Sequence
atgc intronic sequence ATGC exonic sequencegtaagttggatatcaatcctcctaataaatcctttgaattgcttcagagttcatctcttttaacattatttcaatttctccttcagATCATTAAGTCAATTGCTCCGTCAATATATGGCCACGAAGATATCAAAACAGCTCTTGCTCTTGCTATGTTTGGTGGCCAAGAGAAAAATATCAAAGGGA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G44900.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G44900.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os11g29380.1 (Oryza sativa), 3'ss of exon 9
gtaagttggatatcaatcctcctaataaatcctttgaattgcttcaga---gttcatctcttttaac-attatttcaatttctcctt-cagATCATTAAGTCAATTGCTCCGTCAATATATGGCCACGAAGATATCAAAACAGCTCTTGCTCTTGCTATGTTTGGTGGCCAAGAGAAAAATATCAAAGGGA
||| | | |||||| ||| || |||| | || | | | ||| | || | | | | || | || ||||| | || |||||||| || || |||||||| || ||||||||||| || || |||| || ||||||||||| || |||||||| ||| |||| || |
----gtttgtgcttaatcct-----taagccccttgactcaattataataagctaatcagtattgtctgacaaatgacttattgtttacagATTGTCAAATCAATTGCACCATCCATATATGGTCATGAAGATATCAAGACTGCCATTGCACTAGCTATGTTTGGGGGGCAAGAGAAGAATGTCAAGGGAA
upper sequence: AT1G44900.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G139894_T01 (Zea mays), 3'ss of exon 9
gtaagttggatatcaatcctcctaataaatcctttgaattgcttcagagttcatctcttttaacattatttcaatttctccttcagATCATTAAGTCAATTGCTCCGTCAATATATGGCCACGAAGATATCAAAACAGCTCTTGCTCTTGCTATGTTTGGTGGCCAAGAGAAAAATATCAAAGGGA
||| | || | | |||| | | || || | | || | || | |||| | | || | | ||||| || || |||||||| || || || || || || ||||||||||| || || |||| ||||||||||||||||| |||||||| ||| | || || |
----gtttgttactcaactctttaatctcttgatgaaaatgtgtta-agctaatatacgctaacttaag--cacctaactcaacagATTATCAAATCAATTGCACCATCCATTTACGGGCATGAAGATATCAAGACTGCCATTGCACTTGCTATGTTTGGTGGACAAGAGAAGAATGTGAAGGGAA
upper sequence: AT1G44900.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv01s0150g00390.t01 (Vitis vinifera), 3'ss of exon 8
gtaagttggatatcaatcctcctaataaatcctttgaattgcttcagagttcatctcttttaacattatttcaatttctccttcagATCATTAAGTCAATTGCTCCGTCAATATATGGCCACGAAGATATCAAAACAGCTCTTGCTCTTGCTATGTTTGGTGGCCAAGAGAAAAATATCAAAGGGA
|| ||| || || | || | || || || | || ||| || | ||| || |||| | | ||||||| | ||||| ||||| || ||||| ||||||||||| ||||| ||||| || | |||||||| |||||||| |||||||| |||||| | ||||||
gtttgttacttagca-tgctttttatcaactctctctgttatatcatgattta-ctcacaaaagtttat---gactaaaatttcagATTGTCAAGTCCATTGCACCATCAATCTATGGCCACGAGGATATAAAAACTGCAATGGCTCTTGCAATGTTTGGAGGCCAAGAAAAAAATGTTGAAGGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttgaattgcttcagagttcatctcttttaacattatttcaatttctccttcagATCATTAAGTCAATTGCTCCGTCAATATATGGCCACGAAGATATCAAAACAGCTCTTGCTCTTGCTATGTTTGGTGGCCAAGAGAAAAATATCAAAGGGA
ttttaac putative branch site (score: 2)
tttcaatttctccttc putative PPT
tcttttaacattattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttggatatcaatcctcctaataaatcctttgaattgcttcagagttcatctcttttaacattatttcaatttctccttcagATCATTAAGTCAATTGCTCCGTCAATATATGGCCACGAAGATATCAAAACAGCTCTTGCTCTTGCTATGTTTGGTGGCCAAGAGAAAAATATCAAAGGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA