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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCTCTGTGACTAAGAAGCCTGCTAAGGGAGCCAAAGGTGCTGCTAAAGATCCAAACAAACCTAAGAGGCCTTCCAGTGCCTTCTTCGTTTTCATgtaatccttcgaatcttcacttttatctctgtttagtacttgtggtttgtttctatggaataactttattctggtaaaaagtttttgagtattgactttg...

Basic information

species Arabidopsis thaliana
transcript AT1G20696.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G20696.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA04G01840.8 (Glycine max), 5'ss of exon 3
-------GCTCTCTGTGACTAAGAAGCCTGCTAAGGGAGCCAAAGGTGCTGCTAAAGATCCAAACAAACCTAAGAGGCCTTCCAGTGCCTTCTTCGTTTTCATgtaatccttcgaatcttcacttttatctctgtttagtacttgtggtttgtttctatggaataactttattctggtaaaaagtttttgagtattgactttg--------
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AGGGCGCCGCCACCAAGACTAGGAAACCCGCCGGAAAGGGGAAGG---CAGCGAAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCATgtaattat---aatat--attgttatctctacgattcatttgacttccgatgcgctctcttatctttcctccg---aataattttatcgtcaaaacttttatccttgt

upper sequence: AT1G20696.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA06G01970.4 (Glycine max), 5'ss of exon 2
-------GCTCTCTGTGACTAAGAAGCCTGCTAAGGGAGCCAAAGGTGCTGCTAAAGATCCAAACAAACCTAAGAGGCCTTCCAGTGCCTTCTTCGTTTTCATgtaatccttcgaatcttcacttttatctctgtttagtacttg--------tggtttgtttctatggaataactttattctggtaaaaagtttttgagtattgactttg
| | | ||| ||| || || | || | | || ||||| || ||||| || ||||||||| | ||||| ||||||||||||||||||| || | | | ||| | || || | | | | | |||| | |||||| ||||| || |||| |||| | |||| |
AGGGAGCCGCCACCAAGGCTAGGAAACCCGCCGGCAAGGGGAAGG---CAGCGAAAGACCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCATgtaattattatatttctaactatacgatccattcgatttccgatgcgctctcttctctttccaccgaataattttatc---gtcaaaactttt--atcattgtcc---

upper sequence: AT1G20696.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv18s0122g01190.t01 (Vitis vinifera), 5'ss of exon 3
GCTCTCTGTGACTAAGAAGCCTGCTAAGGGAGCCAAAGGTG------CTGCTAAAGATCCAAACAAACCTAAGAGGCCTTCCAGTGCCTTCTTCGTTTTCATgtaatccttcgaatcttcacttttatctctgtttagtacttgtggtttgtttctatggaataactttattctggtaaaaagtttttgagtattgactttg
||| ||| |||| | | ||| | | || | | | || || || ||||| ||||||||||| |||||||||| ||||||||||||||| || | | || | ||| | | ||| | |||| | | | |||||||| | | | |||| | |||||
--GGGCTGCTGCTACGAAGGCAGGAAAGAAAACAAAGAAGGAAAAGCCAGTAAAGGACCCTAACAAGCCTAAGAGGCCAGCCAGTGCCTTTTTCGTTTTCATgtaaaatctcaatttttttttcctatttaaaaatcttacaaattgtttttagattattatctactttatttactttatta--ttttaacgattgaag---

upper sequence: AT1G20696.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv04s0044g00110.t01 (Vitis vinifera), 5'ss of exon 2
--------GCTCTCTGTGACTAAGAAGCCTGCTAAGGGAGCCAAAGGTGCTGCTAAAGATCCAAACAAACCTAAGAGGCCTTCCAGTGCCTTCTTCGTTTTCATgtaat------ccttcgaatcttcacttttatctct-gtttagtacttgtggtttgttt-ctatggaataactttattctg--gtaaaaagtttttgagtattgactttg-----
||| | || || ||| | |||||| | | |||| || ||||||||||| || ||||||||| | ||||||||||||||||||||||| | | | ||| | | |||| | ||| | ||| | ||| | | | | | | | |||||| || | || | || | || |
AAGGTGCCGCTGCC-GTCGGAAAAAAGACGGCTAAGAAGG---AGAAGGCTGTAAAGGATCCAAACAAGCCGAAGAGGCCTGCTAGTGCCTTCTTCGTTTTCATgtactgaatctcgctagaaacgttgaccagatctgtcattttttccttccgatttttaggttttttatttaatccattctgatgtgagaatctctttatccttcgttgaatgaag

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|125231433|gb|EL245518.1|EL245518
EST:     AAAGATCCAAACAAACCTAAGAGGCCTTCCAGTGCCTTCTTCGTTTTCAT                         GGAAGATTTCCGTGTGACGTACAAGGAGGAGCACCCTAAGAACAAGTCTGT
genomic: AAAGATCCAAACAAACCTAAGAGGCCTTCCAGTGCCTTCTTCGTTTTCATgtaatccttc ... tgatttgtagGGAAGATTTCCGTGTGACGTACAAGGAGGAGCACCCTAAGAACAAGTCTGT
EST: gi|125295611|gb|EL309696.1|EL309696
EST:     AAAGATCCAAACAAACCTACGAGGCCTTCCAGTGCCTTCTTCGTTTTCAT                         GGAAGATTTCCGTGTGACGTACAAGG
genomic: AAAGATCCAAACAAACCTAAGAGGCCTTCCAGTGCCTTCTTCGTTTTCATgtaatccttc ... tgatttgtagGGAAGATTTCCGTGTGACGTACAAGG
EST: gi|124828250|gb|EH913116.1|EH913116
EST:     TCCAGTGCCTTCTTCGTTTTCAT                         GGAAGATTTCCGTGTGACGTACAAGGAGGAGCACCCTAAGAACAAGTCTGT
genomic: TCCAGTGCCTTCTTCGTTTTCATgtaatccttc ... tgatttgtagGGAAGATTTCCGTGTGACGTACAAGGAGGAGCACCCTAAGAACAAGTCTGT
EST: gi|301502423|gb|HO207963.1|HO207963
EST:     AAAGATCCAAACAAACCTAAGAGGCCTTCCAGTGCCTTCTTCGTTTTCAT                         GGAAGATTTCCGTGTGACGTACAAGGAGGAGCACCCTAAGAACAAGTCTGT
genomic: AAAGATCCAAACAAACCTAAGAGGCCTTCCAGTGCCTTCTTCGTTTTCATgtaatccttc ... tgatttgtagGGAAGATTTCCGTGTGACGTACAAGGAGGAGCACCCTAAGAACAAGTCTGT
EST: gi|164160537|gb|EL999155.1|EL999155
EST:     GTGCCTTCTTCGTTTTCAT                         GGAAGATTTCCGTGTGACGTACAAGGAGGAGCACCCTAAGAACAAGTCTGT
genomic: GTGCCTTCTTCGTTTTCATgtaatccttc ... tgatttgtagGGAAGATTTCCGTGTGACGTACAAGGAGGAGCACCCTAAGAACAAGTCTGT
EST: gi|164208171|gb|ES067428.1|ES067428
EST:     GGCCTTCCAGTGCCTTCTTCGTTTTCAT                         GGAAGA-TTCCGTGTGACGTACAAGGAGGAGCACCCTAAGAACAAGTCTGT
genomic: GGCCTTCCAGTGCCTTCTTCGTTTTCATgtaatccttc ... tgatttgtagGGAAGATTTCCGTGTGACGTACAAGGAGGAGCACCCTAAGAACAAGTCTGT
EST: gi|163994112|gb|ES210616.1|ES210616
EST:     AAGATCCAAATAAACCTAAGAGGCCTTCCAGTGTCCTTCTTCGTTTTCAT                         GGAAGATTTCCGTGTGACGTACA
genomic: AAGATCCAAACAAACCTAAGAGGCCTTCCAGTG-CCTTCTTCGTTTTCATgtaatccttc ... tgatttgtagGGAAGATTTCCGTGTGACGTACA
EST: gi|125272191|gb|EL286276.1|EL286276
EST:     AAAGATCCAAACAAACCTAAGAGGCCTTCCAGTGCCTTCTTCGTTTTCAT                         GGAAGATTTCCGTGTGACG
genomic: AAAGATCCAAACAAACCTAAGAGGCCTTCCAGTGCCTTCTTCGTTTTCATgtaatccttc ... tgatttgtagGGAAGATTTCCGTGTGACG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTCTCTGTGACTAAGAAGCCTGCTAAGGGAGCCAAAGGTGCTGCTAAAGATCCAAACAAACCTAAGAGGCCTTCCAGTGCCTTCTTCGTTTTCATgtaatccttcgaatcttcacttttatctctgtttagtacttgtggtttgtttctatggaataactttattctggtaaaaagtttttgagtattgactttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtaaaaa