Sequence
atgc intronic sequence ATGC exonic sequencegtttgtagcttaactcacgtatactctctccctaatgttgcactcatctttgaggtaagagaaaatgaatcagaaagaggagctgattttatgcaaacgtaatcaccatgtgcagGATCTGGGAAATCAAAGAGTCTGCAAAATCTAACGATGCAATTAAGAAAGTGTTGTAACCATCCTTATCTATTTGTTGGAGGAGACTACAATATGTGGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G06010.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G06010.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA10G39630.1 (Glycine max), 3'ss of exon 8
gtttgtagcttaactcacgtatactctctccctaatgttgcactcatctttgaggtaagagaaaatgaatcagaaagaggagctgattttatgcaaacgtaatcaccatgtgcagGATCTGGGAAATCAAAGAGTCTGCAAAATCTAACGATGCAATTAAGAAAGTGTTGTAACCATCCTTATCTATTTGTTGGAGGAGACTACAATATGTGGAA---
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gtacctagcctgg-taacat-tacttgttttagatccctgtatgactgcttgatttcttagaacttgct--------aacaattttttatac-caaatgtg----cattttacagGTTCTGGAAAATCAAAAAGTCTGCAAAACTTAACAATGCAACTCAGAAAGTGTTGTAACCATCCCTATCTCTTTGT---GGGAGATTATGATATGTATAGACG
upper sequence: AT3G06010.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA20G28120.1 (Glycine max), 3'ss of exon 11
gtttgtagcttaactcacgtatactctctccctaatgttgcactcatctttgaggtaagagaaaatgaatcagaaagaggagctgattttatgcaaacgtaatcaccatgtgcagGATCTGGGAAATCAAAGAGTCTGCAAAATCTAACGATGCAATTAAGAAAGTGTTGTAACCATCCTTATCTATTTGTTGGAGGAGACTACAATATGTGGAA---
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--atctagcctgg-taacat-tacttgttttagatccctgtatgactgcttgatttcttagaacttgct--------aacaattttttttttaccaa-atatgcat--tttacagGTTCTGGAAAATCAAAAAGTTTACAAAACTTAACAATGCAACTCAGAAAGTGTTGTAACCATCCCTACCTCTTCGT---GGGCGATTATGATATGTATAGACG
upper sequence: AT3G06010.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv05s0020g02960.t01 (Vitis vinifera), 3'ss of exon 10
gtttgtagcttaactcacgtatactctctccctaatgttgcactcatctttgaggtaagagaaaatgaatcagaaagaggagctgattttatgcaaacgtaatcaccatgtgcagGATCTGGGAAATCAAAGAGTCTGCAAAATCTAACGATGCAATTAAGAAAGTGTTGTAACCATCCTTATCTATTTGTTGGAGGAGACTACAATATGTGGAA---
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---------tgaaatcatgtttaaccttctatacttgccaaactagtcataattacttgccgaaagaga---aaacctgcacctg--tttactaaaaca-aagtacgatttgcagGATCTGGGAAGTCAAAAAGTTTACAGAACCTGTCCATGCAACTCAGAAAGTGTTGTAACCACCCATACCTATTTGTTGG---AGATTATAATATCTGGCAGAAMapped 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|125079268|gb|EL141335.1|EL141335EST: AGTGTATTACAAACAAGTTACAGACATGGGCAGGGTTGGCCTTCAAACAG GATCTGGGAAATCAAAGAGTCTGCAAAATCTAACGATGCAATTAAGAAAGT
genomic: AGTGTATTACAAACAAGTTACAGACATGGGCAGGGTTGGCCTTCAAACAGgtttgtagct ... ccatgtgcagGATCTGGGAAATCAAAGAGTCTGCAAAATCTAACGATGCAATTAAGAAAGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaaatgaatcagaaagaggagctgattttatgcaaacgtaatcaccatgtgcagGATCTGGGAAATCAAAGAGTCTGCAAAATCTAACGATGCAATTAAGAAAGTGTTGTAACCATCCTTATCTATTTGTTGGAGGAGACTACAATATGTGGAA
agctgat putative branch site (score: 4)
tgattttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtagcttaactcacgtatactctctccctaatgttgcactcatctttgaggtaagagaaaatgaatcagaaagaggagctgattttatgcaaacgtaatcaccatgtgcagGATCTGGGAAATCAAAGAGTCTGCAAAATCTAACGATGCAATTAAGAAAGTGTTGTAACCATCCTTATCTATTTGTTGGAGGAGACTACAATATGTGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA