Sequence
atgc intronic sequence ATGC exonic sequencegtaaactttttcttgtttcttgaacctcttatccacggttactgattcgccttcttttctttgcattctgatattttatgttgtttgctgttatttgcagATTGCTCTGGGAAATATTTTAAAGTTCAGGAAAAAGAACTGGCAATTTGATTTCATTGGTGGCATCATATACTTTCTCTTGGTCTTTTCCTTGTTCCCTC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G23000.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G23000.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA17G36310.1 (Glycine max), 3'ss of exon 10
------------------------------gtaaactttttcttgtttcttg-aacctcttatccacggttactgattcgccttcttttctttgcattctgatatt-ttatgttgtttgctgttatttgcagATTGCTCTGGGAAATATTTTAAAGTTCAGGAAAAAGAACTGGCAATTTGATTTCATTGGTGGCATCATATACTTTCTCTTGGTCTTTTCCTTGTTCCCTC
|| | | | || |||| || | | | | | || | | | |||| | ||| | || | | | ||| || |||||||||| |||||||||| |||| || ||||||||||||||||||||||||| ||||||||||| ||||| ||| | || |||||||| |||| ||
ggtatgtagaatgtcaattaattgcttattatagttctccttctcttacttgtaagcacaaaatcgctttttttaaaaaaaaatattttactagcacgttatggttgtaacatatttttaaatttgatgcaGATTGCATTGGGAAATATCCTAAAATTTCGGAAAAAGAACTGGCAATTTGATTTTATTGGTGGCATTATATATTTTGTATTAGTCTTTTCAATGTTTCCA-
upper sequence: AT4G23000.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA14G08860.1 (Glycine max), 3'ss of exon 10
-------gtaaactttttcttgtttcttgaac--------ctcttatccacggttactgattcgccttcttttctttgcatt-ctgatattttatgttgt------ttgctgttatttgcagATTGCTCTGGGAAATATTTTAAAGTTCAGGAAAAAGAACTGGCAATTTGATTTCATTGGTGGCATCATATACTTTCTCTTGGTCTTTTCCTTGTTCCCTC
| | | || | ||| || || || |||||| ||| | || || | || | || || | ||||| ||| || || |||||||||| |||||||||| ||||| || |||| |||||||||||||||||||| ||||||||||| ||||| ||| | | |||||||| |||| || |
gtatgcagaatatttataattgcttattatacttctccttctcttacttgtaagcactaaatcattttttcttaaatattttactagcacattatggtgtaacatttttaaatttgatgcagATTGCATTGGGAAATATCTTAAAATTTCGGAAGAAGAACTGGCAATTTGATTTTATTGGTGGCATTATATATTTTGTACTAGTCTTTTCAATGTTTCCAC
upper sequence: AT4G23000.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv18s0001g11060.t01 (Vitis vinifera), 3'ss of exon 11
--------------gtaaactttttcttgtttcttgaacctcttatccacggttactgattcgccttcttttctttgcattctgatattttatgttgttt--gctgttatttgcagATTGCTCTGGGAAATATTTTAAAGTTCAGGAAAAAGAACTGGCAATTTGATTTCATTGGTGGCATCATATACTTTCTCTTGGTCTTTTCCTTGTTCCCTC
|| | || | | || | | | | | || | | | || ||| |||| ||| || |||| ||| | | || |||||||||| ||||||||||||| |||||| | || ||||| ||||| |||||||||||||||||||| ||||| ||| | ||||| ||||| |||| || |
gtaaatctgaaaatctacagttccattggcttgtcaataccaaaaatttcattttatattcctttttttttccttttaatttctcaataatatggtgtattggtcatttgatgcagATTGCATTGGGAAATATTTTGAAGTTCCGAAAGAAGAATTGGCAGTTTGATTTCATTGGTGGCATTATATATTTTGTATTGGTTTTTTCTATGTTTCCAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcgccttcttttctttgcattctgatattttatgttgtttgctgttatttgcagATTGCTCTGGGAAATATTTTAAAGTTCAGGAAAAAGAACTGGCAATTTGATTTCATTGGTGGCATCATATACTTTCTCTTGGTCTTTTCCTTGTTCCCTC
ttctgat putative branch site (score: 3)
atattttatgttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaactttttcttgtttcttgaacctcttatccacggttactgattcgccttcttttctttgcattctgatattttatgttgtttgctgttatttgcagATTGCTCTGGGAAATATTTTAAAGTTCAGGAAAAAGAACTGGCAATTTGATTTCATTGGTGGCATCATATACTTTCTCTTGGTCTTTTCCTTGTTCCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG