Sequence
atgc intronic sequence ATGC exonic sequence...ttgtgtttgatatctacaaactaaagagagattttactgtcccaagaagtatcttttgtttataacttaattgaacttttagttttttttttgctgccagATTTTGGTATGATGGGGGACTTTAGGCCAGAATTACGTGATGGATTCATGGAAGCATGTCTTCATCTTGTAAATCGTGACTTCAAAGCGCTGGCTAAAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G71810.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G71810.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G305007_T01 (Zea mays), 3'ss of exon 10
------ttgtgtttgatatctacaaactaaagagagattttactgtcccaagaagtatcttttgtttataacttaattgaacttttagttttttttttgctgccagATTTTGGTATGATGGGGGACTTTAGGCCAGAATTACGTGATGGATTCATGGAAGCATGTCTTCATCTTGTAAATCGTGACTTCAAAGCGCTGGCTAAAGA
| ||| || | | ||| |||| | | ||||| | ||| | | |||| || ||| || | | ||| | ||||||||| |||||||| || || | | |||| | ||||||||||| || ||||| |||||||||||||| || ||||| || | || | || |||||
caactttcctgtgtgtttaggaaaaaaagaagaaaaactttacaaccaattgaatgaagctcaaattat--tttgattaaatgtgacactattt----gtcaatagATTTTGGGATGATGGGAGAATTCCGACAAGAACTTCGTGATGGATTTATTGAAGCTTGTCTTCATCTTGTTAACCGTGATTTTGATGCTTTAGCAAAAGA
upper sequence: AT1G71810.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA16G27500.1 (Glycine max), 3'ss of exon 10
----------------------------------------------------------------------ttgtgtttgatatctacaaactaaagagagattttactgtcccaagaagtatcttttgtttataacttaattgaacttttagttttttttttgctgc--cagATTTTGGTATGATGGGGGACTTTAGGCCAGAATTACGTGATGGATTCATGGAAGCATGTCTTCATCTTGTAAATCGTGACTTCAAAGCGCTGGCTAAAGA
|||| | ||| | | || | | | || | || || | | | | | || ||||| | | || ||| || | ||| |||||||||||||| || || || | | ||||||||| || |||||||| ||||| ||||| ||||||||||| ||||| || | || |||| || ||
gtaattgaagattgaatatttaatatttcaaattctttggtttcttggttgatgtttacatagatttgtcttgtttctgaggatttaatgatagaaataagcgaaacacttggaataacttgttcatttcttgaatttaatggtgcattctttttcccttcttttgcaatagATTTTGGTATGACTGGTGAGTTCAAACAAGAATTACGCGACGGATTCATCGAAGCTTGTCTACATCTTGTAAACCGTGATTTTGATGCATTGGCCAAGGA
upper sequence: AT1G71810.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv18s0001g01620.t01 (Vitis vinifera), 3'ss of exon 10
---ttgt-gtttgatatctacaaactaaagagagattttactgtcccaagaagtatcttttgtttataacttaattgaacttttagttttttttttgctgccagATTTTGGTATGATGGGGGACTTTAGGCCAGAATTACGTGATGGATTCATGGAAGCATGTCTTCATCTTGTAAATCGTGACTTCAAAGCGCTGGCTAAAGA
||| ||| | | | | | | ||| || | | | | || || | |||||| | | || |||||||||||||||||||| || ||| |||||| | || |||||||| || ||||| ||||| ||||||||||| ||||| | | || ||||||| ||
ttactgtcattttgggttcaattgtgttgaccaaactcttgtgtgtgtgtgtgtgtgtgtgtatcatg--ttggaccatcttttaacatctctt--atcaccagATTTTGGTATGATGGGTGAATTTGAACCAGAACTCCGAGATGGATTTATTGAAGCCTGTCTCCATCTTGTAAACCGTGATTATGATGCATTGGCTAAGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaagtatcttttgtttataacttaattgaacttttagttttttttttgctgccagATTTTGGTATGATGGGGGACTTTAGGCCAGAATTACGTGATGGATTCATGGAAGCATGTCTTCATCTTGTAAATCGTGACTTCAAAGCGCTGGCTAAAGA
cttttagttttttttt CT-rich tract
ttttgtttataactta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgtgtttgatatctacaaactaaagagagattttactgtcccaagaagtatcttttgtttataacttaattgaacttttagttttttttttgctgccagATTTTGGTATGATGGGGGACTTTAGGCCAGAATTACGTGATGGATTCATGGAAGCATGTCTTCATCTTGTAAATCGTGACTTCAAAGCGCTGGCTAAAGA
- -tgtttga
- - - - - - - - - aactaaa
- - - - - - - - - - - - - - - - - - - - cccaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacttaa