGCCAGGCTTGTTCAATTGTCCTAAGAGGGGCCAG                         TCACCAATGTCCTAGATGAGGCTGAAAGAT
genomic: TCTGGTTGTGAAATGGGCCAGGCTTGTTCAATTGTCCTAAGAGGGGCCAGgtatccattt ... tttcttgcagTCACCA-TGTCCTAGATGAGGCTGAAAGAT
EST: gi|163993948|gb|ES203130.1|ES203130
EST:     ATTGTCCTAAGAGGGGCCAG                         TCACCATGTCCTAGATGAGGCTGAAAGATCACTCCATGATGCCTTATGTGT
genomic: ATTGTCCTAAGAGGGGCCAGgtatccattt ... tttcttgcagTCACCATGTCCTAGATGAGGCTGAAAGATCACTCCATGATGCCTTATGTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattctgtttctaattcactaatcaatttttgtatgggttcttttttcttgcagTCACCATGTCCTAGATGAGGCTGAAAGATCACTCCATGATGCCTTATGTGTACTCTCTCAAACAGTGAATGATACTAGAGTTTTGCTTGGAGGTGGATGG
                 cactaat  putative branch site (score: 2)
                                       ttcttttttcttgc  putative PPT
                    taatcaatttttgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatccattttcactcccattacttgaaagacttcgtctaaactttattctgtttctaattcactaatcaatttttgtatgggttcttttttcttgcagTCACCATGTCCTAGATGAGGCTGAAAGATCACTCCATGATGCCTTATGTGTACTCTCTCAAACAGTGAATGATACTAGAGTTTTGCTTGGAGGTGGATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA