Sequence
atgc intronic sequence ATGC exonic sequencegtaactcaagcggtttcaacttcaccgttctaaatcagattttctcaaaacatcgaaaaatgtctacgtttttagcgtctctaactcgtctgtttttttgcttctgttcagACAATGGTGAGGTTAGTCACAAACTCATGGCAAAGGTTGAAGCACACAAGAGGATCATATGGGCATGTTCATGGAACCCGTTTGGCCACCAATTTGCAAC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G49540.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G49540.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os08g38570.1 (Oryza sativa), 3'ss of exon 9
gtaactcaagcggtttcaacttcaccgttctaaatcagattttctcaaaacatcgaaaaatgtctacgtttttagcgtctctaactcgtc-tgtttttttgcttctgtt-cagACAATGGTGAGGTTAGTCACAAACTCATGGCAAAGGTTGAAGCACACAAGAGGATCATATGGGCATGTTCATGGAACCCGTTTGGCCACCAATTTGCAAC---
|| ||||| | | | | || ||| | || | | ||| || | | ||| | | | ||| | | ||| || ||| ||| | ||| || | || | || | |||||| ||||||||||||| || || ||||||||||| ||||||||||| || || || ||||||||||
------------gtaaggacttcttc-ctatgatctagtagttcctacaaatttgtaaactgccaatatttatctgttgtgtaattattgatgtcattccacttgtgtaactctagATGATGGAGCAGAGCATCATCTTGTTGCAAAGCTTGAAGCACACAAAAGAATTATATGGGCATGCTCATGGAACCCCTTCAGCTACGAATTTGCAACTGG
upper sequence: AT1G49540.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G042371_T01 (Zea mays), 3'ss of exon 6
gtaactcaagcggtttcaacttcaccgttctaaatcagattttctcaaaacatcgaa----aaatgtctacgtttttagcgtctctaactcgtctgtttttttgcttctgttcagACA-ATGGTGAGGTTAGTCACAAACTCATGGCAAAGGTTGAAGCACACAAGAGGATCATATGGGCATGTTCATGGAACCCGTTTGGCCACCAATTTGCAAC---
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gtaggcataattcttatgataatgtagttcctt-tgaaattatttcataacatttgtcttttcactcatgctgtttcatttgtgctggagctgatatgatatcacttgtgtaattctagAAGGAGGAGCAGAGCATCGTCTGGTTGCGAAGCTCGAAGCACACAAAAGAATTATATGGGCATGCTCATGGAACCCCTTCGGCTATGAATTTGCAACTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaatgtctacgtttttagcgtctctaactcgtctgtttttttgcttctgttcagACAATGGTGAGGTTAGTCACAAACTCATGGCAAAGGTTGAAGCACACAAGAGGATCATATGGGCATGTTCATGGAACCCGTTTGGCCACCAATTTGCAAC
ctctaac putative branch site (score: 2)
ctcgtctgtttttttg CT-rich tract
tgttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaactcaagcggtttcaacttcaccgttctaaatcagattttctcaaaacatcgaaaaatgtctacgtttttagcgtctctaactcgtctgtttttttgcttctgttcagACAATGGTGAGGTTAGTCACAAACTCATGGCAAAGGTTGAAGCACACAAGAGGATCATATGGGCATGTTCATGGAACCCGTTTGGCCACCAATTTGCAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA