Sequence
atgc intronic sequence ATGC exonic sequencegtatctggaaactgggatgctttacacttattgtttcagaaatggagagtattgtttattggtttctgaagcattgaaaattatctcttcatagGAACCTGCATTCCAGAGGCTTATATTCATCACAATGCTCGCGTGGGCGAATCCATATTGTAAAGAAAGAAATGCACGCAATGATGCCTCAGGAAAACCTT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G71240.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G71240.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G19800.2 (Glycine max), 3'ss of exon 4
-------------------gtatctggaaactggg-atgctttacacttattgtttcagaaatggagagtattgtttattggtttctgaagcattgaaaattatctcttcatagGAACCTGCATTCCAGAGGCTTATATTCATCACAATGCTCGCGTGGGCGAATCCATATTGTAAAGAA------AGAAATGCACGCAATGATGCCTCAGGAAAACCTT
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ttgtccatttaattatcaaatactgtaatactgaataaactttattattttattttcaaaaaataaatgcaatgctcattgcttttgga------------catgtct--atagGACCCTGCATTCCAGAGGCTGATATTCATAACCATGCTTGCCTGGGAAAATCCTTACACTAATGACCTTTCCAGCAATTCAGAGAAGGCTTCTTTACAG-------
upper sequence: AT1G71240.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G05220.1 (Glycine max), 3'ss of exon 1
-------------------gtatctggaaactggg-atgctttacacttattgtttcagaaatggagagtattgtttattggtttctgaagcattgaaaattatctcttcatagGAACCTGCATTCCAGAGGCTTATATTCATCACAATGCTCGCGTGGGCGAATCCATATTGTAAAGAA------AGAAATGCACGCAATGATGCCTCAGGAAAACCTT
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ttgtccatttaattatcaaatactgtaatactgaataaacattattattatatttccataaaagaaatgcagtgctcattgcttttgga------------catgtct--atagGACCCTGCATTCCAGAGGCTGATATTCATAACCATGCTTGCCTGGGAAAATCCTTACACTAATGACCTTTCCAGCAATGCAGAGAAGGCTTCTTTACAG-------
upper sequence: AT1G71240.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv12s0034g01220.t01 (Vitis vinifera), 3'ss of exon 3
---gtatctggaaact----gggatgctttacacttattgtttcag--aaatggagagtattgtttattggtttctgaagcattgaaaattatctcttcatagGAACCTGCATTCCAGAGGCTTATATTCATCACAATGCTCGCGTGGGCGAATCCATATTGTAAAGAAAGAAATGCACGCAATGATGCCTCAGGAAAACCTT
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gatttatcataatcttttgtgagacctgtaggacttactaaattatctgattggccagttgggtttttttttttttttgggat---aaatttggtgcttacagGAACCTGCATTCCAGAGACTGATTTTCATTACAATGCTCGCATGGGAGAATCCTTACTATGAAGCAAATGATTCAAATGCTATTGGTTTAGAGAAAGCTTMapped 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|116431230|gb|EG473822.1|EG473822EST: GTTTCAGGTTTTTATCGAGGGATAACTCGGAGTTTCATCCGTGTCTCAAG GAACCTGCATTCCAGAGGCTTATATTCATCACAATGCTCGCGTGGGCGAAT
genomic: GTTTCAGGTTTTTATCGAGGGATAGCTCGGAGTTTCATCCGTGTCTCAAGgtatctggaa ... ctcttcatagGAACCTGCATTCCAGAGGCTTATATTCATCACAATGCTCGCGTGGGCGAAT
EST:
gi|116431231|gb|EG473823.1|EG473823EST: GTTTCAGGTTTTTATCGAGGGATAACTCGGAGTTTCATCCGTGTCTCAAG GAACCTGCATTCCAAAGGCTTATATTCATCACAATGCTCGCGTGGGC
genomic: GTTTCAGGTTTTTATCGAGGGATAGCTCGGAGTTTCATCCGTGTCTCAAGgtatctggaa ... ctcttcatagGAACCTGCATTCCAGAGGCTTATATTCATCACAATGCTCGCGTGGGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatggagagtattgtttattggtttctgaagcattgaaaattatctcttcatagGAACCTGCATTCCAGAGGCTTATATTCATCACAATGCTCGCGTGGGCGAATCCATATTGTAAAGAAAGAAATGCACGCAATGATGCCTCAGGAAAACCTT
ttatctcttc CT-rich tract
attgaaaattatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatctggaaactgggatgctttacacttattgtttcagaaatggagagtattgtttattggtttctgaagcattgaaaattatctcttcatagGAACCTGCATTCCAGAGGCTTATATTCATCACAATGCTCGCGTGGGCGAATCCATATTGTAAAGAAAGAAATGCACGCAATGATGCCTCAGGAAAACCTT
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA