Sequence
atgc intronic sequence ATGC exonic sequence...gactcaacttatgtggctaatagtattttctttctttgccaaacctgggagtttaatctgtcaactgtatgattgatggctaattgatgatggaaaacagGGAATAATGGTAGCATCAACGGGCAGGGACAAACGTGGTGGAAGAAGTATCGCCAAAAGCTGCTTAACCACACGAGAGGACCACTGGTGCAGATAATGTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G42950.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G42950.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G08270.1 (Glycine max), 3'ss of exon 2
------gactcaacttatgtggctaatagtattttctttctttgccaaacctgggagtttaatctgtcaactgtatgattgatggctaattgatgatggaaaacagGGAATAATGGTAGCATCAACGGGCAGGGACAAACGTGGTGGAAGAAGTATCGCCAAAAGCTGCTTAACCACACGAGAGGACCACTGGTGCAGATAATGTG
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caagcagggtgaactaattagg--aacag-acatgccacagtactgatctcttttacttttctttgtgcaatacttactctctatgttttctcttgttga---cagGCCATAATGGTACCATAAATGGACAGGGACAAACATGGTGGACAAAGTATCGCCAGAAGCTTCTGAACCACACAAGGGGGCCACTTGTTCAGATATTGTG
upper sequence: AT3G42950.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G19820.1 (Glycine max), 3'ss of exon 2
--gac-tcaacttatgtggctaatagtattttctttctttgccaaacctgggagtttaatctgtcaactgtatgattgatggctaattgatgatggaaaacagGGAATAATGGTAGCATCAACGGGCAGGGACAAACGTGGTGGAAGAAGTATCGCCAAAAGCTGCTTAACCACACGAGAGGACCACTGGTGCAGATAATGTG
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tagacattagtttaagtgtccgtttccgtgttgttttagagtccgtgcttcatac---atttctttgtgttatactttctctctatgtttctcttgtttacagGCCACAATGGTACCATAAATGGACAGGGACAAACATGGTGGACAAAGTATCGCCAGAAGCTTCTGAACCACACAAGGGGGCCACTTGTTCAGATATTGTG
upper sequence: AT3G42950.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G17170.1 (Glycine max), 3'ss of exon 2
gactcaacttatgtggctaatagtattttctttctttgccaaacctgg-----gagtttaatctgtcaact-gtatgattgatggctaattgatgatggaaaacagGGAATAATGGTAGCATCAACGGGCAGGGACAAACGTGGTGGAAGAAGTATCGCCAAAAGCTGCTTAACCACACGAGAGGACCACTGGTGCAGATAATGTG
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---tctttttttttttttaaatctccccttcccccttgttctatgtgatgcttaagcttaatttacaaatttatctgatt--tcatctattg-tcataactgacagGGCATAACGGTACCATAAATGGACAGGGACAAACATGGTGGAAAAAATATCGCCAGAAGCGTCTCAACCACACTAGGGGGCCACTTGTTCAGATCATGTT
upper sequence: AT3G42950.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv11s0016g00720.t01 (Vitis vinifera), 3'ss of exon 2
gactcaacttatgtggctaatagtattttctttctttgccaaacctgggagtttaatctgtcaactgtatgattgatggctaattg--atgatggaa-aacagGGAATAATGGTAGCATCAACGGGCAGGGACAAACGTGGTGGAAGAAGTATCGCCAAAAGCTGCTTAACCACACGAGAGGACCACTGGTGCAGATAATGTG
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ggttgtagccacgctggacactataccttcatacttttt---gtcttgaagattacttcgttgctgactttgtctgattctatctgtcatcactgaccaacagGGCATAATGGTACCATAAATGGACAGGGCCAAACTTGGTGGAAGAAGTATCGCCAAAAGCTTCTCAACCACACTAGGGGTCCACTTGTTCAGATAATGTGMapped 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|164090913|gb|ES067712.1|ES067712EST: TGGAAGTTTCATTCATGGACAGAATCTTAGAGATGTTGTTGTTACAG GGAATAATGGTAGCATCAACGGGCAGGGACAAACGTGGTGGAAGAAGTATC
genomic: TGGAAGTTTCATTCATGGACAGAATCTTAGAGATGTTGTTGTTACAGgttagttgat ... tggaaaacagGGAATAATGGTAGCATCAACGGGCAGGGACAAACGTGGTGGAAGAAGTATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgggagtttaatctgtcaactgtatgattgatggctaattgatgatggaaaacagGGAATAATGGTAGCATCAACGGGCAGGGACAAACGTGGTGGAAGAAGTATCGCCAAAAGCTGCTTAACCACACGAGAGGACCACTGGTGCAGATAATGTG
tttaatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gactcaacttatgtggctaatagtattttctttctttgccaaacctgggagtttaatctgtcaactgtatgattgatggctaattgatgatggaaaacagGGAATAATGGTAGCATCAACGGGCAGGGACAAACGTGGTGGAAGAAGTATCGCCAAAAGCTGCTTAACCACACGAGAGGACCACTGGTGCAGATAATGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- ctcaact
- - - - - - - - - - - - - - - - - - - ccaaacc