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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctagtaactttgcagagctagcgtttgattcctgtatacagttttcaagtgtaatgatgcttcttggtttttagGTTACATTGGCGAGTTTGAGTATGTTGATGACCACAGGTCTGGTAAGATTGTTGTTGAGCTTAATGGAAGGCTGAACAAGTGTGGAGTTATCAGTCCTCG

Basic information

species Arabidopsis thaliana
transcript AT3G46040.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G46040.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G018228_T04 (Zea mays), 3'ss of exon 2
gtatgctagtaactttgcagagctag---cgtttga-ttcctgtatac--agttttcaagtgtaatgatgcttcttggtttttagGTTACATTGGCGAGTTTGAGTATGTTGATGACCACAGGTCTGGTAAGATTGTTGTTGAGCTTAATGGAAGGCTGAACAAGTGTGGAGTTATCAGTCCTCG
    | |||   ||   ||    ||    | ||||| || ||  || |  ||  | |     | || ||  || ||   | |||||||||||||||||||| ||||| || |||||||||||  |||| ||||| || || ||||| |||||||| ||||| || ||||| ||||| || || ||
----gttagcc-ctcctcaaccttatgcccatttgaattgcttcattctgaggatacgcccctgattattattgttctatattagGTTACATTGGCGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATCGTGGTGGAGCTGAATGGAAGACTGAATAAATGTGGTGTTATTAGCCCACG

upper sequence: AT3G46040.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G328578_T01 (Zea mays), 3'ss of exon 2
gtatgctagtaactttgcagagctag---cgtttga-ttcctgtatac--agttttcaagtgtaatgatgcttcttggtttttagGTTACATTGGCGAGTTTGAGTATGTTGATGACCACAGGTCTGGTAAGATTGTTGTTGAGCTTAATGGAAGGCTGAACAAGTGTGGAGTTATCAGTCCTCG
    | |||   ||   ||    ||    | ||||| || ||  || |  ||  | |     | || ||  || ||   | ||||| |||||| ||||||| ||||| || |||||||||||  |||| ||||| || || ||||| |||||||| ||||| || ||||| ||||| || || ||
----gttagcc-ctcctcaaccttatgcccatttgaattgcttcattctgaggatacgtccctgattattattgttctatattagGCTACATTAGCGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATCGTGGTGGAGCTGAATGGAAGACTGAATAAATGTGGTGTTATTAGCCCACG

upper sequence: AT3G46040.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G059624_T01 (Zea mays), 3'ss of exon 1
--------------------gtatgctagtaactttgcagagctagcgtttgattcctgtatacagttttcaagtgtaatga-tgcttcttggtttttagGTTACATTGGCGAGTTTGAGTATGTTGATGACCACAGGTCTGGTAAGATTGTTGTTGAGCTTAATGGAAGGCTGAACAAGTGTGGAGTTATCAGTCCTCG
                     | || | | |||||    ||   |  |    | | ||     || || ||| | ||  ||| || | |    | |  ||| || ||  | |||||| |||||||||| ||||| ||  |||| | ||| || |||||| | || || |||||||||||||||||| | |||||||||||
gttagttatctttatttacattttgtttgcaacttgttggaagcaaggaaatagttct-----caattctcatgagtcgtgaatgttgccctttctacagGGTATATCAGTGAGTTTTAGTATGTTGACGACCATAGAGCTGGAAGGATAGTCGTTGAGTTGAACGGCAGGCTGAACAAGTGTGGACTGATCAGTCCTCG

upper sequence: AT3G46040.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G083497_T04 (Zea mays), 3'ss of exon 1
gtatgctagtaactttgcagagctagcgtttgattcctgtatacagt-tttcaagtgta-----atgat-gcttcttggtttttagGTTACATTGGCGAGTTTGAGTATGTTGATGACCACAGGTCTGGTAAGATTGTTGTTGAGCTTAATGGAAGGCTGAACAAGTGTGGAGTTATCAGTCCTCG
        || | ||  || | || | |    ||| |  |   |||  || | ||  ||      ||||   | ||   || ||||| |||||||||||||| ||||| || |||||||||||  |||| |||||||| || || || || || || || ||||| || || || || || || ||
--------gttagttctca-atctcgtgccccatttcaattggcagcattccgaggatacgtacctgattagtgctatattattagGATACATTGGCGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATTGTGGTGGAACTGAACGGCAGACTAAACAAATGCGGTGTAATTAGCCCCCG

upper sequence: AT3G46040.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G177720_T01 (Zea mays), 3'ss of exon 1
gtatgctagtaactttgcaga-gctagcgtttgattcctgtatacagttttcaagtgtaatgatgcttct--tggtttttagGTTACATTGGCGAGTTTGAGTATGTTGATGACCACAGGTCTGGTAAGATTGTTGTTGAGCTTAATGGAAGGCTGAACAAGTGTGGAGTTATCAGTCCTCG
||  ||||| |      |  | ||     ||  ||  ||  || | |    || ||  | ||||  || |  || | | |||| |||||||| ||||| ||||| |||||||||||| | || || ||||| || || || || || || |||||||||||||| || || ||||| |||||
gttagctagcactcgaccttatgccctgtttcaatgactccattccgaggacatgtcca-tgatcattgtgctgttatgtagGCTACATTGGAGAGTTCGAGTACGTTGATGACCACCGATCGGGCAAGATCGTGGTCGAACTCAACGGGAGGCTGAACAAGTGCGGCGTCATCAGCCCTCG

upper sequence: AT3G46040.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S426_18V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------gtatgctagtaactttgcagagctagcgtttgattcctgtatacagttttcaagtgtaatgatgcttcttgg---tttttagGTTACATTGGCGAGTTTGAGTATGTTGATGACCACAGGTCTGGTAAGATTGTTGTTGAGCTTAATGGAAGGCTGAACAAGTGTGGAGTTATCAGTCCTCG
                    || |  | |||  |        | |||| | | |       |  | |  |   |    |  |   | ||||   |||| |||||| ||||| |||||||||  ||||||||||||| |  |||| |||||||| || ||||| ||||||||  |||||||||| || || |||||||||||
ctctctctctctctctcatctacgaaaataaactatttatcttcgcgtctaagttgca-gcattgatagcggatcgttttctctcttttggctcttttcagGTTATATTGGAGAGTTTGAGCTTGTTGATGACCACCGAGCTGGCAAGATTGTGGTAGAGCTCAATGGAAGATTGAACAAGTGCGGTGTCATCAGTCCTCG

upper sequence: AT3G46040.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S41_94V6.2 (Physcomitrella patens), 3'ss of exon 2
----------gtatgctagtaact-ttgcagagctagcgtttgattcctgta--------tacagttttcaagtgtaatgatgctt--cttggtttttagGTTACATTGGCGAGTTTGAGTATGTTGATGACCACAGGTCTGGTAAGATTGTTGTTGAGCTTAATGGAAGGCTGAACAAGTGTGGAGTTATCAGTCCTCG
           |   || | |||| | | | || |     | || ||    |        || ||||||    |||  | |  |||  ||| ||||  ||| |||||||||||||||||    || |||||||||||  | || ||||||||||||||| | || ||||| || |||||||| |||||||||||||||||
tttgttttaatttaacttgaaactgtcgaaaagatctatgtcgagtcacacaattgaatttagagttttggtttgttcttaaccttaccttcgtttgcagGCTACATTGGCGAGTTTGAACTGGTAGATGACCACAGAGCAGGCAAGATTGTTGTTGAGTTAAACGGAAGACTTAACAAGTGCGGAGTTATCAGTCCTCG

upper sequence: AT3G46040.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S45_88V6.2 (Physcomitrella patens), 3'ss of exon 1
--------------------gtatgctagtaactttgcagagctagcgtttgattcctgtatacagttttcaagtgtaatgatgcttcttggt--ttttagGTTACATTGGCGAGTTTGAGTATGTTGATGACCACAGGTCTGGTAAGATTGTTGTTGAGCTTAATGGAAGGCTGAACAAGTGTGGAGTTATCAGTCCTCG
                    | |   | || |   ||   |||  || ||  |   ||| | | |  | ||      | |  || |     ||  ||||||| |||||||| || ||||||   || ||||||||| |  |||| ||||| || || ||||||||||| ||| |||||||||| || || |||||||| ||
tgtttttgtcttccccttatggaatttggttatcctgtt-agcgtgctttacaacgctgaagaaatctctctgactaattagtgttctcctgtctttttagGATACATTGGAGAATTTGAGCTGGTAGATGACCACCGAGCTGGAAAGATCGTAGTGGAGCTTAATGGCAGGTTGAACAAGTGCGGTGTCATCAGTCCCCG

upper sequence: AT3G46040.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S115_101V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------------gtatgctagtaactttg-cagagctagcgtttgatt-----cctgtatacagttttcaagtgtaatgatgcttcttggtttttagGTTACATTGGCGAGTTTGAGTATGTTGATGACCACAGGTCTGGTAAGATTGTTGTTGAGCTTAATGGAAGGCTGAACAAGTGTGGAGTTATCAGTCCTCG
                 |||   |||| |  |||   || | |||||    |      | || |       |||   |  ||| || | | ||  |||  ||| |||||||| ||||||||   ||| |||||||||||| | || || ||||| || ||||| || || ||| ||||||||||||| || |||||||| ||
taatagtaagggaacatgtaacgtagtcatgttggtggatcgagcgtcctttcatgagcttgaacctgacgttcttttaaaat-atacatattcatttc-agGCTACATTGGAGAGTTTGAACTTGTGGATGACCACAGGGCAGGGAAAATTGTGGTGGAGCTGAACGGCAGGTTGAACAAGTGTGGTGTGATCAGTCCCCG

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|116412289|gb|EG454881.1|EG454881
EST:     GCCTTCTTCTAAAGTTATCATCAAGTTCCTTATCGTCATGCAAAAGCACG                         GTTACATTGGCGAGTTTGAGTATGTTGATGACCACAGGTCTGGTAAGATTG
genomic: GCCTTCTTCTAAAGTTATCATCAAGTTCCTTATCGTCATGCAAAAGCACGgtatgctagt ... tggtttttagGTTACATTGGCGAGTTTGAGTATGTTGATGACCACAGGTCTGGTAAGATTG
EST: gi|125034567|gb|EL106836.1|EL106836
EST:     TATCATCAAGTTCCTTATCGTCATGCAAAAGCACG                         GTTACATTGGCGAGTTTGAGTATGTTGATGACCACAGGTCT
genomic: TATCATCAAGTTCCTTATCGTCATGCAAAAGCACGgtatgctagt ... tggtttttagGTTACATTGGCGAGTTTGAGTATGTTGATGACCACAGGTCT
EST: gi|116402443|gb|EG445035.1|EG445035
EST:     GCCTTCTTCTAAAGTTATCATCAAGTTCCTTATCGTCATGCAAAAGCACG                         GTTACATTGGCGAGTTTGGGTATGTTGATGACCACAGGTCTGGTAGGATTG
genomic: GCCTTCTTCTAAAGTTATCATCAAGTTCCTTATCGTCATGCAAAAGCACGgtatgctagt ... tggtttttagGTTACATTGGCGAGTTTGAGTATGTTGATGACCACAGGTCTGGTAAGATTG
EST: gi|125282356|gb|EL296441.1|EL296441
EST:     TGCAAAAGCACG                         GTTACATTGGCGAGTTTGAGTATGTTGATGACCACAGGTCTGGTAAGATTG
genomic: TGCAAAAGCACGgtatgctagt ... tggtttttagGTTACATTGGCGAGTTTGAGTATGTTGATGACCACAGGTCTGGTAAGATTG
EST: gi|116401733|gb|EG444325.1|EG444325
EST:     CCCTTCTTCTAAAGTTATCATCAAGTTCCTTATCGTCATGCAAAAGCACG                         GTTCCATTGGCGAGTTTGGGTATGTTGATGACCCCAGGTCTGGTAGGATTG
genomic: GCCTTCTTCTAAAGTTATCATCAAGTTCCTTATCGTCATGCAAAAGCACGgtatgctagt ... tggtttttagGTTACATTGGCGAGTTTGAGTATGTTGATGACCACAGGTCTGGTAAGATTG
EST: gi|116401724|gb|EG444316.1|EG444316
EST:     GCCTTCTTCTAAAGTTATCATCAAGTTCCTTATCGTCATGCAAAAGCACG                         GTTACATTGGCGAGTTTGGGTATGTTGATGACCACAGGTCTGGTAGGATTG
genomic: GCCTTCTTCTAAAGTTATCATCAAGTTCCTTATCGTCATGCAAAAGCACGgtatgctagt ... tggtttttagGTTACATTGGCGAGTTTGAGTATGTTGATGACCACAGGTCTGGTAAGATTG
EST: gi|116462642|gb|EG505234.1|EG505234
EST:     GCCTTCTTCTAAAGTTATCATCAAGTTCCTTATCGTCATGCAAAAGCACG                         GTTACATTGGCGAGTTTGAGTATGTTGATGACCACAGGTCTGGTAAGATTG
genomic: GCCTTCTTCTAAAGTTATCATCAAGTTCCTTATCGTCATGCAAAAGCACGgtatgctagt ... tggtttttagGTTACATTGGCGAGTTTGAGTATGTTGATGACCACAGGTCTGGTAAGATTG
EST: gi|164150567|gb|ES106104.1|ES106104
EST:     AAGTTCCTTATCGTCATGC-AAAGCACG                         GTTACATTGGCGAGTTTGAGTATGTTGATGACCACAGGTCTGGTAAGATTG
genomic: AAGTTCCTTATCGTCATGCAAAAGCACGgtatgctagt ... tggtttttagGTTACATTGGCGAGTTTGAGTATGTTGATGACCACAGGTCTGGTAAGATTG
EST: gi|125036735|gb|EL109004.1|EL109004
EST:     TTATCGTCATGCAAAAGCACG                         GTTACATTGGCGAGTTTGAGTATGTTGATGACCACAGGTCTGGTAAGATTG
genomic: TTATCGTCATGCAAAAGCACGgtatgctagt ... tggtttttagGTTACATTGGCGAGTTTGAGTATGTTGATGACCACAGGTCTGGTAAGATTG
EST: gi|164147887|gb|ES104385.1|ES104385
EST:     AAGTTCCTTATCGTCATGCAAAAGCACG                         GTTACATTGGCGAGTTTGAGTATGTTGATGACCACAGGTCTGGTAAGATTG
genomic: AAGTTCCTTATCGTCATGCAAAAGCACGgtatgctagt ... tggtttttagGTTACATTGGCGAGTTTGAGTATGTTGATGACCACAGGTCTGGTAAGATTG
EST: gi|125195849|gb|EL210803.1|EL210803
EST:     ATCAAGTTCCTTATCGTCATGCAAAAGCACG                         GTTACATTGGCGAGTTTGAGTATGTTGATGACCACAGGTCTGGTAAGATTG
genomic: ATCAAGTTCCTTATCGTCATGCAAAAGCACGgtatgctagt ... tggtttttagGTTACATTGGCGAGTTTGAGTATGTTGATGACCACAGGTCTGGTAAGATTG
EST: gi|116412290|gb|EG454882.1|EG454882
EST:     CCCTTTTTCTAAAGTTATCATCAAGTTCCTTATCGTCATGCAAAAGCACG                         GTTACATTGGCGAGTTTGAGTATGTTGATGACCACAGGTCTGGTAAGATTG
genomic: GCCTTCTTCTAAAGTTATCATCAAGTTCCTTATCGTCATGCAAAAGCACGgtatgctagt ... tggtttttagGTTACATTGGCGAGTTTGAGTATGTTGATGACCACAGGTCTGGTAAGATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcgtttgattcctgtatacagttttcaagtgtaatgatgcttcttggtttttagGTTACATTGGCGAGTTTGAGTATGTTGATGACCACAGGTCTGGTAAGATTGTTGTTGAGCTTAATGGAAGGCTGAACAAGTGTGGAGTTATCAGTCCTCG
   gtttgat  putative branch site (score: 5)
                                      tgcttctt  putative PPT
                                                ttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctagtaactttgcagagctagcgtttgattcctgtatacagttttcaagtgtaatgatgcttcttggtttttagGTTACATTGGCGAGTTTGAGTATGTTGATGACCACAGGTCTGGTAAGATTGTTGTTGAGCTTAATGGAAGGCTGAACAAGTGTGGAGTTATCAGTCCTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG