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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctagtctatcacacacccatagaagcttggaatagttgatattattcgtctaaggttgggttcactgtttactgatgttgtttgttgtgcctttctacagGATCCTGCTTTCTATGTTCTTAAAGAAGATATTTCCCCTTGCATATTTGGTTCAATTGAGAAGCAGAGGTGGTCATATGCGTGTGCAAAGCAACTGATTG

Basic information

species Arabidopsis thaliana
transcript AT2G27860.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G19550.1 (Glycine max), 3'ss of exon 3
ctagtctatcacacacccatagaagcttggaatagttgatattattcgtctaaggttgggttcactgtttactgatgttgtttgttgtgc---ctttctacagGATCCTGCTTTCTATGTTCTTAAAGAAGATATTTCCCCTTGCATATTTGGTTCAATTGAGAAGCAGAGGTGGTCATATGCGTGTGCAAAGCAACTGATTG
 |  | |||     | | |  |  | ||||  | |||| | ||  |    |  | |  | || |  | | |    ||||||||  | |||    |||    ||||||| || | ||||||||||||||||||    || |||||||| |||||||| || ||||||||||||||||| ||||| |||||||| ||  ||||||
gttttgtattggg-agcaagggttggttgggttggttgttgtttctttcttgtgatgagattga--gctgagatgtgttgttttgtttgcaatgttttgttagGATCCGGCATACTATGTTCTTAAAGAAGACGAATCTCCTTGCATTTTTGGTTCTATCGAGAAGCAGAGGTGGTCTTATGCATGTGCAAAACAGTTGATTG

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA12G08930.1 (Glycine max), 3'ss of exon 3
ctagtctatcac--acacccatagaagcttggaatagttgatattattcgtctaaggttgggttcactgtttactgatgttgtttgtt-gtgcctttctacagGATCCTGCTTTCTATGTTCTTAAAGAAGATATTTCCCCTTGCATATTTGGTTCAATTGAGAAGCAGAGGTGGTCATATGCGTGTGCAAAGCAACTGATTG
|| || |   |     | | |  |  | ||||  |  ||| | ||  |    |  | | || || |  | | |    ||||||||||| |    ||     ||||||| || | ||||||||||||||||||    || |||||||| |||||||| ||||| || ||||||||||| ||||| ||||| || ||  ||||||
ctggttttgtattgggagcaagggttggttggt-tgtttgttgtttctttcttctgatgggattga--gctgatatgtgttgtttgtttgcaatttgtgttagGATCCGGCATACTATGTTCTTAAAGAAGACGAGTCTCCTTGCATTTTTGGTTCTATTGAAAAACAGAGGTGGTCTTATGCCTGTGCGAAACAGTTGATTG

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G05440.1 (Glycine max), 3'ss of exon 1
---ctagtctatcacacaccca-tagaagcttggaatagttgata-ttattcgtctaaggttgggttcactgtttactgatgttgtttgttgtgcctttctacagGATCCTGCTTTCTATGTTCTTAAAGAAGATATTTCCCCTTGCATATTTGGTTCAATTGAGAAGCAGAGGTGGTCATATGCGTGTGCAAAGCAACTGATTG
    ||  | |  |    |  |  |   |  | |  | |||| |  || ||  | |     || | | |  |||   | |||||||||    |   ||| |  |||||||||| | ||| || ||||| || |||   || ||||| || |||||||||||||| |||||||| ||||| ||||| ||||| |||||  ||||||
actttatccaaataggatcttagcaagggagttgtttggttgttgcttttttttttggtaatgagctga--gttatattatgttgttttcaat---tttgtgtagGATCCTGCATACTACGTACTTAAGGAGGATGAATCTCCTTGTATTTTTGGTTCAATTGAAAAGCAGAGATGGTCCTATGCATGTGCTAAGCAGTTGATTG

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA12G30490.2 (Glycine max), 3'ss of exon 3
ctagtctatcacacacccatagaagcttggaatagtt--gatattattcgtctaaggttgggttcactgtttactgatgttgt-ttgttgtgcctttc-tacagGATCCTGCTTTCTATGTTCTTAAAGAAGATATTTCCCCTTGCATATTTGGTTCAATTGAGAAGCAGAGGTGGTCATATGCGTGTGCAAAGCAACTGATTG
 |  ||||  | |    | ||| |    ||| | |||  | | ||     |||    || |||       | | | ||||| | ||||| |   |||  |  |||||||||| | ||| || ||||| || |||   || ||||| || |||||||||||||| |||||||| ||||| ||||| ||||| |||||  ||||||
-ttatctaa-ataggatcttagcaag--ggagttgtttggttgttgcgtttcttttttttggtaatgaactgagttatgttatgttgttttcaatttggtgtagGATCCTGCATACTACGTACTTAAGGAGGATGAGTCTCCTTGTATTTTTGGTTCAATTGAAAAGCAGAGATGGTCCTATGCCTGTGCTAAGCAGTTGATTG

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 3
ctagtctatcacacacccatagaagcttggaatagttgat-attattcgtctaaggttgggttcactgttt-actgatgttgtttgttgtgcctttctac------agGATCCTGCTTTCTATGTTCTTAAAGAAGATATTTCCCCTTGCATATTTGGTTCAATTGAGAAGCAGAGGTGGTCATATGCGTGTGCAAAGCAACTGATTG
        |   ||  |  | ||||||     | | |  |  || || || |   | | |  | | ||||  | |||      |   | ||| ||  ||       ||||||| |||| |||| |||| |||||||||   ||||| ||||| ||||||||||||||||||||||| ||||| ||||| |||||||||||| | ||||
--------ttgaactgctttggaagctatcgtttgctatttgttctttgttttctgcttgccttattgttggaatgaaccaagtccatatgctttgatatgatattagGATCCAGCTTACTATCTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGTTCAATTGAGAAGCAGAGATGGTCCTATGCCTGTGCAAAGCAATTAATTG

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv06s0061g01120.t01 (Vitis vinifera), 3'ss of exon 3
ctagtctatcacacacccatagaagcttggaata-gttgatattattcgtctaaggttgggttcactgtttactgatgttgtttgttgtgcctttctac-agGATCCTGCTTTCTATGTTCTTAAAGAAGATATTTCCCCTTGCATATTTGGTTCAATTGAGAAGCAGAGGTGGTCATATGCGTGTGCAAAGCAACTGATTG
  |  || |     |  |  |     |||  ||  |||  |  | |||  ||   |||    |     |  |   |  |||| |  ||||   |  ||  |||||||  ||| |||||| || |||||||||   ||||| ||||| |||||| | |||||||||||||||||||| ||||| |||||||||||| ||||||
--aaactgtttttgaagcgcaatcatttgctatttgttctttgttttctgcttgtgttattgtttgaatgaatcaaatttgtatactgtgatatgatattagGATCCCACTTACTATGTCCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGTCCGATTGAGAAGCAGAGGTGGTCCTATGCCTGTGCAAAGCAATTGATTG

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ07025 (Selaginella moellendorffii), 3'ss of exon 3
ctagtctatcacacacccatagaagcttggaatagttgatattattcgtctaaggttgggttcactgtttactgatgttgtttgttgtgccttt--ctacagGATCCTGCTTTCTATGTTCTTAAAGAAGATATTTCCCCTTGCATATTTGGTTCAATTGAGAAGCAGAGGTGGTCATATGCGTGTGCAAAGCAACTGATTG
                       | ||      ||||     | ||||||| |  ||   ||  || | ||  |   || ||| || ||    |  | |||||| ||   || ||| || ||||| || ||    || |||||||| |||||  | |||||||||||| | ||||| ||||| ||||||||||| ||||| |
--------------------gtgatctctatccagtt---tctcttcgtctgactttaccttttct-tctatcgtgtttttttattctgttcgtggcgacagGACCCGAGTTACTACGTCCTTAAGGAGGACGAGTCTCCTTGCATTTTTGGCCCGATTGAGAAGCAGCGATGGTCGTATGCTTGTGCAAAGCAGCTGATCG

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ18978 (Selaginella moellendorffii), 3'ss of exon 3
ctagtctatcacacacccatagaagcttggaatagttgatattattcgtctaaggttgggttcactgtttactgatgttgtttgttgtgccttt--ctacagGATCCTGCTTTCTATGTTCTTAAAGAAGATATTTCCCCTTGCATATTTGGTTCAATTGAGAAGCAGAGGTGGTCATATGCGTGTGCAAAGCAACTGATTG
                       | ||      ||||     | ||||||| |  ||   ||  || | ||  |   || ||| || ||    |  | |||||| ||   || ||| || ||||| || ||    || |||||||| |||||  | |||||||||||| | ||||| ||||| ||||||||||| ||||| |
--------------------gtgatctctatccagtt---tctcttcgtctgactttaccttttct-tctatcgtgtttttttattctgttcgtggcgacagGACCCGAGTTACTACGTGCTTAAGGAGGACGAGTCTCCTTGCATTTTTGGCCCGATTGAGAAGCAGCGATGGTCGTATGCTTGTGCAAAGCAGCTGATCG

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|116380180|gb|EG422772.1|EG422772
EST:     ATGGAAAAACCATTGGAAGCCTTCTTCCTAAGGATCATCCTCTGCGTGAT                         GATCCTGCTTTCTATG
genomic: ATGGAAAAACCATTGGAAGCTTTCTTCCTAAGGATCATCCTCTGCGTGATgtaatgcctt ... ctttctacagGATCCTGCTTTCTATG
EST: gi|116380179|gb|EG422771.1|EG422771
EST:     ATGGAAAAACCATTGGAAGCTTTCTTCCTAAGGATCATCCTCTGCGTGAT                         GATCCTGCTTTCTATGTTCTTAAAGAAGATATTTCCCCTTGCATATTTGGT
genomic: ATGGAAAAACCATTGGAAGCTTTCTTCCTAAGGATCATCCTCTGCGTGATgtaatgcctt ... ctttctacagGATCCTGCTTTCTATGTTCTTAAAGAAGATATTTCCCCTTGCATATTTGGT
EST: gi|116377085|gb|EG419677.1|EG419677
EST:     ATGGAAAAACCATTGGAAGCTTTCTTCCTAAGGATCATCCTCTGCGTGAT                         GATCCTGCTTTCTATGTTCTTAAAGAAGATATTTCCCCTTGCATATTTGGT
genomic: ATGGAAAAACCATTGGAAGCTTTCTTCCTAAGGATCATCCTCTGCGTGATgtaatgcctt ... ctttctacagGATCCTGCTTTCTATGTTCTTAAAGAAGATATTTCCCCTTGCATATTTGGT
EST: gi|116377081|gb|EG419673.1|EG419673
EST:     CTTCGTAAGGATCATCCTCTGCGTGAT                         GATCCTGCTTTCTATGTTCTTAAAGAAGATATTTCCCCTTGCATATTTGGT
genomic: CTTCCTAAGGATCATCCTCTGCGTGATgtaatgcctt ... ctttctacagGATCCTGCTTTCTATGTTCTTAAAGAAGATATTTCCCCTTGCATATTTGGT
EST: gi|125186650|gb|EL201604.1|EL201604
EST:     ATGG-AAAACCATTGGAAGCTTTCTTCCTAAGGATCATCCTCTGCGTGAT                         GATCCTGCTTTCTATGTTCTTAAAGAAGATATTT
genomic: ATGGAAAAACCATTGGAAGCTTTCTTCCTAAGGATCATCCTCTGCGTGATgtaatgcctt ... ctttctacagGATCCTGCTTTCTATGTTCTTAAAGAAGATATTT
EST: gi|116377084|gb|EG419676.1|EG419676
EST:     ATGGAAAAACCATTGGAAGCTTTCTTCCTAAGGATCATCCTCTGCGTGAT                         GATCCTGCTTTCTATGTTCTTAAAGAAGATATTTCCCCTTGCATATTTGGT
genomic: ATGGAAAAACCATTGGAAGCTTTCTTCCTAAGGATCATCCTCTGCGTGATgtaatgcctt ... ctttctacagGATCCTGCTTTCTATGTTCTTAAAGAAGATATTTCCCCTTGCATATTTGGT
EST: gi|125289760|gb|EL303845.1|EL303845
EST:     ATGGAAAAACCATTGGAAGCTTTCTTCCTAAGGATCATCCTCTGCGTGAT                         GATCCTGCTTTCTATGTTCTTAAAG
genomic: ATGGAAAAACCATTGGAAGCTTTCTTCCTAAGGATCATCCTCTGCGTGATgtaatgcctt ... ctttctacagGATCCTGCTTTCTATGTTCTTAAAG
EST: gi|116377086|gb|EG419678.1|EG419678
EST:     ATCATCCTCTGCGTGAT                         GATCCTGCTTTCTATGTTCTTAAAGAAGATATTTCCCCTTGCATATTTGGT
genomic: ATCATCCTCTGCGTGATgtaatgcctt ... ctttctacagGATCCTGCTTTCTATGTTCTTAAAGAAGATATTTCCCCTTGCATATTTGGT
EST: gi|116380174|gb|EG422766.1|EG422766
EST:     ATGGAAAAACCATTGGAGGCTTTCTTCCTAAGGATCATCCTCTGCGTGAT                         GATCCTGCTTTCTATGTTCTTAAAGAAGATATTTCCCCTTGCATATTTGGT
genomic: ATGGAAAAACCATTGGAAGCTTTCTTCCTAAGGATCATCCTCTGCGTGATgtaatgcctt ... ctttctacagGATCCTGCTTTCTATGTTCTTAAAGAAGATATTTCCCCTTGCATATTTGGT
EST: gi|116380171|gb|EG422763.1|EG422763
EST:     ATGGAAAAACCATTGGAGGCTTTCTTCCTAAGGATCATCCTCTGCGTGAT                         GATCCTTCTTTCTATGTTCTTAAAGAAGATATTTCCCCTTGCATA
genomic: ATGGAAAAACCATTGGAAGCTTTCTTCCTAAGGATCATCCTCTGCGTGATgtaatgcctt ... ctttctacagGATCCTGCTTTCTATGTTCTTAAAGAAGATATTTCCCCTTGCATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgtctaaggttgggttcactgtttactgatgttgtttgttgtgcctttctacagGATCCTGCTTTCTATGTTCTTAAAGAAGATATTTCCCCTTGCATATTTGGTTCAATTGAGAAGCAGAGGTGGTCATATGCGTGTGCAAAGCAACTGATTG
                        tactgat  putative branch site (score: 2)
                                          tgcctttct  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctagtctatcacacacccatagaagcttggaatagttgatattattcgtctaaggttgggttcactgtttactgatgttgtttgttgtgcctttctacagGATCCTGCTTTCTATGTTCTTAAAGAAGATATTTCCCCTTGCATATTTGGTTCAATTGAGAAGCAGAGGTGGTCATATGCGTGTGCAAAGCAACTGATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - -cacacac
- - - - - - - - -catagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - -ggttggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttgt