Sequence
atgc intronic sequence ATGC exonic sequencegttagtgaaccagacccctctcttttacactctacaattaatttattcagttgaaattctaaaaactgttctacaatagGTGGTCTCTTGGAGCAATCATGTTCGAGATGCTTGTAGGGTTTCCGCCATTCTATTCCGAAGAACCTTTGGCAACATGTAGAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G30640.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G30640.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S22_429V6.1 (Physcomitrella patens), 3'ss of exon 6
-----------gttagtgaaccagacccct-----ctcttttacactctacaattaatttattcagttgaaattctaaaaactgttctacaatagGTGGTCTCTTGGAGCAATCATGTTCGAGATGCTTGTAGGGTTTCCGCCATTCTATTCCGAAGAACCTTTGGCAACATGTAGAAAG
||| | | ||||| | || || | || | ||| || || || || ||| | |||||||| | ||||||||||||| ||||||||| || |||| || ||||| || ||||| |||||| || |||||||| | |||
gtatgtagcaagttgtgctccttggcccctgaatgcatttcctagctttttaagttgttttttttccggaggtttgaacgtaagtttctctgcagGTGGTCATTGGGAGCAATCATGTACGAGATGCTGGTTGGGTACCCTCCATTTTACTCCGATGAACCTATGACAACATGTCGCAAG
upper sequence: AT1G30640.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S86_100V6.1 (Physcomitrella patens), 3'ss of exon 6
--------------------------------------gttagtgaaccagacccctctcttttacactctacaattaatttattcagttgaaat---tctaaaaactgttctacaatagGTGGTCTCTTGGAGCAATCATGTTCGAGATGCTTGTAGGGTTTCCGCCATTCTATTCCGAAGAACCTTTGGCAACATGTAGAAAG
| || || || ||| || | || || || ||| ||| | || ||| | | | |||||||| |||||||||||||||| ||||||||| || || | || ||||| || || || |||||| || |||| ||| | |||
gtatgtgacaagtcgttctcctgaatctttctctttttatccttggctcatgatgtacttgctta-gcttgataaagttcttgttgtgttcaaaaaggttgaacgtaagttttcctacagGTGGTCACTTGGAGCAATCATGTACGAGATGCTAGTTGGCTACCCTCCATTTTACTCTGACGAACCTATGACAACTTGTCGCAAG
upper sequence: AT1G30640.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ29515 (Selaginella moellendorffii), 3'ss of exon 6
gttagtgaaccagacccctctcttttacactctacaattaatttattcagttgaaattctaaaaactgttctacaatagGTGGTCTCTTGGAGCAATCATGTTCGAGATGCTTGTAGGGTTTCCGCCATTCTATTCCGAAGAACCTTTGGCAACATGTAGAAAG
| | || | ||| || | | | | | || ||| | || | | |||||||||||||||||| || |||| ||||||||| || |||| |||||| ||||||||||| ||||| || | || || | |||
------gtaagaggcatttctgattgaaaatatctaccggcttgattgatttatggtgcc----------------tagGTGGTCTCTTGGAGCTATAATGTACGAGATGCTAGTCGGGTATCCGCCCTTCTATTCCGACGAACCGATGTCTACTTGCCGGAAG
upper sequence: AT1G30640.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ28086 (Selaginella moellendorffii), 3'ss of exon 6
gttagtgaaccagacccctctcttttacactctacaattaatttattcagttgaaattctaaaaactgttctacaatagGTGGTCTCTTGGAGCAATCATGTTCGAGATGCTTGTAGGGTTTCCGCCATTCTATTCCGAAGAACCTTTGGCAACATGTAGAAAG
| | || | | ||| || | | | | | || ||| | || | | |||||||||||||||||| || |||| ||||||||| || |||| |||||| ||||||||||| ||||| || | || || | |||
------gtaagaggcacttctgattgaaaatatctaccggcttgattgatttatggtgcc----------------tagGTGGTCTCTTGGAGCTATAATGTACGAGATGCTAGTCGGGTATCCGCCCTTCTATTCCGACGAACCGATGTCTACTTGCCGGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttacactctacaattaatttattcagttgaaattctaaaaactgttctacaatagGTGGTCTCTTGGAGCAATCATGTTCGAGATGCTTGTAGGGTTTCCGCCATTCTATTCCGAAGAACCTTTGGCAACATGTAGAAAG
ttctaaa putative branch site (score: 2)
ctgttct putative PPT
aattaatttattcagt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtgaaccagacccctctcttttacactctacaattaatttattcagttgaaattctaaaaactgttctacaatagGTGGTCTCTTGGAGCAATCATGTTCGAGATGCTTGTAGGGTTTCCGCCATTCTATTCCGAAGAACCTTTGGCAACATGTAGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC