Sequence
atgc intronic sequence ATGC exonic sequencegtttgctattttatttacaaaaagtttacagagaagcaagtctattcatatatctaagatgaatctctagctatgtgatcattgatgaataccttgtcatttaaattttaatgtgtgtgcagAGTAAAGCCAAAGCAGAAAAGAATCAGGCAATGGAGAATTCAATGAGTGAGAATTCCTGCCAGTTATGTGCGGTGGAGAAGCTTACATTTGAGCCACCAC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G16710.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G16710.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 6
gtttgctattttatttacaaaaagtttacagagaagcaagtctattcatatatctaagatgaatctctagctatgtgatcattgatgaataccttgtcatttaaattttaatgtgtgtgcagAGTAAAGCCAAAGCAGAAAAGAATCAGGCAATGGAGAATTCAATGAGTGAGAATTCCTGCCAGTTATGTGCGGTGGAGAAGCTTACATTTGAGCCACCAC
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-------------------taaggtttgggtaagcattatattgttcatgtggt--atatttcccacataatatttctctatttatccacaagttgtcataacatcatcttcttgtg-acagAGCAAGTCAAAAGCAGAGAAGAATCAAGCAATGGAGCATTCAATGAGTGAGAACTCCTGCCAATTGTGTGCTGTAGAGAAGCTTACCTTTGAACCACCGC
upper sequence: AT1G16710.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 8
gtttgctattttatttacaaaaagtttacagagaagcaagtctattcatatatctaagatgaatctctagctatgtgatcattgatgaataccttgtcatttaaattttaatgtgtgtgcagAGTAAAGCCAAAGCAGAAAAGAATCAGGCAATGGAGAATTCAATGAGTGAGAATTCCTGCCAGTTATGTGCGGTGGAGAAGCTTACATTTGAGCCACCAC
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--------tactagtttttaattgttcat---gtggcatat---ttcctacat----agtatttctctaattat---atctggtatccacatgttaccataacatcattttcttgt-cacagAGCAAGTCAAAAGCAGAGAAGAATCAAGCAATGGAGCATTCAATGAGTGAGAACTCCTGTCAATTGTGTGCTGTTGAGAAGCTTACCTTTGAACCACCGC
upper sequence: AT1G16710.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 6
gtttgctattttatttacaaaaagtttacagagaagcaagtctattcatatatctaagatgaatctctagctatgtgatcattgatgaataccttgtcatttaaattttaatgtgtgtgcagAGTAAAGCCAAAGCAGAAAAGAATCAGGCAATGGAGAATTCAATGAGTGAGAATTCCTGCCAGTTATGTGCGGTGGAGAAGCTTACATTTGAGCCACCAC
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---------ttcagttgctgtatgtcctccttaattcct-tatagtcttatacttctt-taattgtcttggtatcctaattttaccgaga----tg-catcta---tttattgtg---acagAGCAAATCAAAAGCAGAGAAGAATCAAGCAATGGAGCATTCAATGAGTGAGAACTCCTGTCAATTGTGTGCTGTAGAAAAACTAACTTTTGAACCATCCC
upper sequence: AT1G16710.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 5
gtttgctattttatttacaaaaagtttacagagaagcaagtctattcatatatctaagatgaatctctagctatgtgatcattgatgaataccttgtcatttaaattttaatgtgtgtgcagAGTAAAGCCAAAGCAGAAAAGAATCAGGCAATGGAGAATTCAATGAGTGAGAATTCCTGCCAGTTATGTGCGGTGGAGAAGCTTACATTTGAGCCACCAC
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-------tggctgttgagaatgatttttctgttttgt--ttttatttttattttttatgta---ctttgtctaggt--ttggtggtgattttttttcctcttccctttt--------tctagAGCAAGGCCAAGGCAGAAAAGAATCAAGCAATGGAGCGTTCGATGAGTGAGAACTCTTGTCAGCTGTGTGCAGTTGAGAAGCTTACTTTTGAACCTCCAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagctatgtgatcattgatgaataccttgtcatttaaattttaatgtgtgtgcagAGTAAAGCCAAAGCAGAAAAGAATCAGGCAATGGAGAATTCAATGAGTGAGAATTCCTGCCAGTTATGTGCGGTGGAGAAGCTTACATTTGAGCCACCAC
ttttaat putative branch site (score: 3)
ttgtcatttaaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgctattttatttacaaaaagtttacagagaagcaagtctattcatatatctaagatgaatctctagctatgtgatcattgatgaataccttgtcatttaaattttaatgtgtgtgcagAGTAAAGCCAAAGCAGAAAAGAATCAGGCAATGGAGAATTCAATGAGTGAGAATTCCTGCCAGTTATGTGCGGTGGAGAAGCTTACATTTGAGCCACCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC