Sequence
atgc intronic sequence ATGC exonic sequencegtacatgtgcactcatttcttggtgactctgggtgggtttgtctacatttaaatgtatgaaaggaaactttgaggtacgaaactgtatttgttcatgtcattagaaaatgttatttatccttttttcccggaattggctagGCTAGAGAGTTCCTTTACTTCAAACTTTATGGAAAGCAATGTGTCACACCTGTTGCCATTATGACAAGTGCTGCAAAGAACAACCATGAGCATGTAAGTT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G56040.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G56040.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G35520.1 (Glycine max), 3'ss of exon 3
gtacatgtgcactcatttcttggtgactctgggtgggtttgtctacatttaaatgtatgaaaggaaactttgaggtacgaaactgtatttgttcatgtcattagaaaatgttatttatccttttttcccggaattggctagGCTAGAGAGTTCCTTTACTTCAAACTTTATGGAAAGCAATGTGTCACACCTGTTGCCATTATGACAAGTGCTGCAAAGAACAACCATGAGCATGTAAGTT
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--------------------------------------------------gtatattagatatccaactatcaaacac--aatcgtacttcttatgcccactgaaatat-ctatttctgctgtttcac---atttga--agGCTAGGGAATTCTTGTACTTCAAGTTATATGGGAAACAATGCATCACACCTGTTGCAATAATGACAAGTTCTGCAAAGAACAACCACAAACATGTCACCT
upper sequence: AT3G56040.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G02900.1 (Glycine max), 3'ss of exon 3
gtacatgtgcactcatttcttggtgactctgggtgggtttgtctacatttaaatgtatgaaaggaaactttgaggtacgaaactgtatttgttcatgtcattagaaaatgttatttatccttttttcccggaattggctagGCTAGAGAGTTCCTTTACTTCAAACTTTATGGAAAGCAATGTGTCACACCTGTTGCCATTATGACAAGTGCTGCAAAGAACAACCATGAGCATGTAAGTT
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----gtatatagatataccactatcaaacacaatcatacttcttatgcccaattttttttaataaaa--tggagacaagattaatcatttatgctgggcgt--ggaaatatc--taattctgctgtttcacatttga--agGCTAGAGAATTCTTGTACTTCAAGTTATATGGGAAACAATGCATCACACCTGTTGCAATAATGACAAGTTCCGCAAAGAACAACCACAAACATGTCACCT
upper sequence: AT3G56040.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv13s0067g01470.t01 (Vitis vinifera), 3'ss of exon 3
-------------gtacatgtgcactcatttcttggtgactctgggtgggtttgtctacatttaaatgtatgaaaggaaactttgaggtacgaaactgtatttgttcatgtcattagaaaatgttatttatccttttttcccggaattggctagGCTAGAGAGTTCCTTTACTTCAAACTTTATGGAAAGCAATGTGTCACACCTGTTGCCATTATGACAAGTGCTGCAAAGAACAACCATGAGCATGTAAGTT
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gtataggatctctgtttgtcaagcttgaatatttgtttatgcctttgatgcttgacaagaagaacgagttagtactggaactattagttaaatca-tgaaattatgcatatgcatttcaaatgatatttatc-taattttttgcaactg-caagGCTAGGGAGTTCCTTTACTTCAAGATCTATGGAAAACAATGCATCACTCCTGTTGCAATTATGACAAGTGCAGCAAAGAACAACCACGAACATATCACTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttgttcatgtcattagaaaatgttatttatccttttttcccggaattggctagGCTAGAGAGTTCCTTTACTTCAAACTTTATGGAAAGCAATGTGTCACACCTGTTGCCATTATGACAAGTGCTGCAAAGAACAACCATGAGCATGTAAGTT
attagaaaatgttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacatgtgcactcatttcttggtgactctgggtgggtttgtctacatttaaatgtatgaaaggaaactttgaggtacgaaactgtatttgttcatgtcattagaaaatgttatttatccttttttcccggaattggctagGCTAGAGAGTTCCTTTACTTCAAACTTTATGGAAAGCAATGTGTCACACCTGTTGCCATTATGACAAGTGCTGCAAAGAACAACCATGAGCATGTAAGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC