Sequence
atgc intronic sequence ATGC exonic sequencegtaaaaatttaaatttaccttcattttatcctttctacacgcaagttctcatgtgttgataatactctttcccacagGTCATGAACCTAATCGGTGATGTTAAAGGGAAGGTGGCAGTAATGGTGGATGATATTATTGATACAGCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G32380.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G32380.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os02g03540.1 (Oryza sativa), 3'ss of exon 5
--------------------gtaaaaatt-taaatttaccttcatttt-atcctttctacacgcaagttctcatgtgttgataatactc--tttcccacagGTCATGAACCTAATCGGTGATGTTAAAGGGAAGGTGGCAGTAATGGTGGATGATATTATTGATACAGCTG
|| | || | | || | ||||| || |||| | || | ||| || || || ||| |||||| ||||| || || || ||||||| ||| || ||||| || ||| |||||||||| |||||||||||||
tttcagacgagtctatatcactacatgttgcatacttgtttaaattttcatgctttgtgagattaaaccactaca-gtttatcatgttcatttttttacagGTAATGAATCTTATTGGAGATGTTAGAGGAAAAGTGGCTGTTATGATGGATGATATGATTGATACAGCTG
upper sequence: AT1G32380.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G06110.1 (Glycine max), 3'ss of exon 5
-------------------gtaaaaatttaaatttaccttcattttatcctttctacacgcaagt--tctcatgtgttgataatactctttcc----cacagGTCATGAACCTAATCGGTGATGTTAAAGGGAAGGTGGCAGTAATGGTGGATGATATTATTGATACAGCTG
| | |||| || || || ||| || || | | | || || ||| | | | | ||||| |||||||| || |||||||| ||||| || || || ||||||||||||||||| ||||| || ||||
attgttagttttgaatgtgctcatggtttag--ctagttttatggtatactaattatcctcgggcaaacttatctgtcttctgtcttatgtttgtgatgcagGTGATGAACCTGATTGGTGATGTAAAAGGAAAAGTTGCTGTAATGGTGGATGATATGATTGACACTGCTG
upper sequence: AT1G32380.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv02s0012g00530.t01 (Vitis vinifera), 3'ss of exon 5
------------------gtaaaaatttaaatttaccttcattttatcctttctacacgcaagttctcatgt---gttgata---atactctttcccacagGTCATGAACCTAATCGGTGATGTTAAAGGGAAGGTGGCAGTAATGGTGGATGATATTATTGATACAGCTG
| ||| || | | || | || ||| | ||| | | | | | || || || || || | | | |||||| ||||| || || |||||||| ||||| || || ||||| ||||||||||| || |||||||| ||||
agctttgaagatatggatggaaagatgttgaatt-cttttctttgttacttatgagatgtcattcctggagtcaagtctgtatttattgtttaccttacagGTGATGAATCTGATTGGTGATGTCAAAGGAAAAGTTGCAGTCATGGTGGATGACATGATTGATACTGCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttatcctttctacacgcaagttctcatgtgttgataatactctttcccacagGTCATGAACCTAATCGGTGATGTTAAAGGGAAGGTGGCAGTAATGGTGGATGATATTATTGATACAGCTG
tgttgat putative branch site (score: 4)
tactctttccc putative PPT
ttgataata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaaatttaaatttaccttcattttatcctttctacacgcaagttctcatgtgttgataatactctttcccacagGTCATGAACCTAATCGGTGATGTTAAAGGGAAGGTGGCAGTAATGGTGGATGATATTATTGATACAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG