Sequence
atgc intronic sequence ATGC exonic sequencegtattgaattttcttcttgaagctgcaaccactttctttgtttacatatgtttcactgacaaattctgtttatctgttataaagcttacgatgaaaatttactggtatatgacagGAGGAGATTCAAAAACCCTCATGTTTGTACAAATCAGTCCTAACGAGAATGATCAAAGTGAGACACTATGCTCACTGAATTTTGCTAGCAGAGTGAGAGG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G72250.2 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G72250.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GRMZM2G400223_T01 (Zea mays), 3'ss of exon 11
gtattgaattttcttcttgaagctgcaaccactttctttgtttacatatgtttcactgacaaattctgtttatctgttataaagcttacgatgaaaatttactggtatatgacagGAGGAGATTCAAAAACCCTCATGTTTGTACAAATCAGTCCTAACGAGAATGATCAAAGTGAGACACTATGCTCACTGAATTTTGCTAGCAGAGTGAGAGG
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------------------------gtatgtagtttttttgttt-cataga----attgtgtaatcttacactttagttt--agttttatgattcaa---tgtttaaacaatacagGTGGAGATTCCAAAACTTTGATGTTTGTTCAAATCAGTCCTAATGAGAACGACGTGGGTGAAACTCTTTGTTCATTGAACTTCGCGAGCAGAGTACGAGG
upper sequence: AT1G72250.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA08G18590.1 (Glycine max), 3'ss of exon 14
gtattgaattttcttcttgaagctgc--aacca--ctttctttgtttacatatgtttcactgacaaattctgtttatctgttataaagcttacgatgaaaatttactggta-------tatgacagGAGGAGATTCAAAAACCCTCATGTTTGTACAAATCAGTCCTAACGAGAATGATCAAAGTGAGACACTATGCTCACTGAATTTTGCTAGCAGAGTGAGAGG
||| | | || || ||| | | | | ||| || ||| || ||| | ||||| |||| | |||| | ||| | | || ||| || | | | |||||||||||||||| | |||||||||||||| ||||||||||| || || ||| ||||||||| | ||||| ||||| |||||||| ||||| |||||
gtacttatttctccatgcaaagaaacttatctaggcttgtttcttttgcacgtgtatgcctgac---ttctatctatcctatgcaaatatgaaaataaaatttgttgaacaatcttgtttttccagGAGGAGATTCAAAGGCACTCATGTTTGTACAGATCAGTCCTAATGAAAACGATTTGAGTGAGACAATTTGCTCTCTGAACTTTGCTAGTAGAGTAAGAGG
upper sequence: AT1G72250.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA15G40350.1 (Glycine max), 3'ss of exon 14
gtattgaattttcttcttgaag--------ctgcaaccactttctttgtttacatatgtttcactgacaaattctgtttatctgtta-taaagcttacga---tgaaaatttactggtatatgacagGAGGAGATTCAAAAACCCTCATGTTTGTACAAATCAGTCCTAACGAGAATGATCAAAGTGAGACACTATGCTCACTGAATTTTGCTAGCAGAGTGAGAGG
||| | | || || ||| || ||| |||| | |||| | ||| | || | | || | || | || | ||| | | | ||||||||| ||||| | |||||||||||||| ||||||||||| || |||||| ||||||||| | ||||| ||||| |||||||| ||||| |||||
gtacttatttctccatgcaaagaaacttatctagggttgcttcttttgctcgtgtatgcctgacttctatcctccacatgtatgcaaatataactagaaaatttgatggacaatcttgtttttctagGAGGAGACTCAAAGGCACTCATGTTTGTACAGATCAGTCCTAATGAAAATGATTTGAGTGAGACAATTTGCTCTCTGAACTTTGCTAGTAGAGTAAGAGG
upper sequence: AT1G72250.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: Vv19s0027g00080.t01 (Vitis vinifera), 3'ss of exon 13
gtattgaattttcttcttgaagctgcaaccactttctttgtttacatatgtttcactgacaaattctgtttatctgttataaagcttacgatgaaaatttactggtatatgacagGAGGAGATTCAAAAACCCTCATGTTTGTACAAATCAGTCCTAACGAGAATGATCAAAGTGAGACACTATGCTCACTGAATTTTGCTAGCAGAGTGAGAGG
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-----------ttttgtcggtttcttggaaattaactttaatt-cagcttttatctttacaatttatatggagacaaga-acaactgatgatgc--gcgagcttttctttgttagGAGGAGACTCCAAGACGCTCATGTTTGTACAGATCAGTCCTAATGAGAATGACTTGAGTGAGACTCTTTGCTCCCTCAATTTTGCAAGTAGAGTGAAAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaattctgtttatctgttataaagcttacgatgaaaatttactggtatatgacagGAGGAGATTCAAAAACCCTCATGTTTGTACAAATCAGTCCTAACGAGAATGATCAAAGTGAGACACTATGCTCACTGAATTTTGCTAGCAGAGTGAGAGG
agcttac putative branch site (score: 3)
tttatctgttataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattgaattttcttcttgaagctgcaaccactttctttgtttacatatgtttcactgacaaattctgtttatctgttataaagcttacgatgaaaatttactggtatatgacagGAGGAGATTCAAAAACCCTCATGTTTGTACAAATCAGTCCTAACGAGAATGATCAAAGTGAGACACTATGCTCACTGAATTTTGCTAGCAGAGTGAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG