Sequence
atgc intronic sequence ATGC exonic sequence...ttgaaagattgtttagatggactagttgttgcatttaattcgtgttcgaggaatatcttagagctttatattgaatacaggtaaatcaaattgaatgcagGAGATGGATTACTTGAATGAAGCTCAAAACGGAATAAAATTTAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G71810.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G71810.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os04g54790.1 (Oryza sativa), 3'ss of exon 6
--ttgaaagattgtttagatggactagttgttgcatttaattcgtgttcgaggaatatcttagagctttatattgaatacaggtaaatcaaattgaatgcagGAGATGGATTACTTGAATGAAGCTCAAAACGGAATAAAATTTAG
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tattctatgtacacttagctag-ttagctacctgattttaaaaataaggttcatat-tcttagagctacacattgaatacaggtaaatcacatttaatgcagGAGATGGATTACAGAGCAGAAGCAAGAAGTGGGCTTAAATTCAG
upper sequence: AT1G71810.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G305007_T02 (Zea mays), 3'ss of exon 5
-ttgaaagattgtttagatggactagttgttgcatttaattcgtgttcgaggaatat---cttagagctttatattgaatacaggtaaatcaaattgaatgcagGAGATGGATTACTTGAATGAAGCTCAAAACGGAATAAAATTTAG
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gtgctagcagtattc---taggcta-ttgcagattctgactaaaacattaggtgtatatccttagatattcacattgaatacaggtaaatcacatttgatgcagGAGATGGATTATAGAGAAGAAGCAAGAAATGGACTTAAGTTCAG
upper sequence: AT1G71810.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA16G27500.1 (Glycine max), 3'ss of exon 6
-ttgaaagattgtttagatggactagttgttgcatttaattcgtgttcgaggaatatcttagagctttatattgaatacaggtaaatcaaattgaatgcagGAGATGGATTACTTGAATGAAGCTCAAAACGGAATAAAATTTAG
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acggcaataagatgtcagcatattaatt-tcatatataatgtttcaaaaataaaattcttagaaattcaaattgaatacaggtaaatcaccttgaatgcagGAGATGGACTACAATAATGAAGCAAGCAATGGTATCAAGTTCAG
upper sequence: AT1G71810.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv18s0001g01620.t01 (Vitis vinifera), 3'ss of exon 6
ttgaaagattgtttagatggactagttgttg--catttaattcgtgttcgaggaatat-cttagagctttatattgaatacaggtaaatcaaattgaatgcagGAGATGGATTACTTGAATGAAGCTCAAAACGGAATAAAATTTAG
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---aagcattttaaaacttcttttttttttttccttttatcctttgctctaggcattttcttagtgcttcatattgaatacaggtaaatcacattgaatgcagGAGATGGACTATAGAAAAGAAGCGAAGAATGGGATCAAGTTTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcgaggaatatcttagagctttatattgaatacaggtaaatcaaattgaatgcagGAGATGGATTACTTGAATGAAGCTCAAAACGGAATAAAATTTAG
tttatattgaataca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgaaagattgtttagatggactagttgttgcatttaattcgtgttcgaggaatatcttagagctttatattgaatacaggtaaatcaaattgaatgcagGAGATGGATTACTTGAATGAAGCTCAAAACGGAATAAAATTTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - -tgtttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaataca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatcaaa