Sequence
atgc intronic sequence ATGC exonic sequence...actactgttgaatcattcatcaattgaaataactttttactaatagttgattcctgactctttttgtctatcttttcttgttgaaaatgtcgatatatagGTCACGGAGGATGGGAAACAGGAGCGTCATGTGGTAGCTACTGTTGGCAAGTTCAGTGTGATATGGAACTTTCAGCAGGTGAAGAATGGATCTCATGAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G33400.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G33400.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os02g54780.1 (Oryza sativa), 3'ss of exon 1
----actactgttgaatcattcatcaattgaaataactttttactaatagttgatt-cctgactctttttgtctatcttttcttgttgaaaatgtcgatatatagGTCACGGAGGATGGGAAACAGGAGCGTCATGTGGTAGCTACTGTTGGCAAGTTCAGTGTGATATGGAACTTTCAGCAGGTGAAGAATGGATCTCATGAAT
| || | ||| | | | || | || | | | | ||| | | || | | | | | | || | |||| | | || |||| || ||| ||||||| || || ||| | || || || |||||||| || ||||| || ||||||||||||||||||||| | | ||||| |
taactttcttgctaaattaatgcctacatgctgcataattattcaatttgttaagtatatgtccttatgtatgttcctctatatgttctgattttcc-----cagGTAACAGAGAATGGGAAGCAAGAAAAGCATCTTGTTGCGACAGTTGGCAAATTTAGTGTCATTTGGAACTTTCAGCAGGTGAAGGACAGCAACCATGAGT
upper sequence: AT4G33400.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA04G04120.1 (Glycine max), 3'ss of exon 1
-----actactgttgaatcattcatcaattgaaataactttttactaatagttgattcctgactctttttgtctatcttttcttgttgaaaatgtcg-atatatagGTCACGGAGGATGGGAAACAGGAGCGTCATGTGGTAGCTACTGTTGGCAAGTTCAGTGTGATATGGAACTTTCAGCAGGTGAAGAATGGATCTCATGAAT
|| ||| ||| | | || || | || | ||| || | || || | | ||| ||| | | || | | | || ||||| || ||| |||||||||||||||| ||| | ||||| ||||| || ||||||||||||||||||||||| || || || ||| |||| |||||||| |
ccacatctgctgagaaatgacatcttggtttttattgtgtctttc--atattttaatcatg----tggaaatatatttttattattccaacttcttggatgcttagGTGACAGAGAATGGGAAACAGGAGCGGCATATAGTAGCCACTGTGGGGAAGTTCAGTGTGATATGGAACTTCCAACAAGTCAAGGATGGTTCTCATGAGT
upper sequence: AT4G33400.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA06G04290.1 (Glycine max), 3'ss of exon 1
-actactgttgaatcattcatcaattgaaataactttttactaatagttgattcctgact--ctttttgtctatcttttcttgttgaaaatgtcgatatat-agGTCACGGAGGATGGGAAACAGGAGCGTCATGTGGTAGCTACTGTTGGCAAGTTCAGTGTGATATGGAACTTTCAGCAGGTGAAGAATGGATCTCATGAAT
|| ||| ||| | ||| || | | | ||| || | || | | | | | | ||| || | ||| | | | | | | |||| || ||| |||||||||||||||| ||| | ||||| || || || ||||||||||||||||||||||| || || || ||| |||| |||||||| |
gtctgctgagaaatgacatatcttggtttttactgtgtctttcatattttaatcataaggaaatatatttttataattccaagttt----tattggtgtcttagGTGACAGAGAATGGGAAACAGGAGCGACATATAGTAGCCACCGTGGGGAAGTTCAGTGTGATATGGAACTTCCAACAAGTCAAGGATGGTTCTCATGAGT
upper sequence: AT4G33400.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv18s0001g10540.t01 (Vitis vinifera), 3'ss of exon 1
---actactgttgaatcattcatcaattgaaataactttttactaatagttgattcctgactctttttgtctatcttttcttgttgaaaatgtcgatat---atagGTCACGGAGGATGGGAAACAGGAGCGTCATGTGGTAGCTACTGTTGGCAAGTTCAGTGTGATATGGAACTTTCAGCAGGTGAAGAATGGATCTCATGAAT
| | | | | ||| || || || | | | || || ||| ||| | |||| || |||| | || || || | || || ||||||||| ||| ||||||| |||||||| || |||| || || || || ||||| |||||||||||||| ||||| |||||||||||||| || ||||| |
tgtattctttcttatacatgcagca--tgtttctcttatatccttatgattggttctttggc--ttttaactgtcttgt--ggtccaacattttgaaattccatagGTCACAGAGAATGGGAAGCAGGAGCGCCACCTGGTTGCCACAGTAGGAAAGTTTAGTGTGATATGGAATTTTCAACAGGTGAAGAATGGCTCCCATGAGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgattcctgactctttttgtctatcttttcttgttgaaaatgtcgatatatagGTCACGGAGGATGGGAAACAGGAGCGTCATGTGGTAGCTACTGTTGGCAAGTTCAGTGTGATATGGAACTTTCAGCAGGTGAAGAATGGATCTCATGAAT
tcctgac putative branch site (score: 2)
atatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actactgttgaatcattcatcaattgaaataactttttactaatagttgattcctgactctttttgtctatcttttcttgttgaaaatgtcgatatatagGTCACGGAGGATGGGAAACAGGAGCGTCATGTGGTAGCTACTGTTGGCAAGTTCAGTGTGATATGGAACTTTCAGCAGGTGAAGAATGGATCTCATGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - tcatcaa
- - - - - - - - - - - - -gaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaatg