Sequence
atgc intronic sequence ATGC exonic sequencegtttgtatgctcccccccctcaaactcaaaccagcataaaactgttgacagaatactcactgtggcatttccagGTTTTGAGCCTATTGGAGACACAACTTATACTAGTGATGTAAACTGGGGTTGCATGCTTCGAAGCGGCCAGATGCTCTTCGCACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G59950.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G59950.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os04g58560.1 (Oryza sativa), 3'ss of exon 2
--------gtttgtatgctcccccccctcaaact-caaaccagcat---aaaactgttgacagaatactcactgtggcatttc----cagGTTTTGAGCCTATTGGAGACACAACTTATACTAGTGATGTAAACTGGGGTTGCATGCTTCGAAGCGGCCAGATGCTCTTCGCACAG
|||| | | | ||| || || | | ||| | | | | || | ||| |||| ||||| | || || | | |||||||||||||| |||||||| |||||| | ||||| |||||||||| | || |||
gtaggtttgtttacacgaccatatgcctggtacagcatgttaatgtgtggaaatcagttgtgagttgtttgcactgtctttttgttgcagGCTTTGATGCCATCTCTGATTCCAAGTATACTAGTGATGTGAACTGGGGCTGCATGGTCAGAAGCAGCCAGATGCTGGTTGCTCAG
upper sequence: AT3G59950.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G48380.1 (Glycine max), 3'ss of exon 2
-------gtttgtatgct-cccccccctcaaactca-aaccagcataaaactgttgacagaatactcactgtggcatttccagGTTTTGAGCCTATTGGAGACACAACTTATACTAGTGATGTAAACTGGGGTTGCATGCTTCGAAGCGGCCAGATGCTCTTCGCACAG
| ||||| || | || ||| | | | || ||||| ||| | | | | || | ||| ||||| |||||||||| |||| ||||| |||||||| || |||||||| |||||||||||| | |||||||| | || |||
gtctgttgaatgtatactacttccttttcagggatatgataaatattaaacta---acaaatt--ttaacatgcatactatagGCTTTGATGCTATTGGAGATACAAAGTATACCAGTGATGTTAATTGGGGTTGTATGCTTCGAAGCAGTCAGATGCTGGTTGCTCAG
upper sequence: AT3G59950.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G38000.1 (Glycine max), 3'ss of exon 2
-------gtttgtatgctccc-ccccctcaaactcaaaccagcataa-aactgttgacagaata---ctcactgtggcatttccagGTTTTGAGCCTATTGGAGACACAACTTATACTAGTGATGTAAACTGGGGTTGCATGCTTCGAAGCGGCCAGATGCTCTTCGCACAG
| ||||| || | || ||| | | || | || |||| | || | | | || | ||| ||||| |||||||||| |||| ||||| |||||||| | |||||||| |||||||||||| | |||||||| | ||||||
gtctgttgaatgtatactactaccttttcagggatgtattaagatgataaatgttaaactaacaaattttaacatgcatactatagGCTTTGATGCTATTGGAGATACAAAGTATACCAGTGATGTTCATTGGGGTTGTATGCTTCGAAGCAGTCAGATGCTTGTTGCACAG
upper sequence: AT3G59950.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv00s0215g00030.t01 (Vitis vinifera), 3'ss of exon 3
---------------------gtttgtatgctcccccccctcaaactcaaac-cagcataaaactgttgacagaatactcactgtggcatttccagGTTTTGAGCCTATTGGAGACACAACTTATACTAGTGATGTAAACTGGGGTTGCATGCTTCGAAGCGGCCAGATGCTCTTCGCACAG
| || | || | | | | | | | |||||| | | | | ||| |||||||||| ||||||| || ||| | ||||||||||| || |||||||||||||||||||| | |||||||| | ||||||
gtgcttcacatgtaaaatggtgctttctttcttcttcttattgttattagttgtattgctcacctgttgcttctctctctatccttgattttatagGTTTTGAGGCTATTGGGGATTCAAAGTTAACTAGTGATGTGAATTGGGGTTGCATGCTTCGAAGTAGTCAGATGCTTGTTGCACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaaactcaaaccagcataaaactgttgacagaatactcactgtggcatttccagGTTTTGAGCCTATTGGAGACACAACTTATACTAGTGATGTAAACTGGGGTTGCATGCTTCGAAGCGGCCAGATGCTCTTCGCACAG
tactcac putative branch site (score: 1)
catttcc putative PPT
ataaaact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtatgctcccccccctcaaactcaaaccagcataaaactgttgacagaatactcactgtggcatttccagGTTTTGAGCCTATTGGAGACACAACTTATACTAGTGATGTAAACTGGGGTTGCATGCTTCGAAGCGGCCAGATGCTCTTCGCACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG