Sequence
atgc intronic sequence ATGC exonic sequencegtaaaatatttatgcatgaacctttcaatatttcccaacaaagttttcacacttttctgttgggacttatttatatggtttacagGACCGTTGCTTACACCAATCACACTGTCCTTCCTGAAGCGTTGGAGAAATGGTCACAATCTTTGATGTGGAAGCTTCTTCCTCGTCATATGGAAATAATA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G46970.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G46970.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os01g63270.1 (Oryza sativa), 3'ss of exon 7
--------------------------------------------------------gtaaaatatttatgcatgaacctttcaatatttcccaacaaagt---tttcacacttttctgttgggacttatttatatggtt--tacagGACCGTTGCTTACACCAATCACACTGTCCTTCCTGAAGCGTTGGAGAAATGGTCACAATCTTTGATGTGGAAGCTTCTTCCTCGTCATATGGAAATAATA
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gtgagctctaatatgacaagtgacaatataatttgatctcttttcttatctttttccaccattgtttatttttccgcttttcattttaacaagagtaattcaacttaaaagcttgacctaatcaataaattatttgaatggtccagAACAATTGCCTACACCAATCACACTGTTCTTCCTGAAGCCCTTGAGAAATGGTCGCAGATTGTAATGAGGAAATTACTTCCACGACACATGGAAATTATC
upper sequence: AT3G46970.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA08G45210.1 (Glycine max), 3'ss of exon 8
-----------------------------------------gtaaaatatttatgcatgaacctttcaatatttcccaacaaagttttcac-acttttctgttgggacttatttatatggttta--cagGACCGTTGCTTACACCAATCACACTGTCCTTCCTGAAGCGTTGGAGAAATGGTCACAATCTTTGATGTGGAAGCTTCTTCCTCGTCATATGGAAATAATA
| | ||||| | ||| ||| ||| | | | ||| || | | || | | ||| ||| |||||| |||| ||||| ||||| |||||||| |||||||| ||||||||||||| ||| || | |||||||| || ||||| || ||||||||||| |||
gtcagttaattgtagaaaatgttgttagcaatgattattttccattttctttattccaccacccctcacaattgt--agtgtattactcattacctcatcactaaaacatgatgctatatcttaaccagGACTATTGCGTACACTAATCATACTGTCCTCCCTGAAGCACTGGAGAAATGGTCTCAACCTGTAATGTGGAAACTACTTCCACGCCATATGGAAATCATA
upper sequence: AT3G46970.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA18G07480.1 (Glycine max), 3'ss of exon 7
-----------------------------------------gtaaaatatttatgcatgaacctttca-----atatttcccaacaaagttttcacacttttctgttgggacttatttatatggttta--cagGACCGTTGCTTACACCAATCACACTGTCCTTCCTGAAGCGTTGGAGAAATGGTCACAATCTTTGATGTGGAAGCTTCTTCCTCGTCATATGGAAATAATA
| | ||| | | ||| ||| || | | | | | || | | || | | || ||| |||||| |||||||||| ||||| |||||||| |||||||| | ||||||||||| ||| || | |||||||| || ||||| || ||||||||||| |||
gtcagtaaattgtagataatgtttttaggaatggttattttccattttctttgttccaccacccctcacagttgtagtgtattattacacctcattaacttgccactaaaacatgatgctacatcttaaccagGACTATTGCTTACACTAATCATACTGTCCTCCCTGAAGCACTAGAGAAATGGTCTCAACCTGTAATGTGGAAACTGCTTCCACGCCATATGGAAATCATA
upper sequence: AT3G46970.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv06s0004g06020.t01 (Vitis vinifera), 3'ss of exon 7
---------------------gtaaaatatttatgcatgaacctttcaatatttcccaacaaagttttcacacttttctgttgggacttatttatatggttta----------cagGACCGTTGCTTACACCAATCACACTGTCCTTCCTGAAGCGTTGGAGAAATGGTCACAATCTTTGATGTGGAAGCTTCTTCCTCGTCATATGGAAATAATA
|| || | | |||| || || || || | | | ||| | | | | | ||||| | ||| || |||| || || ||||||||||||||||||||||| | ||||||||||||||| | | ||||||||||||||||| || ||||||||||| |||
gttcactatgttttttgtttgatagaacactcgctcatgggttttccagcatgaccttctttgtctgttgctttttcttatgttaatacaactttatggcaaaaatattgaatcagAACAATTGCCTATACAAATCACACTGTCCTTCCTGAAGCACTTGAGAAATGGTCACAAGTTGTAATGTGGAAGCTTCTTCCACGCCATATGGAAATCATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcccaacaaagttttcacacttttctgttgggacttatttatatggtttacagGACCGTTGCTTACACCAATCACACTGTCCTTCCTGAAGCGTTGGAGAAATGGTCACAATCTTTGATGTGGAAGCTTCTTCCTCGTCATATGGAAATAATA
ttatttatatggttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaatatttatgcatgaacctttcaatatttcccaacaaagttttcacacttttctgttgggacttatttatatggtttacagGACCGTTGCTTACACCAATCACACTGTCCTTCCTGAAGCGTTGGAGAAATGGTCACAATCTTTGATGTGGAAGCTTCTTCCTCGTCATATGGAAATAATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG