Sequence
atgc intronic sequence ATGC exonic sequencegtttaaaacccaaatcacagaatcctctgcttctttctatattctattatatgcttaagaaactaagttctttttgttgcagATTATAAATGTGTATAACCAAGAGTATGAGAGTGCTGCAGCGTTCTGGCCAGATGTTCATAGACGTGTAGTGATTGCACTGATCGTATCTCAGCTTCTTT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G21620.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G21620.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os01g35050.4 (Oryza sativa), 3'ss of exon 10
--------------gtttaaaacccaa---atcacagaatcctctgcttct-ttctatattctattatatgcttaagaaactaagttctttttgttgcagATTATAAATGTGTATAACCAAGAGTATGAGAGTGCTGCAGCGTTCTGGCCAGATGTTCATAGACGTGTAGTGATTGCACTGATCGTATCTCAGCTTCTTT
|| | ||| | || ||| || | || | |||| | | || | |||| || | ||||| ||||| ||||||||||| |||||||| ||||| ||||| ||||| || |||||| ||||||| |||| || | | ||| | |||||||| ||||| |||
tgtgtgacaatttagtcttcggtgcaatagaacaagtaattctacattctgattatgtattaaaatgattgacttcctaactgagggttcattgtttcagATAATAAATGTGTACAACCAAGAATATGAAAGTGCAGCAGCATTTTGGCCAAGTGTTCATGGACGCATAATTGTAGCATTAATCGTATCACAGCTGCTTC
upper sequence: AT3G21620.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G064189_T01 (Zea mays), 3'ss of exon 3
-------------------------------------------------------------------------------------------------gtttaaaacccaaatcacagaat--cctctgcttctttctatattctattat----atgcttaagaaactaagttctttttgttgcagATTATAAATGTGTATAACCAAGAGTATGAGAGTGCTGCAGCGTTCTGGCCAGATGTTCATAGACGTGTAGTGATTGCACTGATCGTATCTCAGCTTCTTT
|| | | | | | | | | | || || || | ||| ||| |||| ||| || || | | |||| ||||| |||||||||||||| ||||| || |||||||| ||||| || |||||| ||||||| |||| || | | || |||| ||||| ||||| |||
gtaagcaagcatatcataaatgtcctcatgtgttttctttagcattgcatctggcattgtgttgtttatcgtgctgtgctacatttgcatgcgcataattatacatattagttagtgtgttgcatttgtttggttagaaattgacttaccctgatgcataacttacacagct-taactgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCAAGTGTTCATGGACGCATAATCACAGCGTTGATTGTATCACAGCTGCTTC
upper sequence: AT3G21620.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G021194_T01 (Zea mays), 3'ss of exon 10
-------------gtttaaaacccaaatcacagaat--cctctgcttctttctatattctattat----atgcttaagaaactaagttctttttgttgcagATTATAAATGTGTATAACCAAGAGTATGAGAGTGCTGCAGCGTTCTGGCCAGATGTTCATAGACGTGTAGTGATTGCACTGATCGTATCTCAGCTTCTTT
| | | | | | | | || || || | ||| ||| |||| ||| || || | | |||| ||||| |||||||||||||| ||||| || |||||||| ||||| || |||||| ||||||| |||| || | | || |||| ||||| ||||| |||
aactaaaacgaaacagaggagtattagttagtgtgttgcatttgtttggttagaaattgacttaccctgatgcataacttacacagct-taactgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCAAGTGTTCATGGACGCATAATCACAGCGTTGATTGTATCACAGCTGCTTC
upper sequence: AT3G21620.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA02G43910.1 (Glycine max), 3'ss of exon 10
---------------------------------------------------------------------------------------------gtttaaaacccaaatcacagaatcctctgcttctttctatattctattatatgcttaagaaactaagttctttttgttgcagATTATAAATGTGTATAACCAAGAGTATGAGAGTGCTGCAGCGTTCTGGCCAGATGTTCATAGACGTGTAGTGATTGCACTGATCGTATCTCAGCTTCTTT
| | | || | |||| || | || ||||| | |||| | | || | ||| || ||||||||| ||||| || |||||||||||||||||||||||||| |||||||| ||||| ||| ||||| | | |||| | | | || ||||| || |
gtaaaagttagctcatgaaaggtcttctgtttcaatgcaatttaatctttgtttttacaaactgaccatagacacgagaaattttaaggatgaatatttactatgtattattcaatcttcaacaa--ttgaatattttgttatgtagcataatgcctgaaatctaaatg--gcagATTATTAATGTCTACAACCAAGAGTATGAGAGTGCTGCAGCATTCTGGCCTGATGTCCATGGACGTATTATATTTGCGTTAGTGATCTCACAGCTGCTGT
upper sequence: AT3G21620.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv12s0059g01090.t01 (Vitis vinifera), 3'ss of exon 9
--------------------------------------------------------------------------------------------------------gtttaaaacccaaatc--acagaatcctctgcttctttctatattctattatatgcttaagaaactaagttctttttgt---tgcagATTATAAATGTGTATAACCAAGAGTATGAGAGTGCTGCAGCGTTCTGGCCAGATGTTCATAGACGTGTAGTGATTGCACTGATCGTATCTCAGCTTCTTT
||| ||| | || | ||| | ||| || | | | || || || || | || || |||| |||||||| || || || ||||||||||||||||| || |||||||| |||||||| | || | | ||||| | | || || ||||| ||
gtaaaagttggtattccttcacatttgtgtggaggaatctcctcctaccctaatcatattttccctgcccagttgttttacagtatagtgtttttcagttggtggttggaaaggaatctctgatgtaatatattatctctgtcctctctgcccaaattctttctctaataaaatttctggtggatatgtagATCATAAATGTATACAATCAGGAGTATGAGAGTGCTGCTGCATTCTGGCCTGATGTTCACATGCGCATCATAGTTGCATTAGTTGTCTCACAGCTGCTAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcttctttctatattctattatatgcttaagaaactaagttctttttgttgcagATTATAAATGTGTATAACCAAGAGTATGAGAGTGCTGCAGCGTTCTGGCCAGATGTTCATAGACGTGTAGTGATTGCACTGATCGTATCTCAGCTTCTTT
ttctttttgtt CT-rich tract
tatattctattatatg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttaaaacccaaatcacagaatcctctgcttctttctatattctattatatgcttaagaaactaagttctttttgttgcagATTATAAATGTGTATAACCAAGAGTATGAGAGTGCTGCAGCGTTCTGGCCAGATGTTCATAGACGTGTAGTGATTGCACTGATCGTATCTCAGCTTCTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT