Sequence
atgc intronic sequence ATGC exonic sequencegtatgctaatcttttatgctattttcccgttataacctacccttttcatcatgtcatgctaagaaatctatgcttttgtatcacagTTGAACAATTTGGAGCTTGCTGTCAATCTTGCTAAAAGAGGAAACCTCCCAGGTGCAGAAAATCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G08530.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 9
gtatgctaat--cttttatgctattttcccgttataacctacccttttcatcatgtcatgctaagaaat-ctatgcttttgt-atcacagTTGAACAATTTGGAGCTTGCTGTCAATCTTGCTAAAAGAGGAAACCTCCCAGGTGCAGAAAATCTG
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gtatgtttctgaccttgttataacttttttgttgtaaagtggggtatgaa--atggcatttttacaaattccatttggttattatcacagTTAAACAATTTGGAGCTAGCAGTTAGTCTTGCCAAAAGAGGAAATCTTCCTGGTGCTGAGAAGCTG
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 9
gtatgctaat--cttttatgctattttcccgttataacctacccttttcatcatgtcatgctaagaaatctatgcttttgtatcacagTTGAACAATTTGGAGCTTGCTGTCAATCTTGCTAAAAGAGGAAACCTCCCAGGTGCAGAAAATCTG
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gtatgtttctgaccatgttataacttttttgttgtaaagtggggtatgaa--atgccatttttacaaattt-catttggttatcacagCTAAACAATTTGGAGCTAGCAGTTAGTCTTGCCAAAAGAGGAAATCTTCCTGGTGCTGAAAAGCTG
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 9
gtatgctaatcttttatgctattttcccgttataacctacccttttcatcatgtcatgctaagaaatctatgcttttgtatcacagTTGAACAATTTGGAGCTTGCTGTCAATCTTGCTAAAAGAGGAAACCTCCCAGGTGCAGAAAATCTG
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gtatgtttctgagctg-atttcctttgtggcatgtcagaaaattatcttc-tgtgcttatggatgttatctgattct-tattgtagTTGAACAACTTGGAGCTAGCTGTCAATCTCGCAAAAAGGGGAAATCTCCCTGGTGCAGAGAACTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataacctacccttttcatcatgtcatgctaagaaatctatgcttttgtatcacagTTGAACAATTTGGAGCTTGCTGTCAATCTTGCTAAAAGAGGAAACCTCCCAGGTGCAGAAAATCTG
ttataac putative branch site (score: 2)
tgctttt putative PPT
taagaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgctaatcttttatgctattttcccgttataacctacccttttcatcatgtcatgctaagaaatctatgcttttgtatcacagTTGAACAATTTGGAGCTTGCTGTCAATCTTGCTAAAAGAGGAAACCTCCCAGGTGCAGAAAATCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA