Sequence
atgc intronic sequence ATGC exonic sequencegttaagtggaatgaaaggtttacacaactcagtaattgatatgatttttcttactaacttcctgaatttgcttattcagGGCCGTGATCTTACTGAGATTGGAGAACGTGGGGTGAATATTAGCGGAGGGCAGAAGCAGAGAGTCTCAATGGCTAGGGCAGTCTACTCAAATTCAGATG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G30410.1 |
intron # | 20 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G30410.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GRMZM2G084181_T01 (Zea mays), 3'ss of exon 18
gttaagtggaatgaaaggtttacacaactcagtaat--tgatatgatttttcttactaacttcc------------tgaatttgcttat--------tcagGGCCGTGATCTTACTGAGATTGGAGAACGTGGGGTGAATATTAGCGGAGGGCAGAAGCAGAGAGTCTCAATGGCTAGGGCAGTCTACTCAAATTCAGATG
|| | | | ||| ||| | | | || | | || ||| ||| ||| | | || ||||| |||| |||||| | ||||| || |||||||| ||| | || || |||||||| |||||||||||||| ||||| |||||||| || || || || || |||||||||
-tttaatccagtgatgcctttgtattttttaatactggcgcactgttttaacttgctactgtacattaacaaataatgcatttggttatgctttctatcagGGAGGCGATCTGACAGAGATTGGTGAAAGAGGAGTTAATATTAGTGGAGGGCAGAAGCAAAGAGTTTCAATGGCAAGAGCTGTGTATTCTGATTCAGATG
upper sequence: AT1G30410.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA06G46940.1 (Glycine max), 3'ss of exon 20
gttaagtgg--aatgaaaggtttacacaactcagtaattgatatgatttttcttactaacttcctgaatttgcttattcagGGCCGTGATCTTACTGAGATTGGAGAACGTGGGGTGAATATTAGCGGAGGGCAGAAGCAGAGAGTCTCAATGGCTAGGGCAGTCTACTCAAATTCAGATG
|| | | | || ||| || | || | | || | || || ||| | | || | | | |||||| |||||| |||| ||||| |||||| | || || |||||||| || || || ||||| ||||| || || |||||||| || ||||||||||| |||
gtaagattgtttataaaatgtcatcttctctaaactaatgggaattttctttttataatcatctcatttatatcttctcagGGACGTGATTTTACAGAGATCGGAGAAAGAGGAGTCAATATTAGTGGTGGTCAAAAGCAAAGAGTTTCCATAGCTAGGGCTGTATACTCAAATTCGGATA
upper sequence: AT1G30410.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: Vv10s0003g04470.t01 (Vitis vinifera), 3'ss of exon 19
gttaagtggaatgaaaggtttacacaactcagtaattgatatgatttttcttactaacttcctgaatttgcttattcagGGCCGTGATCTTACTGAGATTGGAGAACGTGGGGTGAATATTAGCGGAGGGCAGAAGCAGAGAGTCTCAATGGCTAGGGCAGTCTACTCAAATTCAGATG
| |||| | | | | ||| | | ||| | ||||| | | | || ||| || ||||||| | ||||||||| ||||| || ||| | ||||||||||| ||||| ||||| ||||| ||||| |||||||||||||| || || || ||||||||||
-gtgagtgtattcacaaagttatgtcgtttcatt-ttgttttgattgcctgttttgatttatc---tttcttttttcagGGTCATGATCTTACAGAGATCGGTGAAAGGGGGGTGAATATCAGCGGTGGGCAAAAGCAAAGAGTTTCAATGGCTAGGGCTGTATATTCTAATTCAGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caactcagtaattgatatgatttttcttactaacttcctgaatttgcttattcagGGCCGTGATCTTACTGAGATTGGAGAACGTGGGGTGAATATTAGCGGAGGGCAGAAGCAGAGAGTCTCAATGGCTAGGGCAGTCTACTCAAATTCAGATG
tactaac putative branch site (score: 0)
tttgctt putative PPT
taattgatatgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaagtggaatgaaaggtttacacaactcagtaattgatatgatttttcttactaacttcctgaatttgcttattcagGGCCGTGATCTTACTGAGATTGGAGAACGTGGGGTGAATATTAGCGGAGGGCAGAAGCAGAGAGTCTCAATGGCTAGGGCAGTCTACTCAAATTCAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG