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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtaaaataaaacactttataagcactggtgagttactaagaaagggttgtgaaaacatatttgctctgttctcaacaaaaccatagTTTATCGGGAAGAAAGCTGCATATGCATTGAGTGAGGGTCTTGGAGTGATAGCTTGTATTGGGGAAAAGCTAGAAGAGAGGGAAGCAGGCAAGACGTTTG

Basic information

species Arabidopsis thaliana
transcript AT2G21170.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM5G852968_T02 (Zea mays), 3'ss of exon 5
---gtcagtaaaataaaacactttataagcactggtgagttactaagaaagggttgtgaaaacatatttgctctgttctcaacaaaaccatagTTTATCGGGAAGAAAGCTGCATATGCATTGAGTGAGGGTCTTGGAGTGATAGCTTGTATTGGGGAAAAGCTAGAAGAGAGGGAAGCAGGCAAGACGTTTG
    | | |  |     | |   ||   |   || ||  |    ||  |  | ||||||   || || |     |||     |  ||    ||||||| |||||||| |||||||||||||||||  |   | ||   || || || || || || ||    || ||||||||||||||||| || || ||||
gtgattattttatgtgcatatgctactggt-ttgatgcttgcagaaacatagtttgtgattgca-atataacaagtt----gctcaaatgcagTTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATTGCCTGCATAGGAGAGCTTCTGGAAGAGAGGGAAGCAGGGAAAACTTTTG

upper sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G20930.1 (Glycine max), 3'ss of exon 5
---------------gtcagtaaaataaaacactttataagcactggtgagttactaagaaagggttgtgaaaacatatttgctctgttctcaaca------aaaccatagTTTATCGGGAAGAAAGCTGCATATGCATTGAGTGAGGGTCTTGGAGTGATAGCTTGTATTGGGGAAAAGCTAGAAGAGAGGGAAGCAGGCAAGACGTTTG
                | | |   |||  |   ||  || | ||  ||   ||| |   ||| | | |  ||   ||| |   | |  |  | | |      ||||   ||||||| || |||||| |||| ||||| ||||||||||||||||| |||||||| ||||||||||||   ||| |||| || ||||| ||  | || || |
gtgaaaattttggagataatttctatagtagttttcctatggaccagta--ttatttgtaaaagat-gaaaatgtataataattataataaccaaagattgcaaactccagTTTATAGGAAAGAAAACTGCCTATGCTTTGAGTGAGGGTCTTGGTGTGATAGCATGTATTGGGGAACTTCTACAAGAAAGAGAAGCTGGTCAAACTTTCG

upper sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G06740.1 (Glycine max), 3'ss of exon 5
---------------gtcagtaaaataaaacactttataagcactggtgag-ttactaagaaagggttgtg-aaaacatatttgctctgttctcaacaaaaccatagTTTATCGGGAAGAAAGCTGCATATGCATTGAGTGAGGGTCTTGGAGTGATAGCTTGTATTGGGGAAAAGCTAGAAGAGAGGGAAGCAGGCAAGACGTTTG
                |   |   |||  |   ||  || | ||  ||    ||  ||| | | |    || | || ||| |  |       |  |   |||   ||||||| |||||||| ||||  ||||| |||||||||||||| || |||||||| ||||||||||||  | || |||| || ||||| || || || || |
gtgaaaattttggagataccttctatagtagttttcctagggaccagtattctttgtaaaagatgaaaatgtataatatactaaccgaagattgca---aactccagTTTATAGGGAAGAAGGCTGTCTATGCTTTGAGTGAGGGTCTGGGTGTGATAGCATGTATTGGGGAACTGTTACAAGAAAGAGAAGCTGGGAAAACTTTCG

upper sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G36990.2 (Glycine max), 3'ss of exon 5
-----------------gtcagtaaaataaaaca-ctttataagca---ctggtgagttactaagaaagggttgtgaaaacatatttgctctgttctcaacaaaacca----tagTTTATCGGGAAGAAAGCTGCATATGCATTGAGTGAGGGTCTTGGAGTGATAGCTTGTATTGGGGAAAAGCTAGAAGAGAGGGAAGCAGGCAAGACGTTTG
                  ||| |    || |  | ||||   ||      || | |||   |  | ||| | ||  |||  || |  | | |   || ||||    ||     ||||||| || ||||||||||| ||||| |||||  | |||||||||||||| || || ||||| |||  | ||||||| |||||||| || || || ||||
gtaaagcaaatccagacatcatttttctacagtagctttgctagagaatatgattagtatatttgcaagagatgctaaa-tatttaagatattaactgaacattgtcaattccagTTTATAGGAAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGAGTGATTGCATGCATTGGAGAATTGTTAGAAGAAAGGGAAGCTGGAAAAACTTTTG

upper sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA03G34300.1 (Glycine max), 3'ss of exon 5
--------------------gtcagtaaaataa----aacactttataag----cactggtgagttactaagaaagggttgtg-aaaacatatttgctctgttctcaacaa----aaccatagTTTATCGGGAAGAAAGCTGCATATGCATTGAGTGAGGGTCTTGGAGTGATAGCTTGTATTGGGGAAAAGCTAGAAGAGAGGGAAGCAGGCAAGACGTTTG
                     |   || | ||         ||||   ||     |    | |  || |   ||  | |  || |||| || |  | |||    | || |     |||   ||||||| |||||||||||||| ||||| |||||  | |||||||| ||||| || || ||||| |||  | ||||||| ||||| || || || || ||||
gtaaagcaaattcagaaatcatttctacagtagctttgctgctttgctagagaatatgattaatatatttgcaagagatgatgcaaaatatttaagatcttacttgaatattgtcaactccagTTTATAGGGAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGGGTGATTGCATGCATTGGAGAATTGTTAGAAGAAAGGGAGGCTGGAAAAACTTTTG

upper sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv03s0038g01780.t01 (Vitis vinifera), 3'ss of exon 5
-------------------------------gtcagtaaaataaaacactttata-agcactggtgagttactaagaaagggttgtgaaaacatatttgctctgttctcaacaaaaccatagTTTATCGGGAAGAAAGCTGCATATGCATTGAGTGAGGGTCTTGGAGTGATAGCTTGTATTGGGGAAAAGCTAGAAGAGAGGGAAGCAGGCAAGACGTTTG
                                |  || |||    |  || |||  || |||  |   ||    | ||  |    |  |  || |  |   ||||       |||     |||| || || ||||||||||| ||||| |||||  ||||||||  ||| |||||||||||||| |||  | || |||| ||||||||||| || || ||||
gtgaaaaactctaatattagattgttactatttatgtgaaacgtgaagctatattcagaactttttttttttggataagtgaagctatattcagaacttgactgtgggtctgaaattttcagTTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATAGCTTGTATTGGAGAACTGTTACAAGAAAGGGAAGCAGGAAAAACTTTTG

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|125206214|gb|EL221168.1|EL221168
EST:     CATTCTTGGGCATTCCGAACGGAGACATGTCATCGGAGAAAAAGATGAG                         TTTATCGGGAAGAAAGCTGCATATGCATTGAGTGAGGGTCTTGGAGTG
genomic: CATTCTTGGGCATTCCGAACGGAGACATGTCATCGGAGAAAAAGATGAGgtcagtaaaa ... aaaaccatagTTTATCGGGAAGAAAGCTGCATATGCATTGAGTGAGGGTCTTGGAGTG
EST: gi|125038661|gb|EL110930.1|EL110930
EST:     CATGTCGTCGGAGAAAAAGATGAG                         TTTATCGGGAAGAAAGCTGCATATGCATTGAGTGAGGGTCTTGGAGTGATA
genomic: CATGTCATCGGAGAAAAAGATGAGgtcagtaaaa ... aaaaccatagTTTATCGGGAAGAAAGCTGCATATGCATTGAGTGAGGGTCTTGGAGTGATA
EST: gi|125223014|gb|EL237099.1|EL237099
EST:     TCATTCTTGGGCATTCCGAACGGAGACATGTCATCGGAGAAAAAGATGAG                         TTTATCGGGAAGAAAG
genomic: TCATTCTTGGGCATTCCGAACGGAGACATGTCATCGGAGAAAAAGATGAGgtcagtaaaa ... aaaaccatagTTTATCGGGAAGAAAG
EST: gi|47828644|gb|CK118328.1|CK118328
EST:     TCATTCTTGGGCATTCCGAACGGAGACATGTCATCGGAGAAAAAGATGAG                         TTTATCGGGAAGAAAGCTGCATATGCATTGAGTGAGGGTCTTGGAGTGATA
genomic: TCATTCTTGGGCATTCCGAACGGAGACATGTCATCGGAGAAAAAGATGAGgtcagtaaaa ... aaaaccatagTTTATCGGGAAGAAAGCTGCATATGCATTGAGTGAGGGTCTTGGAGTGATA
EST: gi|124849934|gb|EH934371.1|EH934371
EST:     TCATTCTTGGGCATTCCGAACGGAGACATGTCATCGGAGAAAAAGATGAG                         TTTATCGGGAAGAAAGCTGCATA
genomic: TCATTCTTGGGCATTCCGAACGGAGACATGTCATCGGAGAAAAAGATGAGgtcagtaaaa ... aaaaccatagTTTATCGGGAAGAAAGCTGCATA
EST: gi|125257208|gb|EL271293.1|EL271293
EST:     ACATGTCATCGGAGAAAAAGATGAG                         TTTATCGGGAAGAAAGCTGCATATGCATTGAGTGAGGGTCTTGGAGTGATA
genomic: ACATGTCATCGGAGAAAAAGATGAGgtcagtaaaa ... aaaaccatagTTTATCGGGAAGAAAGCTGCATATGCATTGAGTGAGGGTCTTGGAGTGATA
EST: gi|47831761|gb|CK121445.1|CK121445
EST:     TCATTCTTGGGCATTCCGAACGGAGACATGTCATCGGAGAAAAAGATGAG                         TTTATCGGGAAGAAAGCTGCATATGCATTGAGTGAGGGTCTTGGAGTGATA
genomic: TCATTCTTGGGCATTCCGAACGGAGACATGTCATCGGAGAAAAAGATGAGgtcagtaaaa ... aaaaccatagTTTATCGGGAAGAAAGCTGCATATGCATTGAGTGAGGGTCTTGGAGTGATA
EST: gi|124800938|gb|EH890525.1|EH890525
EST:     ACATGTCATCGGAGAAAAAGATGAG                         TTTATCGGGAAGAAAGCTGCATATGCATTGAGTGAGGGTCTTGGAGTGATA
genomic: ACATGTCATCGGAGAAAAAGATGAGgtcagtaaaa ... aaaaccatagTTTATCGGGAAGAAAGCTGCATATGCATTGAGTGAGGGTCTTGGAGTGATA
EST: gi|116463095|gb|EG505687.1|EG505687
EST:     TCATTCTTGGGCATTCCGAACGGAGACATGTCATCGGAGAAAAAGATGAG                         TTTATCGGGAAGAAAGCTGCATATGCATTGAGTGAGGGTCTTGGAGTGATA
genomic: TCATTCTTGGGCATTCCGAACGGAGACATGTCATCGGAGAAAAAGATGAGgtcagtaaaa ... aaaaccatagTTTATCGGGAAGAAAGCTGCATATGCATTGAGTGAGGGTCTTGGAGTGATA
EST: gi|116454376|gb|EG496968.1|EG496968
EST:     TCATTCTTGGGCATTCCGAACGGAGACATGTCATCGGAGAAAAAGATGAG                         TTTATCGGGAAGAAAGCTGCATATGCATTGAGTGAGGGTCTTGGAGTGATA
genomic: TCATTCTTGGGCATTCCGAACGGAGACATGTCATCGGAGAAAAAGATGAGgtcagtaaaa ... aaaaccatagTTTATCGGGAAGAAAGCTGCATATGCATTGAGTGAGGGTCTTGGAGTGATA
EST: gi|125187026|gb|EL201980.1|EL201980
EST:     ACATGTCATCGGAGAAAAAGATGAG                         TTTATCGGGAAGAAAGCTGCATATGCATTGAGTGAGGGTCTTGGAGTGATA
genomic: ACATGTCATCGGAGAAAAAGATGAGgtcagtaaaa ... aaaaccatagTTTATCGGGAAGAAAGCTGCATATGCATTGAGTGAGGGTCTTGGAGTGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttactaagaaagggttgtgaaaacatatttgctctgttctcaacaaaaccatagTTTATCGGGAAGAAAGCTGCATATGCATTGAGTGAGGGTCTTGGAGTGATAGCTTGTATTGGGGAAAAGCTAGAAGAGAGGGAAGCAGGCAAGACGTTTG
                    aaaacatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtaaaataaaacactttataagcactggtgagttactaagaaagggttgtgaaaacatatttgctctgttctcaacaaaaccatagTTTATCGGGAAGAAAGCTGCATATGCATTGAGTGAGGGTCTTGGAGTGATAGCTTGTATTGGGGAAAAGCTAGAAGAGAGGGAAGCAGGCAAGACGTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA