Sequence
atgc intronic sequence ATGC exonic sequencegtaatttgttatcctaatagatgatgtgataaaagattatgacatcaactgactacaaaaagttatgcagGCATATATGGTGGAACTTTATCAAGACACACTTGTAGACCTTTTGTTACCAAAAAGTGCAAGACGCTTGAAACTAGAGATTAAAAAAGATTCAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G65930.3 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 18
---------------------gtaatttgt--tatcctaatagatgatgt-gataaaagattatgacatcaactgactacaaaaagt------tatgcagGCATATATGGTGGAACTTTATCAAGACACACTTGTAGACCTTTTGTTACCAAAAAGTGCAAGACGCTTGAAACTAGAGATTAAAAAAGATTCAAAG
| ||| ||| ||| | | | | ||| ||| | | | | | ||| | || |||||||||||||||||| ||||||||||| | ||||| ||||| || || || | || ||||| | |||| ||||||| ||||||||||| |||
aatgacttatatttatatctgacactttcacatattttaacacgttctttagatccaagtatgccttctatattatccttaaattctgttttatacgcagGCATATATGGTGGAGCTTTATCAAGATAATCTTGTGGACCTGTTATTGCCCAGAAATGCAAAGCAGCTGAAGTTAGAGATAAAAAAAGATTCCAAG
upper sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA11G09480.1 (Glycine max), 3'ss of exon 20
-----------------------------gtaatttgttatcctaatagatg-atgtgataaaagattatgacatcaactgactacaaaaagtt--atgcagGCATATATGGTGGAACTTTATCAAGACACACTTGTAGACCTTTTGTTACCAAAAAGTGCAAGACGCTTGAAACTAGAGATTAAAAAAGATTCAAAG
|| | | | || | ||||| | | | ||| | ||| | | || ||||||||||||||| ||||| | |||||||| ||||||||||| ||| ||||||| || | ||||| || || ||| | || ||||| || ||||| |||
tgggtataatgttgagcgacttaaccagaacaaatcacgagatttgcagtagcatgtgtttgttg--tctgatctagacttctttttgtatgtatgatgcagGCATATATGTTGGAATTATATCAAGATACACTTGTAGATCTTCTGTTACCGAAGAATGCAAAGCGTTTAAAATTGGATATTAAGAAGGATTCCAAG
upper sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA01G35950.1 (Glycine max), 3'ss of exon 20
---------------------gtaatttgtta---tcctaatag-atg-atgtgataaaagattatgacatcaactgacta----caaaaagttatgcagGCATATATGGTGGAACTTTATCAAGACACACTTGTAGACCTTTTGTTACCAAAAAGTGCAAGACGCTTGAAACTAGAGATTAAAAAAGATTCAAAG
|| | | | | | ||| ||| | || | ||| ||| | | | | | ||||||||||||||| ||||| | |||||||| ||||||||||| ||| ||||||| || | ||||| || || ||| | || ||||| || ||||| |||
atgttgagtgacttaaccataacaaatcatgaggtttgcagtagcatgtgtttgttgtctgatctagactttttttttttttttttcatctatgatgcagGCATATATGTTGGAATTATATCAAGATACACTTGTAGATCTTCTGTTACCGAAGAATGCAAAGCGTTTAAAATTGGATATTAAGAAGGATTCCAAG
upper sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 19
-------------------------gtaatttgttatcctaatagatgatgtgataaaagattatgacatcaactgactacaaa-----aagttatgcagGCATATATGGTGGAACTTTATCAAGACACACTTGTAGACCTTTTGTTACCAAAAAGTGCAAGACGCTTGAAACTAGAGATTAAAAAAGATTCAAAG
| || | |||| |||| || ||| || | | | | ||| || || || ||||||| |||||||| | |||||||| ||||||||||| ||| | |||||||| | ||||| || ||||| || || ||||| ||||||||||||
aagttcttgtttataggaagcaaaatttatgtagtatctaaataaatattgttctattttgcctttattcacctttgacataaatcgtgaaattgtgtagGCATACATGGTGGAGTTGTATCAAGATACACTTGTAGATCTTCTATTACCAAAGAATGCAAAGCGTTTGAAGCTGGACATTAAGAAAGATTCAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatagatgatgtgataaaagattatgacatcaactgactacaaaaagttatgcagGCATATATGGTGGAACTTTATCAAGACACACTTGTAGACCTTTTGTTACCAAAAAGTGCAAGACGCTTGAAACTAGAGATTAAAAAAGATTCAAAG
aactgac putative branch site (score: 2)
tgataaaagattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatttgttatcctaatagatgatgtgataaaagattatgacatcaactgactacaaaaagttatgcagGCATATATGGTGGAACTTTATCAAGACACACTTGTAGACCTTTTGTTACCAAAAAGTGCAAGACGCTTGAAACTAGAGATTAAAAAAGATTCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA