Sequence
atgc intronic sequence ATGC exonic sequencegtaaatctttgaaacttttgtcctgttcttagttctgttttcacatagttgttcatacttcctagtagttattctttgtgagtgtttcaatagGTTACTGGTGTTGGAATCAACACTGAGTGGGGATTGTTGATGGCAAGTATCTCAGAAGATACTGGTGAAGAAACTCCATTGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G21180.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 11
--------------------------------------------------------------------------------------gtaaatctttgaaacttttgtcctgtt----cttagttctgtt--ttcacatagttgttcatacttcctagtagttattctttgtgagtgtttcaat----agGTTACTGGTGTTGGAATCAACACTGAGTGGGGATTGTTGATGGCAAGTATCTCAGAAGATACTGGTGAAGAAACTCCATTGCAG
| || | ||| | | || | | | | ||| | | |||| ||| | || | | | | | | | | || ||| |||| || | ||||| || |||||||| |||||| || | |||||||| || || |||||| ||||||||||||| || ||||||
gtgagttttctgtttactgtctgcgtactcaatgcctcaatggaggggatgcacagctactttcaccttctaaatatatgtacattatgaagtagtaaaattgtagtagcatcaacattgattactgatgagttacatggttttacaatttgatctatctcaaatatgcataaattcttaaatgctcagGTGACCGCAGTTGGCATTAACACTGAATGGGGACTGCTAATGGCAAGCATTTCTGAAGATTCTGGTGAAGAAACACCTTTGCAG
upper sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os02g08018.1 (Oryza sativa), 3'ss of exon 8
-gtaaatctttgaaactt----ttgtcctgttcttagttctgttttcacatagttgt-tcatacttcctagta-gttattctttgtgagtgtttcaatagGTTACTGGTGTTGGAATCAACACTGAGTGGGGATTGTTGATGGCAAGTATCTCAGAAGATACTGGTGAAGAAACTCCATTGCAG
|| | | | | | || |||| ||| || | || | || || | | | | ||| | | |||| | || ||||| |||| || || | |||||||||||||| || |||||||| || ||||||||||| | ||||||||||||| | |||
cttataccctcaagaattaagtttgtgacgttttttttctaacatttgtaatgtggtgtggaagtcttttgtatatgaaattttgcagtttcttttgtagGTAACTGCAGTCGGTCTAAACACTGAGTGGGGCTTATTGATGGCCAGCATCTCAGAAGACAACAATGAAGAAACTCCACTACAG
upper sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA15G00340.1 (Glycine max), 3'ss of exon 11
-gtaaatctttga-aacttttgtcctgttcttagttctgttttcacatagttgttcatact--tcctagtagtta--ttctttgtgagtgtt-tcaatagGTTACTGGTGTTGGAATCAACACTGAGTGGGGATTGTTGATGGCAAGTATCTCAGAAGATACTGGTGAAGAAACTCCATTGCAG
| ||| ||| | | | | || | || | ||| | || |||| | | | ||| | || ||| | | ||| || ||||| ||||||||||| || || ||||||||||||||||||||||||||||||||||| |||||||| ||||| |||||||| |||
tttgaattttttatgattctagtggcatattttaagcacacgaaacaaattttttcagaatgttactacaccctgacttattttttactgtcatctgtagGTAACTGGTGTTGGTATAAATACTGAGTGGGGATTGTTGATGGCAAGTATCTCAGAGGATACTGGAGAAGAGACTCCATTACAG
upper sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA13G44990.1 (Glycine max), 3'ss of exon 12
----------gtaaatctttgaaacttttgtcctgtt-cttagttctgttttcacatagttgttcatacttcctagtagttattctttgtgagtgtttcaatagGTTACTGGTGTTGGAATCAACACTGAGTGGGGATTGTTGATGGCAAGTATCTCAGAAGATACTGGTGAAGAAACTCCATTGCAG
| || | | | | ||| | | | | ||| |||| | | ||| ||||| ||| | | ||||| ||||||||||| || || |||||||||||| || ||||||||||||||||||| |||||||| ||||| |||||||| |||
ctcctattttgatgattctagtggcatatgtttaatcacatgaaacaaattttttcagaatgttactgcaccctgac--ttattttttactgtcatct--gtagGTAACTGGTGTTGGTATAAATACTGAGTGGGGACTGCTGATGGCAAGTATCTCAGAGGATACTGGAGAAGAGACTCCATTACAG
upper sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA07G00630.1 (Glycine max), 3'ss of exon 13
---gtaaatctttgaaacttttgtcctgttcttagttctgttttcacatagttgttcatacttcctagtagttattc---tttgtgagtgtt-tcaatagGTTACTGGTGTTGGAATCAACACTGAGTGGGGATTGTTGATGGCAAGTATCTCAGAAGATACTGGTGAAGAAACTCCATTGCAG
||| | | | || | || | ||||| | ||| | | | | | | | | || ||| || || | ||||| ||||||||||| || || ||||| ||||||||||||||||||||||||||||| || ||||| ||||| ||||| || |||
tgtgtagaatactcctatcttgattatgcttttagtggtctttaagaacataaataaagtttacagaatgccacctcacattttagactgccatttgtagGTAACTGGTGTTGGTATAAATACTGAATGGGGATTGTTGATGGCAAGTATCTCAGAGGACACTGGAGAAGAGACTCCGTTACAG
upper sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA08G23760.1 (Glycine max), 3'ss of exon 13
------gtaaatctttgaaactttt-gtcctgttcttagttctgttttcacatagttgttcatacttcctagtagttattctttgtgagtgtt-tcaatagGTTACTGGTGTTGGAATCAACACTGAGTGGGGATTGTTGATGGCAAGTATCTCAGAAGATACTGGTGAAGAAACTCCATTGCAG
|| | | | ||||| || | || | | | | | | | ||| | ||| || ||| | ||||| ||||||||||| || || || || ||||||||||||||||| ||||||||||| || | ||| ||||| |||||||| |||
atactcctatcttgattatgcttttagtggtctttaagaacataaatcaaatttacagagtgccaccaccaaaagtcacatttta-gactgtcatttgtagGTAACTGGTGTTGGTATAAATACCGAATGGGGATTGTTGATGGCTAGTATCTCAGAGGACAATGGAGAAGAGACTCCATTACAG
upper sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv09s0018g02130.t01 (Vitis vinifera), 3'ss of exon 12
-----gtaaatctttgaaacttttgtcctgttcttag----ttctgttttcacatagttgttcatacttcctagtagttattc-tttgtgagtgtt-tcaatagGTTACTGGTGTTGGAATCAACACTGAGTGGGGATTGTTGATGGCAAGTATCTCAGAAGATACTGGTGAAGAAACTCCATTGCAG
| | |||| | |||||| | | | | || | | |||| ||| | ||| || |||||| || | | | || ||||| |||||||| |||||||| ||||| ||||||||||||||||||||||||||||| ||||||||||||||||| || ||||||
tcttgttgcacctttc---ttcttgtccaactgtaaaagtatcatgatgttccataagagttggcagcatcta-tatttattcattcttctatatgatctttagGTAACTGGTGTGGGAATCAATACTGAATGGGGATTGTTGATGGCAAGTATCTCAGAGGATACTGGTGAAGAAACCCCCTTGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcacatagttgttcatacttcctagtagttattctttgtgagtgtttcaatagGTTACTGGTGTTGGAATCAACACTGAGTGGGGATTGTTGATGGCAAGTATCTCAGAAGATACTGGTGAAGAAACTCCATTGCAG
ttattcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatctttgaaacttttgtcctgttcttagttctgttttcacatagttgttcatacttcctagtagttattctttgtgagtgtttcaatagGTTACTGGTGTTGGAATCAACACTGAGTGGGGATTGTTGATGGCAAGTATCTCAGAAGATACTGGTGAAGAAACTCCATTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA