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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatataccagtcctacattgttaaaattcttcatagtttgtttataaaacaaacctctaaatgtttttcgattattctagATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTATGTGCCCAGGTGGATGGAAAGTTCTGGTGGATTACTATGAGAGCTTGACTCCGG

Basic information

species Arabidopsis thaliana
transcript AT3G22890.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G22890.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G051270_T02 (Zea mays), 3'ss of exon 5
gtaa---tataccagtcctacattgttaaaattcttcatag------tttgt--ttataaaacaaacctctaaatgtttttcgattattctagATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTATGTGCCCAGGTGGATGGAAAGTTCTGGTGGATTACTATGAGAGCTTGACTCCGG
||||   |  || | | ||    ||||   ||| |    |       |||||  | |  |  |||| | |||| |  |  |   |||||| ||||||||||  | || ||||||  ||| |  || || || |||||||||||||| ||||| |||||||| || || || |||||||| ||||||   ||  
gtaagttttcacaactgctgggatgttgtgattttcagcaccaatcctttgtcgtcactagtcaaatc-ctaactaatcatgccttattc-agATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATGTGCCCGGGTGGCTGGAAAGTGCTCGTTGAATACTATGACAGCTTGGTGCCAT

upper sequence: AT3G22890.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G38760.1 (Glycine max), 3'ss of exon 4
---------------gtaatataccagtcctacattgttaaaattcttcatagtttgtt-----tataaaacaaacctctaaatgtttttcgattattctagATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTATGTGCCCAGGTGGATGGAAAGTTCTGGTGGATTACTATGAGAGCTTGACTCCGG
               || | | |   ||  | |||||| | |||  |   ||  || ||     | |  |  |       ||| |||  | |  | ||  ||||||||||| |||||| |||||| ||||  || || || || ||||||||||| ||||||||||| || ||||| ||||||||||| |||||    |   
aagtactttctagacgtcacaaaatggtgtt-cattgtgataatagtgactatgttcttacatatctgtagtatgttaacaaaggttacttgcat-ttacagATGCGCACACTGGCAAGGAACAAAGAAAGTCCTCCTGATGGATTTATGTGCCCTGGTGGATGGAAGGTGCTGGTTGATTACTATGATAGCTTAGTACTCT

upper sequence: AT3G22890.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G28980.2 (Glycine max), 3'ss of exon 4
------------gtaatataccagtcct-acattgttaaaattcttcatagtttgtt-----tataaaacaaacctctaaatgtttttcgattattctagATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTATGTGCCCAGGTGGATGGAAAGTTCTGGTGGATTACTATGAGAGCTTGACTCCGG
            |||| |||   ||  | |   || ||| | | |   ||  || ||     | |  |  |       ||| |||  | |  | ||  ||||||||||| |||||| |||||| |||| ||| || || || ||||||||||| ||||| ||||| || ||||| || |||||||| |||||    |   
tattttctaggtgtaacataatggtgttcattatgataatagtgtgagtatgttattacatatttgtagtatgttaacaaaggttacttgcattttacagATGCGCACACTGGCAAGGAACAAAGAAAGCCCTCCTGATGGATTTATGTGCCCTGGTGGTTGGAAGGTACTGGTTGAATACTATGATAGCTTAGTACTCT

upper sequence: AT3G22890.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv05s0020g04210.t01 (Vitis vinifera), 3'ss of exon 4
------------------------------------------------------------gtaatataccagtcctacattgttaaaattcttcatagtttgtttataaaac--aaacctctaa------atgtttttcgatta------------ttctagATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTATGTGCCCAGGTGGATGGAAAGTTCTGGTGGATTACTATGAGAGCTTGACTCCGG
                                                             |   | |   |    | ||| || | | |   |||   || |||  || |   |||  | | |      |||||| |  |  |            ||  ||||| | ||  | || |||||||| || ||||| |||||||| ||||||||||| ||||| ||| ||||  ||||||| || ||||| || |||   ||  
gtatattttttgcataggaaaaaaatgcagacctctttttttatttcatatctaatgataatcccaaaatggctgaaaattattcagactgggcatgcatttttttcaacatggaaatatttgatggatgatgtttctgaacaaggccgctacattttgcagATGAGAACTCTAGCGAAGAACAAAGAGAACCCTCCAGACGGATTTATGTGCCCGGGTGGTTGGGAAGTGTTGGTGGAATATTATGACAGTTTGGTGCCCA

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|125035015|gb|EL107284.1|EL107284
EST:     TCTTCGATCCCTCGAGGCCTCAAGATTTCTTGTTCATCTCCGGCACTAAG                         ATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGA
genomic: TCTTCGATCCCTCGAGGCCTCAAGATTTCTTGTTCATCTCCGGCACTAAGgtaatatacc ... attattctagATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGA
EST: gi|86077424|gb|DR373181.1|DR373181
EST:     TCTTCGATCCCTCGAGGCCTCAAGATTTCTTGTTCATCTCCGGCACTAAG                         ATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTATGTGC
genomic: TCTTCGATCCCTCGAGGCCTCAAGATTTCTTGTTCATCTCCGGCACTAAGgtaatatacc ... attattctagATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTATGTGC
EST: gi|125302843|gb|EL316928.1|EL316928
EST:     TTTCTTGTTCATCTCCGGCACTAAG                         ATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTATGTGC
genomic: TTTCTTGTTCATCTCCGGCACTAAGgtaatatacc ... attattctagATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTATGTGC
EST: gi|125134005|gb|EL175164.1|EL175164
EST:     CTTGTTCATCTCCGGCACTAAG                         ATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTATGTGC
genomic: CTTGTTCATCTCCGGCACTAAGgtaatatacc ... attattctagATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTATGTGC
EST: gi|116444819|gb|EG487411.1|EG487411
EST:     TCTTCGATCCCTCGAGGCCTCAAGATTTCTTGTTCATCTCCGGCACTAAG                         ATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTATGTGC
genomic: TCTTCGATCCCTCGAGGCCTCAAGATTTCTTGTTCATCTCCGGCACTAAGgtaatatacc ... attattctagATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTATGTGC
EST: gi|125239841|gb|EL253926.1|EL253926
EST:     ATTTCTTGTTCATCTCCGGCACTAAG                         ATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTATGTGC
genomic: ATTTCTTGTTCATCTCCGGCACTAAGgtaatatacc ... attattctagATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTATGTGC
EST: gi|116460581|gb|EG503173.1|EG503173
EST:     TTTTCGATCCCTCGAGGCCTCAAGATTTTTTGTTCATTTCCGGCACTAAG                         ATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTATGTGC
genomic: TCTTCGATCCCTCGAGGCCTCAAGATTTCTTGTTCATCTCCGGCACTAAGgtaatatacc ... attattctagATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTATGTGC
EST: gi|124772906|gb|EH863035.1|EH863035
EST:     ATCTCCGGCACTAAG                         ATGCGCTTACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTATGT
genomic: ATCTCCGGCACTAAGgtaatatacc ... attattctagATGCGC--ACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTATGT
EST: gi|124780621|gb|EH870564.1|EH870564
EST:     TCTTCGATCCCTCGAGGCCTCAAGATTTCTTGTTCATCTCCGGCACTAAG                         ATAGCGCACATTGGCAAAGAACAACGAAAACCCGCC
genomic: TCTTCGATCCCTCGAGGCCTCAAGATTTCTTGTTCATCTCCGGCACTAAGgtaatatacc ... attattctagAT-GCGCACATTGGCAAAGAACAACGAAAACCCGCC
EST: gi|116460580|gb|EG503172.1|EG503172
EST:     TCTTCGATCCCTCGAGGCCTCAAGATTTCTTGTTCATCTCCGGCACTAAG                         ATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTATGTGC
genomic: TCTTCGATCCCTCGAGGCCTCAAGATTTCTTGTTCATCTCCGGCACTAAGgtaatatacc ... attattctagATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTATGTGC
EST: gi|125203910|gb|EL218864.1|EL218864
EST:     TCTTCGATCCCTCGAGGCCTCAAGATTTCTTGTTCATCTCCGGCACTAAG                         ATGCGCACATTGG
genomic: TCTTCGATCCCTCGAGGCCTCAAGATTTCTTGTTCATCTCCGGCACTAAGgtaatatacc ... attattctagATGCGCACATTGG
EST: gi|125309566|gb|EL323651.1|EL323651
EST:     TCTTCGATCCCTCGAGGCCTCAAGATTTCTTGTTCATCTCCGGCACTAAG                         ATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAG
genomic: TCTTCGATCCCTCGAGGCCTCAAGATTTCTTGTTCATCTCCGGCACTAAGgtaatatacc ... attattctagATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAG
EST: gi|124791335|gb|EH881014.1|EH881014
EST:     TCTTCGATCCCTCGAGGCCTCAAGATTTCTTGTTCATCTCCGGCACTAAG                         ATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTA
genomic: TCTTCGATCCCTCGAGGCCTCAAGATTTCTTGTTCATCTCCGGCACTAAGgtaatatacc ... attattctagATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTA
EST: gi|86082234|gb|DR377993.1|DR377993
EST:     TCTTCGATCCCTCGAGGCCTCAAGATTTCTTGTTCATCTCCGGCACTAAG                         ATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTATGTGC
genomic: TCTTCGATCCCTCGAGGCCTCAAGATTTCTTGTTCATCTCCGGCACTAAGgtaatatacc ... attattctagATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTATGTGC
EST: gi|125185276|gb|EL200230.1|EL200230
EST:     TCTTCGATCCCTCGAGGCCTCAAGATTTCTTGTTCATCTCCGGCACTAAG                         ATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTA
genomic: TCTTCGATCCCTCGAGGCCTCAAGATTTCTTGTTCATCTCCGGCACTAAGgtaatatacc ... attattctagATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTA
EST: gi|125215760|gb|EL229844.1|EL229844
EST:     CTTCGATCCCTCGAGGCCTCAAGATTTCTTGTTCATCTACCGGCACTAAG                         ATGCGCACATTGGC
genomic: CTTCGATCCCTCGAGGCCTCAAGATTTCTTGTTCATCT-CCGGCACTAAGgtaatatacc ... attattctagATGCGCACATTGGC
EST: gi|116453694|gb|EG496286.1|EG496286
EST:     TTTTCGATCCCTCGAGGCCTCAAGATTTTTTGTTCATTTCCGGCACTAAG                         ATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTATGTGC
genomic: TCTTCGATCCCTCGAGGCCTCAAGATTTCTTGTTCATCTCCGGCACTAAGgtaatatacc ... attattctagATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTATGTGC
EST: gi|124860233|gb|EH944670.1|EH944670
EST:     GCCTCAAGATTTCTTGTTCATCTCCGGCACTAAG                         ATGCGCACATTGGCAAAGAACAA
genomic: GCCTCAAGATTTCTTGTTCATCTCCGGCACTAAGgtaatatacc ... attattctagATGCGCACATTGGCAAAGAACAA
EST: gi|116457320|gb|EG499912.1|EG499912
EST:     TCTTCGATCCCTCGAGGCCTCAAGATTTCTTGTTCATCTCCGGCACTAAG                         ATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTATGTGC
genomic: TCTTCGATCCCTCGAGGCCTCAAGATTTCTTGTTCATCTCCGGCACTAAGgtaatatacc ... attattctagATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTATGTGC
EST: gi|116444818|gb|EG487410.1|EG487410
EST:     TTTTCGATCCCTCGAGGCCTCAAGATTTTTTGTTCATTTCCGGCACTAAG                         ATGCGCACATTGGCAAAGAACAACGAAAACCCCCCAGACGGTTTTATGTGC
genomic: TCTTCGATCCCTCGAGGCCTCAAGATTTCTTGTTCATCTCCGGCACTAAGgtaatatacc ... attattctagATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTATGTGC
EST: gi|125024539|gb|EL096808.1|EL096808
EST:     TCGAGGCCTCAAGATTTCTTGTTCATCTCCGGCACTAAG                         ATGCGCACATTGGCAAAGAACTACGAAAACCCGCCAGACGGTTT
genomic: TCGAGGCCTCAAGATTTCTTGTTCATCTCCGGCACTAAGgtaatatacc ... attattctagATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTT
EST: gi|116478451|gb|EG521043.1|EG521043
EST:     TTTTCGATCCCTCGAGGCCTCAAGATTTTTTGTTCATTTCCGGCACTAAG                         ATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTATGTGC
genomic: TCTTCGATCCCTCGAGGCCTCAAGATTTCTTGTTCATCTCCGGCACTAAGgtaatatacc ... attattctagATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTATGTGC
EST: gi|116420530|gb|EG463122.1|EG463122
EST:     TTTTCGATCCCTCGAGGCCTCAAGATTTCTTGTTCATCTCCGGCACTAAG                         ATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTATGTGC
genomic: TCTTCGATCCCTCGAGGCCTCAAGATTTCTTGTTCATCTCCGGCACTAAGgtaatatacc ... attattctagATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTATGTGC
EST: gi|125034532|gb|EL106801.1|EL106801
EST:     TCTTCGATCCCTCGAGGCCTCAAGATTTCTTGTTCATCTCCGGCACTAAG                         ATGCGCACATTGGCAAAGAACA
genomic: TCTTCGATCCCTCGAGGCCTCAAGATTTCTTGTTCATCTCCGGCACTAAGgtaatatacc ... attattctagATGCGCACATTGGCAAAGAACA
EST: gi|125041509|gb|EL113778.1|EL113778
EST:     TCTTCGATCCCTCGAGGCCTCAAGATTTCTTGTTCATCTCCGGCACTAAG                         ATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTT
genomic: TCTTCGATCCCTCGAGGCCTCAAGATTTCTTGTTCATCTCCGGCACTAAGgtaatatacc ... attattctagATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTT
EST: gi|124855245|gb|EH939682.1|EH939682
EST:     TCTTCGATCCCTCGAGGCCTCAAGATTTCTTGTTCATCTCCGGCACTAAG                         ATGCGCACATTGGC
genomic: TCTTCGATCCCTCGAGGCCTCAAGATTTCTTGTTCATCTCCGGCACTAAGgtaatatacc ... attattctagATGCGCACATTGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcttcatagtttgtttataaaacaaacctctaaatgtttttcgattattctagATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTATGTGCCCAGGTGGATGGAAAGTTCTGGTGGATTACTATGAGAGCTTGACTCCGG
                             ctctaaa  putative branch site (score: 3)
                                              ttattct  putative PPT
       atagtttgtttataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatataccagtcctacattgttaaaattcttcatagtttgtttataaaacaaacctctaaatgtttttcgattattctagATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTATGTGCCCAGGTGGATGGAAAGTTCTGGTGGATTACTATGAGAGCTTGACTCCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT