Sequence
atgc intronic sequence ATGC exonic sequence...ttaaatttaagactattatgaatgaagtcaagtttgagttttgactagagtctctatctggtacctattgcttagccttgactttctgtgtggtttaaagAGGAATTTGTGGCACATTCTGCTGCTGTCAATTGTCTTAAGATCGGAAGGAAGTCTTCTAGGGTTCTGGTAACAGGTGGTGAAGATCACAAGGTCAATCT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G23430.2 |
intron # | 2 |
splice site | 3' |
intron type | U12 (go to U12 genes for details) |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G23430.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G00890.1 (Glycine max), 3'ss of exon 2
---------------------------------------------------------------ttaaatttaagactattatgaatgaagtcaagtttgagttttgactagagtctctatctg-gtacctat-tgcttagccttgactttctgtgtggtttaaagAGGAATTTGTGGCACATTCTGCTGCTGTCAATTGTCTTAAGATCGGAAGGAAGTCTTCTAGGGTTCTGGTAACAGGTGGTGAAGATCACAAGGTCAATCT
|| | ||| || || || | |||| || |||||||| | | || || | | || | | || | ||| | || | | |||||||||||| |||||| || || |||||||||| || ||||| ||| |||| || || |||||||| || || || |||||||||||||||||||||||
gtatccttcatctcttgtctgtctgtgctttacattttgtttgatctatctatgcactcgcccttcattttctatctgca--gatctctctctactttgttattatgttagagtctttctttgtgtgtgtgtgtgacttggctggccttgacgagttatgtccagAGGAATTTGTAGCACATGCTTCTACTGTCAATTGCCTCAAGATTGGACGGAAATCATCCAGGGTTCTTGTCACTGGAGGTGAAGATCACAAGGTCAATCT
upper sequence: AT5G23430.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G09360.1 (Glycine max), 3'ss of exon 2
-----------------------------------------------------ttaaatttaagactat-tatgaatgaagtcaagtttgagttttgactagagtctctatctggtacctattgcttagccttgactttctgtgtggtttaaagAGGAATTTGTGGCACATTCTGCTGCTGTCAATTGTCTTAAGATCGGAAGGAAGTCTTCTAGGGTTCTGGTAACAGGTGGTGAAGATCACAAGGTCAATCT
|| | | | | | || | | | | | |||||| |||| | | ||| |||||||| | || | | |||||||||||| |||||| || || | |||||||| || ||||| ||| |||| || || |||||||| || || || |||||||||||||||||||||||
gtatccttcatctcttgtttgtctgtgctttacattttgtttgatctatgcacttgccctccattttctatctgcagatctctctctctctctctctctctctctctctacttggtgtgtgtgacttggccttgac-----gagttatgtccagAGGAATTTGTAGCACATGCTTCTACCGTCAATTGCCTCAAGATTGGACGGAAATCATCCAGGGTTCTTGTCACTGGAGGTGAAGATCACAAGGTCAATCT
upper sequence: AT5G23430.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv10s0071g01150.t01 (Vitis vinifera), 3'ss of exon 1
ttaaatttaagactattatgaatgaagtcaagtttgagttttgactagagtctctatctggtacctattgcttagccttgactttctgtgtggtttaa-agAGGAATTTGTGGCACATTCTGCTGCTGTCAATTGTCTTAAGATCGGAAGGAAGTCTTCTAGGGTTCTGGTAACAGGTGGTGAAGATCACAAGGTCAATCT
| | || | | | | | || | || | | | | ||| | | | | | | || || || |||||||||||| ||||| ||| | ||| || ||||| ||||| || |||||||| || |||||||| || || ||||| |||||||||||||| |||||
-tctgcagatcccttctctacccttgcttcacagcatttgttattttgaattttgaatttttacttctcgagaaaattccttgaccacggtttttgaacagAGGAATTTGTAGCACACTCTTCCAGTGTAAACTGTCTCAAGATTGGGAGGAAGTCATCCAGGGTTCTTGTCACCGGTGGAGAAGATCACAAGGTGAATCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagagtctctatctggtacctattgcttagccttgactttctgtgtggtttaaagAGGAATTTGTGGCACATTCTGCTGCTGTCAATTGTCTTAAGATCGGAAGGAAGTCTTCTAGGGTTCTGGTAACAGGTGGTGAAGATCACAAGGTCAATCT
agccttgac putative branch site
tttaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttaaatttaagactattatgaatgaagtcaagtttgagttttgactagagtctctatctggtacctattgcttagccttgactttctgtgtggtttaaagAGGAATTTGTGGCACATTCTGCTGCTGTCAATTGTCTTAAGATCGGAAGGAAGTCTTCTAGGGTTCTGGTAACAGGTGGTGAAGATCACAAGGTCAATCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA