Sequence
atgc intronic sequence ATGC exonic sequencegttaagtaaaatgacaggcatacacaacccggtacatgacatttcttactaacttcctgaatttgcttattcagGGCCGTGATCGTACTGAGATTGGAGAACGTGGGGTGAATATTAGTGGAGGGCAGAAGCAGAGAGTTTCAATGGCTAGGGCAGTCTACTCAAATTCAGATA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G30420.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G30420.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GRMZM2G084181_T01 (Zea mays), 3'ss of exon 18
----------------------gttaagtaa-aatgacaggcatacacaacccggtacatgacatttcttactaactt-cctgaatttgcttat--tcagGGCCGTGATCGTACTGAGATTGGAGAACGTGGGGTGAATATTAGTGGAGGGCAGAAGCAGAGAGTTTCAATGGCTAGGGCAGTCTACTCAAATTCAGATA
|| ||| | || | | ||| | ||| ||||| | ||| || | ||||| |||||| | |||| || |||||||| ||| | || || ||||||||||||||||||||||| |||||||||||||| || || || || || ||||||||
tttaatccagtgatgcctttgtattttttaatactggcgcactgttttaacttgctactgtacattaacaaataatgcatttggttatgctttctatcagGGAGGCGATCTGACAGAGATTGGTGAAAGAGGAGTTAATATTAGTGGAGGGCAGAAGCAAAGAGTTTCAATGGCAAGAGCTGTGTATTCTGATTCAGATG
upper sequence: AT1G30420.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA06G46940.1 (Glycine max), 3'ss of exon 20
--------gttaagtaaaatgacaggcatacacaacccggtacatgacatttcttactaacttcctgaatt-tgcttattcagGGCCGTGATCGTACTGAGATTGGAGAACGTGGGGTGAATATTAGTGGAGGGCAGAAGCAGAGAGTTTCAATGGCTAGGGCAGTCTACTCAAATTCAGATA
||| | ||||||| || | | || | | | | || ||| || | || | | |||||| |||||| ||| ||||| |||||| | || || ||||||||||| || || ||||| |||||||| || |||||||| || ||||||||||| ||||
gtaagattgttta-taaaatgtcat-cttctctaaactaatgggaattttctttttataatcatctcatttatatcttctcagGGACGTGATTTTACAGAGATCGGAGAAAGAGGAGTCAATATTAGTGGTGGTCAAAAGCAAAGAGTTTCCATAGCTAGGGCTGTATACTCAAATTCGGATA
upper sequence: AT1G30420.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: Vv10s0003g04450.t01 (Vitis vinifera), 3'ss of exon 7
-------------------------------gttaagtaaaatgacag-gcatacacaacccggtacatgacatttcttactaacttcctgaat------ttgcttattcagGGCCGTGATCGTACTGAGATTGGAGAACGTGGGGTGAATATTAGTGGAGGGCAGAAGCAGAGAGTTTCAATGGCTAGGGCAGTCTACTCAAATTCAGATA
||||| | || | | | | || || ||| | |||| || | | || || ||| || | ||||| ||| || ||||| ||| | ||||||||||||||||| ||||| ||||| ||||||||
gttaagtgtattcacaaaattatacattccagttaattctcattaggatgtaattttcattgtgttgataggttttttacctaatgtcttatttatcccttttttttctcaagGTCATGATCTTACAGAAATTGGTGAAAGAGGGGTGAATATTAGTGGTGGGCAAAAGCAAAGAGTTTCC-------------------------------
upper sequence: AT1G30420.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: Vv10s0003g04470.t01 (Vitis vinifera), 3'ss of exon 19
gttaagtaaaatgacaggcatacacaacccggtacatgacatttcttactaacttc---ctgaatttgcttattcagGGCCGTGATCGTACTGAGATTGGAGAACGTGGGGTGAATATTAGTGGAGGGCAGAAGCAGAGAGTTTCAATGGCTAGGGCAGTCTACTCAAATTCAGATA
| ||| | | ||| || | | || || | || | ||| || ||||||| | ||||| ||| ||||| || ||| | ||||||||||| || || ||||| ||||| |||||||||||||||||||| || || || |||||||||
-gtgagtgtattcacaaagttatgtcgttt--cattttgttttgattgcctgttttgatttatctttcttttttcagGGTCATGATCTTACAGAGATCGGTGAAAGGGGGGTGAATATCAGCGGTGGGCAAAAGCAAAGAGTTTCAATGGCTAGGGCTGTATATTCTAATTCAGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atacacaacccggtacatgacatttcttactaacttcctgaatttgcttattcagGGCCGTGATCGTACTGAGATTGGAGAACGTGGGGTGAATATTAGTGGAGGGCAGAAGCAGAGAGTTTCAATGGCTAGGGCAGTCTACTCAAATTCAGATA
tactaac putative branch site (score: 0)
tttgctt putative PPT
atttctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaagtaaaatgacaggcatacacaacccggtacatgacatttcttactaacttcctgaatttgcttattcagGGCCGTGATCGTACTGAGATTGGAGAACGTGGGGTGAATATTAGTGGAGGGCAGAAGCAGAGAGTTTCAATGGCTAGGGCAGTCTACTCAAATTCAGATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC