Sequence
atgc intronic sequence ATGC exonic sequencegtattttgttttgttgaaattgttttgatgttattatagcaatcagttatatttgggtatgcttactatcacagacaatattgtttgtagaatttaatggtttgtatgtttgtttgtctctgacagAACTTTACAAAATGGTTTGTGAACCGGATGAAACTGATTTAGATATACAGATTCCTGCCGTCATGCTCCCGCAAGATGCTGGTGCATCCTTGCAAAAGAT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G63690.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G63690.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA01G42940.1 (Glycine max), 3'ss of exon 3
----------------------gtattttgttttgtt---gaaattg---ttttgat-gttattatagcaa--tcagttatat-ttgggtatgc--ttactatcacagacaatattgtttgtagaatttaatggtttgtatgtttgtttgtctctgacagAACTTTACAAAATGGTTTGTGAACCGGATGAAACTGATTTAGATATACAGATTCCTGCCGTCATGCTCCCGCAAGATGCTGGTGCATCCTTGCAAAAGAT
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gtaaaaattccgttgtccttctggctcttattttttttgggtagttgggtttttgatagttgaagaagttgcttcacttttgtgttgggtgggtcatgtctagtatatacacttttttatttctcttttcatgtcaaatttgttt--ttgttgtttgcagAACTGTACAAGATGGTTTGCGAACCTGATGAAACTGATTTGAACATACACATACCTGCTGTCATGCTTCCACTAGATGCAGGTACAAGGCTGGAAAAAAT
upper sequence: AT1G63690.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G02540.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------------gtattttgttttgttgaaattgtttt-gatgttattatagcaatcagttatatttgggtatgcttactatcacagacaatattgtttgtagaatttaatggtttgtatgtttgtttgtctctgacagAACTTTACAAAATGGTTTGTGAACCGGATGAAACTGATTTAGATATACAGATTCCTGCCGTCATGCTCCCGCAAGATGCTGGTGCATCCTTGCAAAAGAT
| |||| |||| || |||| ||| || ||| | | | ||| | || ||| || ||| | || | | || | | | | ||| | ||||||| | ||||||| ||||| |||||||| ||||| |||||||||||||| | ||||| || ||||| |||||||| || |||||| ||| || || |||| ||
gtaaaaattcctttgtcctttttaattgaggcaactttacttatggtagttttttttttttttttttttaaatagttggagaagttgcttcactgttgtgttgggtg-ggtcatgtctagtat-gtacactttttaaattctcttttcatgtcaagtttatttgtgtttgttgtttgcagAACTGTACAAGATGGTTTGCGAACCTGATGAAACTGATTTGAACATACACATACCTGCTGTCATGCTTCCATTAGATGCAGGTACAAGGCTGGAAAAAAT
upper sequence: AT1G63690.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G20390.1 (Glycine max), 3'ss of exon 2
gtattttgttttgttgaaattgttttgatgttattatagcaatcagttatatttgggtatgcttactatcacagacaatattgtttgtagaatttaatggtttgtatgtttgtttgtctctgacagAACTTTACAAAATGGTTTGTGAACCGGATGAAACTGATTTAGATATACAGATTCCTGCCGTCATGCTCCCGCAAGATGCTGGTGCATCCTTGCAAAAGAT
|| | || | | ||| | || | ||| ||| | ||| | ||| | || | | | ||| ||| | | ||| |||| | | || ||||| |||||||||||||| |||||||||||||| | || || || ||||| |||||||| || | |||||| ||| || || ||||
---------------------gtgcacagtttgtgtttgcagtaagaaagcttttt-tatttct-ctagtatgtacacttttttatttctcttttcatgtcaatttttttttgttgtttgcagAACTGCTGTACAAGATGGTTTGTGAACCTGATGAAACTGATTTGAACATGCACATACCTGCTGTCATGCTTCCACTAGATGCAGGTACAAGGCTGGAAAA--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagacaatattgtttgtagaatttaatggtttgtatgtttgtttgtctctgacagAACTTTACAAAATGGTTTGTGAACCGGATGAAACTGATTTAGATATACAGATTCCTGCCGTCATGCTCCCGCAAGATGCTGGTGCATCCTTGCAAAAGAT
atttaat putative branch site (score: 4)
tttgtctct putative PPT
aatattgtttgtagaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattttgttttgttgaaattgttttgatgttattatagcaatcagttatatttgggtatgcttactatcacagacaatattgtttgtagaatttaatggtttgtatgtttgtttgtctctgacagAACTTTACAAAATGGTTTGTGAACCGGATGAAACTGATTTAGATATACAGATTCCTGCCGTCATGCTCCCGCAAGATGCTGGTGCATCCTTGCAAAAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG