Sequence
atgc intronic sequence ATGC exonic sequence...tctcgttatcaaaggtccttaatcggatttcaataattacaattttacaaagcagtaattggcacatttatcgtgaactagttatttttcaaaaatgtagGTGTCTTCGAAAAAGTGGGGATTGAACCTCAAGTACAAAGGATTGGAAAATACAAAAGTGCTGGAGATCAGCTTTCTCGCAAAAGTATATCTGAGGAAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G73990.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G73990.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G22870.1 (Glycine max), 3'ss of exon 3
tctcgttatcaaaggtccttaatcggatttcaataattacaattttacaaag--cagtaattggc---acatttatcgtgaactagttatttttcaaaaatgt----agGTGTCTTCGAAAAAGTGGGGATTGAACCTCAAGTACAAAGGATTGGAAAATACAAAAGTGCTGGAGATCAGCTTTCTCGCAAAAGTATATCTGAGGAAAA
||| | || | || | ||| |||| ||| |||| || | | | ||| || | | || | ||| | | |||| || ||| |||| | || ||||| | || |||||||| ||||| ||||||||||||||||||||||||| ||||||||||| |||| | || || ||||| |||||
----gttctggaacatgctgca----gtttaaatattta-aattctatgatggctataaataagcctaaaactttttgtgtttgacatcattttattaattgttttcagGTATTTTAGAAAACATAGGAATTGAACCACAAGTGGAAAGGATTGGAAAATACAAAAGTGCAGGAGATCAGCTAGCTCGAAGAACCATGTCTGAAGAAAA
upper sequence: AT1G73990.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA04G31180.1 (Glycine max), 3'ss of exon 3
tctcgttatcaaaggtccttaatcggatttcaataattacaattttacaa-agcagtaattgg---cacatttat-cgtgaactagttatttttcaaaaatgtagGTGTCTTCGAAAAAGTGGGGATTGAACCTCAAGTACAAAGGATTGGAAAATACAAAAGTGCTGGAGATCAGCTTTCTCGCAAAAGTATATCTGAGGAAAA
|||| || | ||| ||| |||| ||| |||| || | || ||| | | | || | ||| | || | || | | ||| || || || || | || |||||||| ||||| ||||||||||||||||||||||||| |||||||| || |||| | || || ||||| |||||
----attattgaatattaataaatcattttaaatattta-aattctatgatggctataaataagcctaaacttgtgtttgacatcattttattacttgttttcagGCGTTTTAGATAACATAGGAATTGAACCACAAGTGGAAAGGATTGGAAAATACAAAAGTGCAGGAGATCAACTAGCTCGAAGAACCATGTCTGAAGAAAA
upper sequence: AT1G73990.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G07540.1 (Glycine max), 3'ss of exon 3
tctcgttatcaaaggtccttaatcggatttcaataattacaattttacaaa-gcagtaattggcacatttatcgtgaactagttatttttcaaaaatgt-agGTGTCTTCGAAAAAGTGGGGATTGAACCTCAAGTACAAAGGATTGGAAAATACAAAAGTGCTGGAGATCAGCTTTCTCGCAAAAGTATATCTGAGGAAAA---------
|| ||| || || || | || | | | || || || | | | | | |||| | || | | | |||| | || || | || |||||||| |||| |||||||||| ||||||||||||| ||||||||||||| | || |||| || ||||| || |
-----------aaaacactttctcaaatcacatagacccttgttctttgattactatagttagcctaaaactattttttttttcatttgttaattctcttatgtgttctagAGAATCTTGGAATTGAACCAGAAGTGGAAAGGATTGGCAAATACAAAAGTGTTGGAGATCAGCTTACCCGTAAAACCATGTCTGAAGATCATCATGAGAT
upper sequence: AT1G73990.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv17s0000g04680.t01 (Vitis vinifera), 3'ss of exon 3
tctcgttatcaaaggtccttaatcggatttcaataattacaattttacaaagcagtaattggcaca-tttatcg---tgaactagttatttttcaaaaa----tgtagGTGTCTTCGAAAAAGTGGGGATTGAACCTCAAGTACAAAGGATTGGAAAATACAAAAGTGCTGGAGATCAGCTTTCTCGCAAAAGTATATCTGAGGAAAA
|| ||| | | | | || || | | | || || || ||| || |||| | | |||||| ||||||||| || || ||||| || |||||||| ||||| ||||||||||| |||||||||||||| || ||||| ||| | ||||||| || ||||| |||||
------aatagaagatgatcttttaaaattggatcactgtg--tgagaggagttgtctttattttggtttctctgactgaagtggagtggcttcaaattgttttgtagGTGTTTTTGAGAAAGTAGGAATTGAACCACAAGTGCAAAGGATTGGTAAATACAAAAGTGCAGGGGATCAACTTACACGCAAAACGATGTCTGAAGAAAA
upper sequence: AT1G73990.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S25_21V6.1 (Physcomitrella patens), 3'ss of exon 6
tctcgttatcaaaggtccttaatcggatttcaataattacaattttacaaagcagtaattggcacatttatcg--tgaactagttatttttcaaaa-atgt---agGTGTCTTCGAAAAAGTGGGGATTGAACCTCAAGTACAAAGGATTGGAAAATACAAAAGTGCTGGAGATCAGCTTTCTCGCAAAAGTATATCTGAGGAAAA
| ||| |||| | || | || || | | | || | | || || | || | | | | | || | | |||| | ||| ||| ||||| || || || || | |||| ||||| ||| | || |||||||||||||||||||||||||| ||||||||||| ||| || |||| ||
----ttgatc--aggttcaatattgcatgacacttaatctaagtcttgaactcaatgatggagttctaccacaactcatctggatgttttatgtgacgtgttccagGGGTCTTGGAGAAGGTAGGTGTGCAACCCCAAGTGCAACGTATAGGAAAATACAAAAGTGCTGGAGATCAACTTTCTCGCAAGGATATGTCAGAGGCCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacaaagcagtaattggcacatttatcgtgaactagttatttttcaaaaatgtagGTGTCTTCGAAAAAGTGGGGATTGAACCTCAAGTACAAAGGATTGGAAAATACAAAAGTGCTGGAGATCAGCTTTCTCGCAAAAGTATATCTGAGGAAAA
tttttca CT-rich tract
aactagttatttttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctcgttatcaaaggtccttaatcggatttcaataattacaattttacaaagcagtaattggcacatttatcgtgaactagttatttttcaaaaatgtagGTGTCTTCGAAAAAGTGGGGATTGAACCTCAAGTACAAAGGATTGGAAAATACAAAAGTGCTGGAGATCAGCTTTCTCGCAAAAGTATATCTGAGGAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - tatcaaa
- - - - - - - - - - - - - - - - - - - - - - - -caaagca