Sequence
atgc intronic sequence ATGC exonic sequence...ccaaaaacagaagaaaaaatgtgttcttgagatttggggtttttgagttttttgtcttcttctacaagaaatctgatgttatgatctttgattttgttagGGTTTCAGAAAGATTGTACCAGATCGATGGGAGTTCGCGAACGAGTTTTTCAAGAGAGGAGAGAAACATTTACTCTGCGAAATCCACCGCCGTAAAACAT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G46264.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G46264.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA04G04200.1 (Glycine max), 3'ss of exon 1
ccaaaaacagaagaaaaaatgtgttcttgag--atttggggtttttgagtt-ttttgtcttcttctacaagaaatctgatgttatgatctttgattttgttagGGTTTCAGAAAGATTGTACCAGATCGATGGGAGTTCGCGAACGAGTTTTTCAAGAGAGGAGAGAAACATTTACTCTGCGAAATCCACCGCCGTAAAACAT
| | | | | | | || | ||| || | || || | | | |||| | ||||| | | | | | | |||||||| ||||||||||| ||||| |||||||||||||||||||| || ||||||| ||||||||||| || || ||||| ||||| | | |||||
---gtattatatttacttacacactgatacactatctctagttcttcaattattgttttcttttctttttatattctgacagttttaaat--ggatgaactagGGTTTTAGAAAGATTGTGCCAGACCGATGGGAGTTCGCGAACGAATTCTTCAAGAAGGGAGAGAAACACTTGCTGTGCGAGATCCATAGAAGAAAAACGG
upper sequence: AT1G46264.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA06G04390.1 (Glycine max), 3'ss of exon 1
ccaaaaacagaagaaaaaatgtgttcttgagatttggggttt-ttgagttttttgtcttcttctacaagaaatctgatgttatgatctttgattttgttagGGTTTCAGAAAGATTGTACCAGATCGATGGGAGTTCGCGAACGAGTTTTTCAAGAGAGGAGAGAAACATTTACTCTGCGAAATCCACCGCCGTAAAACAT
| | | || | | | | | |||| || | | || || || || | | || | || | ||||||||| ||||||||||| ||||| |||||||||||||| ||||| || ||||||| ||||||||||| || || ||||| ||||| | | |||||
------------------gtattatattcacttacacactatatctagttcttcagttattcttataattaacatggt-taattttaaatgcatgaattagGGTTTTAGAAAGATTGTGCCAGACCGATGGGAGTTCGCCAACGAATTCTTCAAGAAGGGAGAGAAACACTTGCTGTGCGAGATCCATAGAAGAAAAACCG
upper sequence: AT1G46264.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA14G09190.1 (Glycine max), 3'ss of exon 1
ccaaaaacagaagaaaaaatgt----gttcttgagatttggggtttttgagttttttgtcttcttcta--caagaaatctgatgttatgatctttgattttgttagGGTTTCAGAAAGATTGTACCAGATCGATGGGAGTTCGCGAACGAGTTTTTCAAGAGAGGAGAGAAACATTTACTCTGCGAAATCCACCGCCGTAAAACAT
||| | | |||| || || || | | || ||||||| | || | | || || || | | ||| |||| ||| |||||||| ||||||||||| || ||| |||||||||||||||| ||||| ||||||| ||||||||| | || | ||||| || ||| | | |||||
---aaattgtgatttaccatgttgtggtaattagtccttcaagatgttacattttttgcatgctcccaattaactaacttg--gctttgaattttg-tttgaatagGGTTTTAGAAAGATTGTGCCTGATAGATGGGAGTTCGCGAATGAGTTCTTCAAGAAAGGAGAGAAGAACTTGTTGTGCGAGATTCACAGAAGAAAAACCC
upper sequence: AT1G46264.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA17G35980.1 (Glycine max), 3'ss of exon 1
ccaaaaacagaagaaaaaatgtgttcttgagatttggggtttttgagttttttgtcttcttctacaagaaatctgatgttatgatctttgattttgt-tagGGTTTCAGAAAGATTGTACCAGATCGATGGGAGTTCGCGAACGAGTTTTTCAAGAGAGGAGAGAAACATTTACTCTGCGAAATCCACCGCCGTAAAACAT
| | | |||| | | || | | || | |||| | || | | | || | ||| | | | ||| | || |||||||| ||||||||||| || ||| |||||||||||||||| ||||| ||||||| ||||| ||| | || || ||||| |||||| | | |||||
-tcccatttaacatacccatgttaatctcactttcaagatgttacatttttgcatgctcctattaattaactaacatggttttacattttttcttaaatagGGTTTTAGAAAGATTGTGCCTGATAGATGGGAGTTCGCGAATGAGTTCTTCAAGAAAGGAGCGAAGAACTTGCTGTGCGAGATCCACAGAAGGAAAACCC
upper sequence: AT1G46264.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv18s0001g10380.t01 (Vitis vinifera), 3'ss of exon 1
----------------------------------ccaaaaa----cagaagaaaaaatgtgttcttgagatttggggtttttgagttttttgtcttcttctacaagaaatctgatgttatgatc-tttgattttg----ttagGGTTTCAGAAAGATTGTACCAGATCGATGGGAGTTCGCGAACGAGTTTTTCAAGAGAGGAGAGAAACATTTACTCTGCGAAATCCACCGCCGTAAAACAT
|||| | | ||| || ||| | | || | || || || | | || | | | |||| || | ||| || | |||||||| |||||||||||||| ||| |||||||||| || |||||||| ||||||| ||||||||| || ||||||||||| ||||| | | ||||| |
gtatgccttctctctcttcccccacttcccttcttcaaatcgtttctggagatgtaactggttatatatatatatatgaaacaagcttcttattgtttttactgatttagattttgttttgcttgcttgcttccggaaactagGGTTTTAGAAAGATTGTACCGGATAGATGGGAGTTTGCCAACGAGTTCTTCAAGAAAGGAGAGAAGCACTTACTCTGCGAGATCCATAGAAGAAAAACCT
upper sequence: AT1G46264.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S207_20V6.1 (Physcomitrella patens), 3'ss of exon 1
ccaaaaacagaagaaaaaatgtgttc-ttgagatttggggtttttgagttttttgtcttcttctacaagaaatctgatgttatgatctttgattttgttagGGTTTCAGAAAGATTGTACCAGATCGATGGGAGTTCGCGAACGAGTTTTTCAAGAGAGGAGAGAAACATTTACTCTGCGAAATCCACCGCCGTAAAACAT
|| || | | || | | ||| || | | | || || | ||| | | | || | | | | | | |||||||||||||||| || ||||||| ||||| ||||| ||| |||||||| | || ||||| || | |||||||| ||||| | | ||| | |
-gaatgacgtggttgagattgcatccgttgtaatgtatgttggttcgattctccaacttgaaagtcttggtgaataatatggttggggcttgtcatttcagGGTTTCAGAAAGATAGTGCCAGATCACTGGGAATTCGCCAACAAGTTTTTCCGACGCGGGGAGAAGCACCTGCTCTGCGAGATCCATAGGAGAAAATCGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttttttgtcttcttctacaagaaatctgatgttatgatctttgattttgttagGGTTTCAGAAAGATTGTACCAGATCGATGGGAGTTCGCGAACGAGTTTTTCAAGAGAGGAGAGAAACATTTACTCTGCGAAATCCACCGCCGTAAAACAT
ttttgtt CT-rich tract
tttgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccaaaaacagaagaaaaaatgtgttcttgagatttggggtttttgagttttttgtcttcttctacaagaaatctgatgttatgatctttgattttgttagGGTTTCAGAAAGATTGTACCAGATCGATGGGAGTTCGCGAACGAGTTTTTCAAGAGAGGAGAGAAACATTTACTCTGCGAAATCCACCGCCGTAAAACAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
-caaaaac
- - - - - - gaaaaaa
- - - - - - - - - - - - - - - gatttgg
- - - - - - - - - - - - - - - - - - - gtttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagaaat