Sequence
atgc intronic sequence ATGC exonic sequencegtaatggcgtcttcattgtttatgctatataaccacaatacttagtttaacaaaaaaaaacgttgctttggacacttattatttagtgtgtttgcagGACTCGCGGCTTGTATACAAGCATTATGCTACACTCTATTTTGTTCTTGTATTTGATGGTTCAGAAAATGAGCTTGCTATGCTTGATCTCATTCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G50860.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G50860.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G06350.2 (Glycine max), 3'ss of exon 4
--gtaatggcgtcttca--ttgtttat-gctatataaccacaatacttagtttaacaaaaaaaaacgttgctttggacacttattatttagtgtgtttgcagGACTCGCGGCTTGTATACAAGCATTATGCTACACTCTATTTTGTTCTTGTATTTGATGGTTCAGAAAATGAGCTTGCTATGCTTGATCTCATTCAAG
| | |||| ||||| | | ||| | | | | | | | ||| || | || | | | || || | |||||||||| || || || |||||||| | ||| || | |||||||| | |||||||| |||| ||||| ||||||||||||||||| | || ||||
ttttgagcaattctttggcttgttcgttgtaatactgttatctcatcttttcttatccgaggaaa-gtaagtgtgaattcat-ttgttgtattctcctgcagGACTCCCGCCTGGTCTACAAGCACTTTGCAACTTTATATTTTGTGTTCATATTTGATAGTTCTGAAAACGAGCTTGCTATGCTTGACTTGATACAAG
upper sequence: AT3G50860.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA16G25400.2 (Glycine max), 3'ss of exon 3
-----------gtaatggcgtcttcattgtttatgctatataaccacaatacttagtttaacaaaaaaaaacgttgctttggacacttattatttagtgtgtttgcagGACTCGCGGCTTGTATACAAGCATTATGCTACACTCTATTTTGTTCTTGTATTTGATGGTTCAGAAAATGAGCTTGCTATGCTTGATCTCATTCAAG
|||| | || | || || || | || | | | | | | ||| || || || || || || | | | |||||||||| || ||||| |||||||| | ||| || | ||||| | | |||||||| |||| ||||| ||||||||||||||||| | || ||||
ttttgagcaattctttggcttgtttgtagta-atactgttatctcatattttcttatctgaggaaaggaagtgtgaatt----cattttttgt---attttcctgcagGACTCTCGCCTTGTCTACAAGCACTTTGCAACTTTATATTTCATGTTCATATTTGATAGTTCTGAAAACGAGCTTGCTATGCTTGACTTGATACAAG
upper sequence: AT3G50860.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv04s0023g01770.t01 (Vitis vinifera), 3'ss of exon 3
gtaatggcgtcttcattgtttatgctatataac---cacaatacttagtttaacaaaaaaaaacgttgctttggacacttat-tatttagtgtgtt----tgcagGACTCGCGGCTTGTATACAAGCATTATGCTACACTCTATTTTGTTCTTGTATTTGATGGTTCAGAAAATGAGCTTGCTATGCTTGATCTCATTCAAG
|| || ||| ||| |||||| | || || || ||| | | || | | | || ||| |||| | | | || |||| | || ||||| |||||||| ||||| || ||||||||||| ||||||||||| |||| ||||||||| | || ||||||||| | || ||||
----catagtttttcatgtatata-tatatacctggcattatgttttgttattccataactcctctgacctaaaacttatatacattttatcttctgtcctgtagGATACTCGTCTTGTGTACAAGCACTATGCAACTCTCTATTTTGTCTTTGTATTTGATAGTTCTGAAAATGAGTTAGCCATGCTTGATTTGATACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagtttaacaaaaaaaaacgttgctttggacacttattatttagtgtgtttgcagGACTCGCGGCTTGTATACAAGCATTATGCTACACTCTATTTTGTTCTTGTATTTGATGGTTCAGAAAATGAGCTTGCTATGCTTGATCTCATTCAAG
gtttaac putative branch site (score: 3)
taacaaaaaaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatggcgtcttcattgtttatgctatataaccacaatacttagtttaacaaaaaaaaacgttgctttggacacttattatttagtgtgtttgcagGACTCGCGGCTTGTATACAAGCATTATGCTACACTCTATTTTGTTCTTGTATTTGATGGTTCAGAAAATGAGCTTGCTATGCTTGATCTCATTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT