Sequence
atgc intronic sequence ATGC exonic sequence...ttttggctaggtgcaaaaacgtagatagtagaaataaccttctcaactcataatatttacgattgtgctactgatcctaatgcaattcttatattgccagCTATTTGAATTTGCGGACAAATACAGAGGCAAATATGACAGCAGCATTACCGTGGCACAAAAATATTACCGATCCGTCAGCGGTTACAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G11050.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G11050.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G36930.1 (Glycine max), 3'ss of exon 3
ttttggctaggtgcaaaaacgtagatagtagaaataaccttctcaactcataat--atttacgattgtgctactgatcctaatgcaattcttatattgccagCTATTTGAATTTGCGGACAAATACAGAGGCAAATATGACAGCAGCATTACCGTGGCACAAAAATATTACCGATCCGTCAGCGGTTACAAT
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gattcatttattg--agaattatggtactcgattgactttactccattccttttccatccggacttgttcaacttactctctctgggtttgttcaatttcagCTATTTGATTTTGCTGACAAATACAGAGGCAAATATGACAGCAGCATTACGGTTGCCCAGAAATATTACAGATCCATCAGTGGTTACAAT
upper sequence: AT4G11050.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G02610.1 (Glycine max), 3'ss of exon 3
ttttggctaggtgcaaaaacgtagatagtagaaataaccttctcaactcataatatttacgattgtgct--actgatcctaatgcaattcttatattgccagCTATTTGAATTTGCGGACAAATACAGAGGCAAATATGACAGCAGCATTACCGTGGCACAAAAATATTACCGATCCGTCAGCGGTTACAAT
|| | || | || | || | || | | ||| | || | | | || |||| ||||| || | | | | ||||||||||| ||||| |||||||||||||||||||||||||||||||| || || || ||||| |||||| ||||| |||| |||||||||
gattcatttattg--agaataatggtactcgattgactttactccattctttttctacccggacctgctcaactgactctctctggggttgttcaatttcagCTATTTGATTTTGCTGACAAATACAGAGGCAAATATGACAGCAGCATCACGGTTGCCCAAAAGTATTACAGATCCATCAGTGGTTACAAT
upper sequence: AT4G11050.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv02s0025g01380.t01 (Vitis vinifera), 3'ss of exon 5
ttttggctaggtgcaaaaacgtagatagtagaaataaccttctcaactcataatatttac--gattgtgctactgatcctaatgcaattctta------tattgccagCTATTTGAATTTGCGGACAAATACAGAGGCAAATATGACAGCAGCATTACCGTGGCACAAAAATATTACCGATCCGTCAGCGGTTACAAT
| ||| | | || || ||||| | || |||| ||| ||| || | | |||| || | || |||| ||||| || || |||| ||||||||||| |||||||||||||||||||| || ||||| || || || ||||| || ||| || ||| |
--------cttcccctcaacctctcttcccaaactacccttcatgttttatcatatctactgaattacccttcagtcactaacacatgttctaaaatcttattttcagCTGTTCGAGTTTGGAGACAAATACAGGGGCAAATATGACAGCAGCATCACAGTGGCCCAGAAGTACTACCGGTCTTACAGTGGATACGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actcataatatttacgattgtgctactgatcctaatgcaattcttatattgccagCTATTTGAATTTGCGGACAAATACAGAGGCAAATATGACAGCAGCATTACCGTGGCACAAAAATATTACCGATCCGTCAGCGGTTACAAT
tcctaat putative branch site (score: 2)
ttcttat putative PPT
taatatttacgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttggctaggtgcaaaaacgtagatagtagaaataaccttctcaactcataatatttacgattgtgctactgatcctaatgcaattcttatattgccagCTATTTGAATTTGCGGACAAATACAGAGGCAAATATGACAGCAGCATTACCGTGGCACAAAAATATTACCGATCCGTCAGCGGTTACAAT
- - - - - - -caaaaac
- - - - - - - - - - - - - - - gaaataa
- - - - - - - - - - - - - - - - - - - cttctca
- - - - - - - - - - - - - - - - - - - - - - -actcata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atcctaa