Sequence
atgc intronic sequence ATGC exonic sequencegtgtgctgttttcttactttttatattaacctgtttgcctttttaaaagattaataacttcccattggtataaaaatgtctgtgactgcgagcatgtgatacttccatccataatcagtttcttttatgttttccatgtatcacatttgtatttataaccaatctttctttctttttggttttgttcagGATCCTTATTTTAGAATGACTCGTGATGTCGCACCCCGGTTAGGCTATAGCAAGCCCGCCCTGATTGAGTCAACATTTTTTCCTGCGTTGCAGGCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G04600.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G04600.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA13G11390.1 (Glycine max), 3'ss of exon 5
gtgtgctgttttcttactttttatattaacctgtttgcctttttaaaagattaataacttcccattggtataaaaatgtctgtgactgcgagcatgtgatacttccatccataatcagtttcttttatgttttccatgtatcacatttgta---tttataaccaatctttctttctttttggttttgttcagGATCCTTATTTTAGAATGACTCGTGATGTCGCACCCCGGTTAGGCTATAGCAAGCCCGCCCTGATTGAGTCAACATTTTTTCCTGCGTTGCAGGCAA
|| || | | | || | | | | || | | ||||||| || ||| ||| ||| || | ||||| || | | |||||||||| |||||||||||||| |||||||| || || | || | |||||| ||| ||||||| ||| ||| || || || || |||
------------------------------------------------------------------------------------------agtattcattcttattcttggtattacatgtgatataggatacatggcaggcacatttttaatttttttaattaatagtt-tatctttatgatat-attcagGATCCATATTTTAGAATGACACGTGATGTTGCTCCTAAAATGGGTTTCCACAAGCCAGCCTTGATTGAATCATTATTCTTCCCAGCATTACAG----
upper sequence: AT3G04600.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA03G25740.1 (Glycine max), 3'ss of exon 5
gtgtgctgttttcttactttttatattaacctgtttgcctttttaaaagattaataacttcccattggtataaaaatgtctgtgactgcgagcatgtgatacttccatccataatcagtttcttttatgttttccatgtatcacatttgtatttataaccaatctttctttctttttggttttgttcagGATCCTTATTTTAGAATGACTCGTGATGTCGCACCCCGGTTAGGCTATAGCAAGCCCGCCCTGATTGAGTCAACATTTTTTCCTGCGTTGCAGGCAA
||| ||||| | | | || | | | | || | | || || | | ||| | ||| || ||||||| || | | |||||||||| |||||||||||||| |||||||| || || | || | |||||| ||| ||||||| ||| ||| || || || || |||
-------------------------------------------------------------------------------------atgcaagcattcattgttattcttggtattgcatgtgatataggatccatgtgcatttaaaaaaaaatta--agtaatagtt-tttctttctgatat-attcagGATCCATATTTTAGAATGACACGTGATGTTGCTCCTAAAATGGGTTTCCACAAGCCAGCCTTGATTGAATCATTATTCTTCCCAGCATTACAG----
upper sequence: AT3G04600.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv12s0028g03370.t01 (Vitis vinifera), 3'ss of exon 6
gtgtgctgttttcttactttttatattaacctgtttgcctttttaaaagattaataacttcccattggtataaaaatgtctgtgactgcgagcatgtgatacttccatccataatcagtttcttttatgttttccatgtatcacatttgtatttataaccaatctttctttctttttggttttgttcagGATCCTTATTTTAGAATGACTCGTGATGTCGCACCCCGGTTAGGCTATAGCAAGCCCGCCCTGATTGAGTCAACATTTTTTCCTGCGTTGCAGGCAA
| | ||| || | | | ||| ||| | || | || ||||| | | || | ||||| || || || | |||||||||||||||||||| |||||||| || ||||| || || ||| |||| ||| ||||||||| ||||||| ||| ||| || ||||| | |||
------------------------------------------------------------------------------------aatattgtcatcatttatccaactttacattcatttttgcatctgatgtcaatgta--ataattat-tttatggt--attgcctttgtttccttaatttgttcagGATCCTTATTTCAGAATGACACGGGATGTTGCTCCTCGGATAGGATATCACAAGCCCGCATTGATTGAATCATTATTCTTCCCTGCCCTTCAG---- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catgtatcacatttgtatttataaccaatctttctttctttttggttttgttcagGATCCTTATTTTAGAATGACTCGTGATGTCGCACCCCGGTTAGGCTATAGCAAGCCCGCCCTGATTGAGTCAACATTTTTTCCTGCGTTGCAGGCAA
ttataac putative branch site (score: 2)
tctttctttctttttg putative PPT
acatttgtatttataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgctgttttcttactttttatattaacctgtttgcctttttaaaagattaataacttcccattggtataaaaatgtctgtgactgcgagcatgtgatacttccatccataatcagtttcttttatgttttccatgtatcacatttgtatttataaccaatctttctttctttttggttttgttcagGATCCTTATTTTAGAATGACTCGTGATGTCGCACCCCGGTTAGGCTATAGCAAGCCCGCCCTGATTGAGTCAACATTTTTTCCTGCGTTGCAGGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG