Sequence
atgc intronic sequence ATGC exonic sequence...gtggagttgtactactttcattatcaatctgttcctgccttcccttttgtaaccaactcatcaagttctcatcctgctctgctataatctactttttcagGTATTATACAAGCACAAGATCATAATTTTTGGTGGCTTCTATGATACTCTACGTGAAGTAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G50310.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G50310.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA04G36770.1 (Glycine max), 3'ss of exon 6
---gtggagttgtactactttcattatcaatctgttcctgccttcccttttgtaaccaactcatcaagttctcatcctgctctgctataatctactttttcagGTATTATACAAGCACAAGATCATAATTTTTGGTGGCTTCTATGATACTCTACGTGAAGTAAG
| | | | || || | ||| | || | | | | || | || || | | |||| | | | | | || |||||||| |||||||||||||| || ||||||||||||||||||| ||||| | ||||| ||
cccccccacccccatcatatggatacccatattaatccagttttttttgtcttcatcatat-atttgtttgttctaatgctttattttggttaa--ttaacagGTATTGTACAAGCACAAGATTATTCTTTTTGGTGGCTTCTATGACACTCTTAGAGAAGTGAG
upper sequence: AT5G50310.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA06G18170.1 (Glycine max), 3'ss of exon 6
-gtggagttgtactactttcat-tatcaatctgttcctgccttcccttttgtaaccaactcatcaagttctcatcctgctctgctataatctactttttcagGTATTATACAAGCACAAGATCATAATTTTTGGTGGCTTCTATGATACTCTACGTGAAGTAAG
||| | | | |||| | || | ||| | || || | | | | || | | |||| | | | | | || |||||||| |||||||||||||| || ||||||||||||||||||| ||||| | ||||| ||
tgtgtgccccccccaatatcatatggcatattaatccagtttttttttgtcttcatcatatagttgtttgttctaatgctttattttggttaa--ttaacagGTATTGTACAAGCACAAGATTATTCTTTTTGGTGGCTTCTATGACACTCTTAGAGAAGTGAG
upper sequence: AT5G50310.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv17s0000g10130.t01 (Vitis vinifera), 3'ss of exon 6
gtggagt-tgtactactttcattatcaatctgttcct-gccttcccttttgtaaccaactcatcaagttctcatcctgctctgctataatctactttttcagGTATTATACAAGCACAAGATCATAATTTTTGGTGGCTTCTATGATACTCTACGTGAAGTAAG
|| | | | || | | | || || || || | ||| | | | ||| | | || | | | | | | | | | || ||||| ||||||||||||||||| || ||||||||||||||||||| ||||| | ||||||||
ctgtattctataggaatgt-atcataggtcatttattcatcttatttgatattttgcactttttcactttttaaattaattttattttggaca-tgttacagGTTTTATACAAGCACAAGATTATTGTTTTTGGTGGCTTCTATGACACTCTCAGAGAAGTAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgtaaccaactcatcaagttctcatcctgctctgctataatctactttttcagGTATTATACAAGCACAAGATCATAATTTTTGGTGGCTTCTATGATACTCTACGTGAAGTAAG
ttgtaac putative branch site (score: 2)
tctactttttc putative PPT
tataatctacttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtggagttgtactactttcattatcaatctgttcctgccttcccttttgtaaccaactcatcaagttctcatcctgctctgctataatctactttttcagGTATTATACAAGCACAAGATCATAATTTTTGGTGGCTTCTATGATACTCTACGTGAAGTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - atcaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - ccaactc