Sequence
atgc intronic sequence ATGC exonic sequence...gatctcattgcttattaatgcagaggaataattccctcttagagttttgtacttccctgtttcgctcaacggatccttattcaattttatatgcttacagGGGCTACAAGCGCTTTTTTCGAAGACTTATGCTGGAAACATCTGATTTTCTGAAGGATGATTGTCTGAAAATTAATTGCACCGTGGGAGTTGTGGTCTCA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G03740.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G03740.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G074323_T02 (Zea mays), 3'ss of exon 1
--gatctcattgcttattaatgcagaggaataattccctcttagagttttgtacttccctgtttcgctcaacggatccttat-tcaattttatatgcttacagGGGCTACAAGCGCTTTTTTCGAAGACTTATGCTGGAAACATCTGATTTTCTGAAGGATGATTGTCTGAAAATTAATTGCACCGTGGGAGTTGTGGTCTCA
| || || | | | | | | | | | | ||| | | | | || || || ||| || || | | || |||||| ||||| || || ||||| || | || ||| ||| || | ||| || ||||||||||||||||| |||||||| ||||||||||| || |||
aatgtttctttacatgtggaacctgtattgtgggaatcatt---gctcttgcaataactggcctctgataattgaattttacgtctatccttctttgtttcagGGGTTACAAACGATTCTTTCGGCGAACTGCCCTTGAATTATCAGACTATCTCAAAGATGATTGTCTGAAAATAAATTGCACTGTGGGAGTTGTAGTGTCA
upper sequence: AT3G03740.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv06s0009g01030.t01 (Vitis vinifera), 3'ss of exon 1
-gatctcattgc-ttattaatgcagagg--aataattccctcttagagttttgtacttccctgtttcgctcaacggatccttattcaattttatatgcttacagGGGCTACAAGCGCTTTTTTCGAAGACTTATGCTGGAAACATCTGATTTTCTGAAGGATGATTGTCTGAAAATTAATTGCACCGTGGGAGTTGTGGTCTCA
|| | ||| ||| ||| || |||| | |||| || || | | | | | | ||| | | || ||| | ||||| |||||||||||||| || || | |||| |||||||| || || || ||||||||||| ||||||| ||||| || || ||||||||||| |||
atatgtttttgggttagaaattggatggttgataactatttcttcacattgcataatcatttacaagatttttggtttgttcatttattcttttattc----agGGGATACAAGCGCTTTTTCAGACGAGCTTTGCTTGAAACATCAGACTTCCTCAAGGATGATTGCTTGAAAATCAATTGTACTGTTGGAGTTGTGGTTTCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgtacttccctgtttcgctcaacggatccttattcaattttatatgcttacagGGGCTACAAGCGCTTTTTTCGAAGACTTATGCTGGAAACATCTGATTTTCTGAAGGATGATTGTCTGAAAATTAATTGCACCGTGGGAGTTGTGGTCTCA
ttattcaattttatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gatctcattgcttattaatgcagaggaataattccctcttagagttttgtacttccctgtttcgctcaacggatccttattcaattttatatgcttacagGGGCTACAAGCGCTTTTTTCGAAGACTTATGCTGGAAACATCTGATTTTCTGAAGGATGATTGTCTGAAAATTAATTGCACCGTGGGAGTTGTGGTCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - -agaggaa
- - - - - - - - - - - - - - - - - cctctta
- - - - - - - - - - - - - - - - - - - - - -gttttgt