Sequence
atgc intronic sequence ATGC exonic sequence...agcttaaaaattctaactagttagaattgctatctaaaaagttgttcggtgttaatttaaatgcatttatatatctgactttacagatgttgttgtgcagGTGAACCCACACACGCATCAGCTAAAAATATGTGATTTCGGGAGTGCAAAAGTGTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G09840.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G09840.6 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os03g62500.1 (Oryza sativa), 3'ss of exon 6
agcttaaaaattctaactagttagaattgctatctaaaaagttgtt-cggtgttaatttaaatgcatttatatatctgactttacagatgttgttg-----tgcagGTGAACCCACACACGCATCAGCTAAAAATATGTGATTTCGGGAGTGCAAAAGTGTTG
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-acttcaattatttattt---taaaaccgtgatcatgcatgtacttacagactgaaattcactaagttttgatggt--actaataaggtcttccttcgcactgtagGTTAACCCACATACACACCAGCTCAAAATATGTGATTTTGGCAGTGCAAAAGTTTTG
upper sequence: AT1G09840.6 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 5
-agcttaaaaattctaactagttagaattgctatctaaaaagttgttcggtgttaatttaaatgcatttatatatctgacttta-cagatgttgtt-gtg-cagGTGAACCCACACACGCATCAGCTAAAAATATGTGATTTCGGGAGTGCAAAAGTGTTG
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tggcttaa----cctaactgaaagatgatacaatttgtagcaaatatacctgtgatgccatttgttactatttggttggctcaaatgcatgttactcatgtcagGTGAACCCACACACTCATCAGCTGAAACTATGTGATTTTGGGAGTGCAAAAGTGTTG
upper sequence: AT1G09840.6 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 6
-agcttaaaaattctaactagttagaattgctatctaaaaagttgttcggtgttaatttaaatgcatttatatatctgacttta-cagatgttgtt-gtg-cagGTGAACCCACACACGCATCAGCTAAAAATATGTGATTTCGGGAGTGCAAAAGTGTTG
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tgacttaa----cctaactgaaagatgatacaatatgtagcaaatatacctgtgatgccatctgttactatttgttgggctcaaatgtatgttactcatgtcagGTGAACCCGCACACTCATCAGCTGAAACTATGTGATTTTGGGAGTGCAAAAGTGTTG
upper sequence: AT1G09840.6 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 5
agcttaaaaattctaactagttagaattgctatctaaaaagttgttcggtgttaatttaaatgcatt----tatatatctgactttacagatgttgttgtgcagGTGAACCCACACACGCATCAGCTAAAAATATGTGATTTCGGGAGTGCAAAAGTGTTG
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--tttggacagacttatcaggctaact--ccatggtgacgacttttaaattttgatcttgttatcttactttgtaagactgatttgttaaattgttatgttcagGTGAACCCACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAAGTTTTGMapped 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|125271163|gb|EL285248.1|EL285248EST: TTCCTTTGGTCTTTGTCACCGTGATATCAAGCCTCAAAACCTGCTG GTGAACCCACACACGCATCAGCTAAAAATATGTGATTTCGGGAGTGCAAAA
genomic: TTCCTTTGGTCTTTGTCACCGTGATATCAAGCCTCAAAACCTGCTGgcaagttcca ... tgttgtgcagGTGAACCCACACACGCATCAGCTAAAAATATGTGATTTCGGGAGTGCAAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcggtgttaatttaaatgcatttatatatctgactttacagatgttgttgtgcagGTGAACCCACACACGCATCAGCTAAAAATATGTGATTTCGGGAGTGCAAAAGTGTTG
atctgac putative branch site (score: 3)
ttaatttaaatgcatt 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
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agcttaaaaattctaactagttagaattgctatctaaaaagttgttcggtgttaatttaaatgcatttatatatctgactttacagatgttgttgtgcagGTGAACCCACACACGCATCAGCTAAAAATATGTGATTTCGGGAGTGCAAAAGTGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT