Sequence
atgc intronic sequence ATGC exonic sequence...tttacattgatcttcggatcttaagatcctctgtgagattatttctgaacatgaaaaaatggttttgagtctaaaaccgattggtcttttgatgtgacagGAATTCAACATTGAGAAATTGCAGCTTGTTGAAGCAGAGAAGAAGAAGATTAGACAAGAGTATGAGAAGAAGGAGAAACAGGTCGATGTCAGAAAGAAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G64200.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G64200.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G030167_T01 (Zea mays), 3'ss of exon 1
tttacattgatcttcggatcttaagatcctctgtgagattatttctgaacatgaaaaaatggttttgagtctaaaaccgattggtcttttgatg-tgacagGAATTCAACATTGAGAAATTGCAGCTTGTTGAAGCAGAGAAGAAGAAGATTAGACAAGAGTATGAGAAGAAGGAGAAACAGGTCGATGTCAGAAAGAAGA
| |||||| | | | || | | | | | || ||| | | || ||| ||| | | ||| | | |||||||||||||||||||| ||||||||||||||||| ||||| |||||||| || ||||||||||| || ||||| ||||| || || | ||||| |
-gtgatttgatcagacagtttcatatctctttttatgtgtgtacttgtcaatgcccttttttctatgcgtcctcaacttttacttgtttaaaaacttgcagGAATTCAACATTGAGAAGTTGCAGCTTGTTGAAGCTGAGAAAAAGAAGATCAGGCAAGAGTATGAACGCAAAGAGAAGCAGGTTGAAGTACGCAAGAAAA
upper sequence: AT1G64200.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G070360_T01 (Zea mays), 3'ss of exon 1
tttacattgatcttcggatcttaagatcctctgtgag--attatttctgaacatgaaaaaatg-gttttgagtctaaaaccgattggtcttttgatgtgacagGAATTCAACATTGAGAAATTGCAGCTTGTTGAAGCAGAGAAGAAGAAGATTAGACAAGAGTATGAGAAGAAGGAGAAACAGGTCGATGTCAGAAAGAAGA
| | || | | |||| | | |||| || || ||| ||| ||| || | | | | || || || | | | ||||||||||||||||||||| |||||||||||||||| ||||| ||||||||||||||||||||||| || ||||| ||||| || || | ||||| |
-tcggacagacaatttca-cttatttttttatgtgcatacttgttaatgaccatttttctatgtgtcctcaattttaatttattttgtttaaaaactt-acagGAATTCAACATTGAGAAGCTGCAGCTTGTTGAAGCTGAGAAAAAGAAGATTAGACAAGAGTATGAACGCAAAGAGAAGCAGGTTGAAGTACGGAAGAAAA
upper sequence: AT1G64200.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv02s0025g01000.t01 (Vitis vinifera), 3'ss of exon 1
tttacattgatcttcggatcttaagatcctctgtgagattatttctgaacatgaaaaaatg-gttttgagtctaaaaccgattggtcttttgatg----tgacagGAATTCAACATTGAGAAATTGCAGCTTGTTGAAGCAGAGAAGAAGAAGATTAGACAAGAGTATGAGAAGAAGGAGAAACAGGTCGATGTCAGAAAGAAGA
| || | || ||| | | ||||| | | ||| | | ||| | || | | | ||| ||| | || | | ||||||||||||||||||| ||||||||||||||||| |||||||||||||| ||||| || |||||| || ||||| || || ||| | | ||||| |
----ttgtagtcgattaagctgtagagtttggatcagattgatacataacgtatatggatgtggatttgttatggtattgat-ggtttagtggcggtttttgtagGAATTCAACATTGAGAAGTTGCAGCTTGTTGAAGCGGAGAAGAAGAAGATCAGACAGGAATATGAGCGAAAAGAGAAGCAAGTTGATATTCGGAAGAAAA
upper sequence: AT1G64200.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S269_15V6.1 (Physcomitrella patens), 3'ss of exon 1
tttacattgatc-ttcggatcttaaga-tcctctgtgagattatttctgaacatgaaaaaatggttttgagtctaaaaccgattggtcttttgatgtg-acagGAATTCAACATTGAGAAATTGCAGCTTGTTGAAGCAGAGAAGAAGAAGATTAGACAAGAGTATGAGAAGAAGGAGAAACAGGTCGATGTCAGAAAGAAGA
| |||||| ||| | | |||| || || || || | | || | | | | | | |||| ||| | | | |||||||||||||||||||| || ||| |||| ||||| || |||||||| ||| | || |||| |||| |||||||| || || || || | || |
--tcaattgatgattccgttggtaaggctcttccatgttatcaactgtgca-acacgtgtcttatatcggaattaaatgttgttgaggggtggttcaacgcagGAATTCAACATTGAGAAGTTACAGATTGTAGAAGCTGAAAAGAAGAAAATTCGGCAGGAGTTTGAGCGTAAGGAGAAGCAAGTGGAAGTTCGCCGTAAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaacatgaaaaaatggttttgagtctaaaaccgattggtcttttgatgtgacagGAATTCAACATTGAGAAATTGCAGCTTGTTGAAGCAGAGAAGAAGAAGATTAGACAAGAGTATGAGAAGAAGGAGAAACAGGTCGATGTCAGAAAGAAGA
tcttttg CT-rich tract
atgaaaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttacattgatcttcggatcttaagatcctctgtgagattatttctgaacatgaaaaaatggttttgagtctaaaaccgattggtcttttgatgtgacagGAATTCAACATTGAGAAATTGCAGCTTGTTGAAGCAGAGAAGAAGAAGATTAGACAAGAGTATGAGAAGAAGGAGAAACAGGTCGATGTCAGAAAGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - -cctctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - gaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctaaaac