Sequence
atgc intronic sequence ATGC exonic sequencegtgagagtcgtggtggattttagtttaccaaagatggttagaaacagaaaatgttaaatagaaaatgttgttttcagGAGTTGCTGGAGGTGCAGCATCCGGGAAAACAACTGTCTGTGATATGATTATGCAGCAACTGCATGATCAGAGAGCTGTTGTTGTAAATCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G55810.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 2
-----------gtgagagtcgtgg-----tggattttagtt-taccaaagatggttagaaacagaaaatgttaaatagaaaatgttgtt------ttcagGAGTTGCTGGAGGTGCAGCATCCGGGAAAACAACTGTCTGTGATATGATTATGCAGCAACTGCATGATCAGAGAGCTGTTGTTGTAAATCAG
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tacttgatgaggtcctaaatttggataccttgttttcaattcttacaacttttcttttatcttaatgattctaacacttattttttgtcatatgatgcagGTGTTGCTGGGGGTGCAGCATCTGGCAAGACAACAGTTTGTGATATGATTATTCAGCAGCTTCATGATCAACGAGTTGTACTTGTTAATCAG
upper sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 2
-----------gtgag---agtcgtggtggattttagtttaccaaagatggttagaaacagaaaatgttaaatagaaaatgttgtttt--------cagGAGTTGCTGGAGGTGCAGCATCCGGGAAAACAACTGTCTGTGATATGATTATGCAGCAACTGCATGATCAGAGAGCTGTTGTTGTAAATCAG-
| || || || || | | | ||| | || | | || | | | || || | | |||| |||||||| ||||||||||| || || ||||| || |||||||||||||| ||||| || |||||||| ||| ||| |||| ||||||
ttcatgaggtcctaagtttggttaccttgttttcaattcttacaacttttcttttatcttaatgattcttactcactcattttttgtcatatgatgcaggTGTTGCTGGGGGTGCAGCATCTGGCAAGACAACAGTTTGTGATATGATTATTCAGCAGCTTCATGATCAACGAGTTGTACTTGTTAATCAGG
upper sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G47270.1 (Glycine max), 3'ss of exon 2
gtgagagtcgtggtggattttagtttaccaaagatggttagaaacagaaa---atgttaaatagaaaatgttgt-tttcagGAGTTGCTGGAGGTGCAGCATCCGGGAAAACAACTGTCTGTGATATGATTATGCAGCAACTGCATGATCAGAGAGCTGTTGTTGTAAATCAG
| ||||| ||| | ||| || || | || | | | || | | | |||| |||||||| || ||||||||||| || ||| | || |||||||||||| | ||||| || |||||||| ||| || |||| ||||||
----------ttaccaatttttatttggtatctatgattctaatccattttctatttacattttggtttggtatgtgacaggtgttgctggtggagcagcatccggtaagACATCAGTTTGTGATATGATTGTTCAGCAGCTTCATGATCAACGAGTCGTACTTGTTAATCAG
upper sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 2
-----------------gtgagagtcgtggtggattttagtttaccaaag-atggttagaaaca-gaaaatgttaaa-tagaaaatgttgttt---tcagGAGTTGCTGGAGGTGCAGCATCCGGGAAAACAACTGTCTGTGATATGATTATGCAGCAACTGCATGATCAGAGAGCTGTTGTTGTAAATCAG
|| | | | | | | ||| || || ||| ||||| | |||| | || ||| || | | ||| |||||||| |||||||| || |||||||| || || ||||| |||||||| |||| |||||||||||| | | ||| | ||||| |||
gtgttgttagatgcttgttgtttggcactctttttatcatttttttaactcatagtttaaaacacgtgtatgtgattctatcaaacattatatgggctagGTGTTGCTGGGGGTGCAGCTTCTGGGAAAACTACAGTTTGTGACATGATTATTGAGCAGCTGCATGATCAGCGTGTTGTACTAGTAAACCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttaccaaagatggttagaaacagaaaatgttaaatagaaaatgttgttttcagGAGTTGCTGGAGGTGCAGCATCCGGGAAAACAACTGTCTGTGATATGATTATGCAGCAACTGCATGATCAGAGAGCTGTTGTTGTAAATCAG
ttgttttc CT-rich tract
aaaatgttaaatagaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagagtcgtggtggattttagtttaccaaagatggttagaaacagaaaatgttaaatagaaaatgttgttttcagGAGTTGCTGGAGGTGCAGCATCCGGGAAAACAACTGTCTGTGATATGATTATGCAGCAACTGCATGATCAGAGAGCTGTTGTTGTAAATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT