Sequence
atgc intronic sequence ATGC exonic sequencegtaacatttgcttcaaatttccctccaacttatagttgacagttttttcatgtttccacttaccttcttctttccagGTGCTCATAAGAGGCTCATTACATCTCCTCCTGTTGCTGTTTTCCCTCACCCTCTCGCGAGTGATCTAAGTTTTGGACG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G19880.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G19880.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA05G35860.1 (Glycine max), 3'ss of exon 8
----------------------gtaacatttgcttca----aatttccctccaacttatagttgacagttttttcatgtttccacttaccttcttctttccagGTGCTCATAAGAGGCTCATTACATCTCCTCCTGTTGCTGTTTTCCCTCACCCTCTCGCGAGTGATCTAAGTTTTGGACG
| ||| |||| | || || ||| || | | | | || | | || |||| | | | |||||||||| || ||||||||||| ||||||||||||||||| || |||||||| || || |||||||| | ||||||| |
cagcttaatagtactgcagtgaattttattagcttaacaagaagtttcctaaaagaatgaagtcctaatattctaacaatta---ttacaatgtatcatacagGTGCTCACAAAAGGCTCATTACTTCTCCTCCTGTTGCTGTCTTTCCTCACCCCCTTGCCAGTGATCTTAATTTTGGAAG
upper sequence: AT2G19880.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G03760.1 (Glycine max), 3'ss of exon 9
--------------------------gtaacatttgcttcaaatttccctccaacttatagttgacagttttttcatgtttccacttaccttcttctttccagGTGCTCATAAGAGGCTCATTACATCTCCTCCTGTTGCTGTTTTCCCTCACCCTCTCGCGAGTGATCTAAGTTTTGGACG
| | | || ||||| | || | | | || | | || |||| | | |||||||||| || ||||||||||| |||||||| ||||| || || || ||||| || || |||||||| | ||||||| |
aattttattactagctcagcttaataagactactaaacagaagtttcctaaaagaataagagtcctaatattcttacaatta---ttacaacgtatcatacagGTGCTCACAAAAGGCTCATTACCTCTCCTCCCGTTGCCGTCTTTCCCCACCCCCTTGCAAGTGATCTTAATTTTGGAAG
upper sequence: AT2G19880.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv11s0016g03130.t01 (Vitis vinifera), 3'ss of exon 9
-------------gtaacatttgcttca--aatttccctccaacttatagttgacagttttttcatg-------tttccacttaccttct-tctttccagGTGCTCATAAGAGGCTCATTACATCTCCTCCTGTTGCTGTTTTCCCTCACCCTCTCGCGAGTGATCTAAGTTTTGGACG
| | |||| || |||| | | ||||| | || | | || | | | | || | ||||| |||| |||||||||||| ||||||||||| || ||||| || || |||||||| || || |||||||| |||||| | |
gttgaaaggaaggggactatttctttggttaattgatggctttttcatagtctatttccttattgagatggtggttgctaatgtcattgtgtctttacagGGAATCATAAGAGGCTGATTACATCTCCGCCAGTTGCCGTCTTTCCTCACCCCCTTGCAAGTGATCTTAGTTTTTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctccaacttatagttgacagttttttcatgtttccacttaccttcttctttccagGTGCTCATAAGAGGCTCATTACATCTCCTCCTGTTGCTGTTTTCCCTCACCCTCTCGCGAGTGATCTAAGTTTTGGACG
cacttac putative branch site (score: 2)
ttttttcatgtttcca CT-rich tract
ttttttcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacatttgcttcaaatttccctccaacttatagttgacagttttttcatgtttccacttaccttcttctttccagGTGCTCATAAGAGGCTCATTACATCTCCTCCTGTTGCTGTTTTCCCTCACCCTCTCGCGAGTGATCTAAGTTTTGGACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT