Sequence
atgc intronic sequence ATGC exonic sequencegtaagttcccattgagctatcatcgttcctttttatttttgtttgttagctagatgtcttcttattcttaacttctgagcagGTGTTACACGAATTTTTGCAAGTGGAAGCTTTTGCTAAATTGAGCAATGCAATTGGAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G75850.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G75850.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os03g58700.1 (Oryza sativa), 3'ss of exon 9
gtaagttcccattgagctatcatcgttcctttttatttttgtttgttagctagatgtcttcttattcttaacttctgagcagGTGTTACACGAATTTTTGCAAGTGGAAGCTTTTGCTAAATTGAGCAATGCAATTGGAAAG
||||| | || | | | | | || | | | |||| | | ||| || | || | | || | ||||| || | ||||| |||||||| ||||||||||| || || |||||||| |||||||||
gtaagcactcactaaaccac--ttcatcatggtaaaatttgcgtat--acta------ttgacaatcatgaattgta--cagGTATTGCCAGAATTCTTGCAAGTTGAAGCTTTTGCAAAGTTCAGCAATGCTATTGGAAAG
upper sequence: AT1G75850.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM5G825524_T02 (Zea mays), 3'ss of exon 9
gtaagttcccattgagctatcatcgttcctttttatttttgtttgttagctagatgtcttcttattcttaacttctgagcagGTGTTACACGAATTTTTGCAAGTGGAAGCTTTTGCTAAATTGAGCAATGCAATTGGAAAG
| ||| || | | || || || || | || ||| ||| || | | || || |||||||||| || || |||||||| |||||||||||||| || || ||||| |||||||||
-----------gtaagcattcgttatatagcttgatcattcaaattttg-tatatg-cttgacataaatgaattatg--cagGTGTTACCAGAGTTCTTGCAAGTTGAAGCTTTTGCTAAGTTCAGTAATGCTATTGGAAAG
upper sequence: AT1G75850.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM5G844195_T02 (Zea mays), 3'ss of exon 10
gtaagttcccattgagctatcatcgttcctttttatttttgtttgtt--agctagatgtcttcttattcttaacttctgagcagGTGTTACACGAATTTTTGCAAGTGGAAGCTTTTGCTAAATTGAGCAATGCAATTGGAAAG
| | ||||||| | ||| | || | | | | | ||| | || | |||| |||| | || || |||||||| |||||||||||||| || || ||||| |||||||||
------------------gtaagtgttccttatatagcttgatcattcaaattttgtatatgcttgacataaatgaatatgcagCTGTTGCCAGAGTTCTTGCAAGTTGAAGCTTTTGCTAAGTTCAGTAATGCTATTGGAAAG
upper sequence: AT1G75850.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv18s0001g14680.t01 (Vitis vinifera), 3'ss of exon 9
gtaagttcccattgagctatcatcgttcctttttatttttgtttgttagctagatgtcttcttattcttaacttctgagcagGTGTTACACGAATTTTTGCAAGTGGAAGCTTTTGCTAAATTGAGCAATGCAATTGGAAAG
| || |||| | ||||| |||||| | | | | | || | | || | |||||| |||| || || ||||||| |||||||||||||||||||||| ||| ||||| |||
-----------gtaagttatccatatgatactttatg--ggtttgt-aattttaagcttcattgataatgtttttggtgcagGTATTACCTGACTTCCTGCAAGTAGAAGCTTTTGCTAAATTGAGCAGTGCCATTGGGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctttttatttttgtttgttagctagatgtcttcttattcttaacttctgagcagGTGTTACACGAATTTTTGCAAGTGGAAGCTTTTGCTAAATTGAGCAATGCAATTGGAAAG
tcttaac putative branch site (score: 2)
cttct CT-rich tract
ttatttttgtttgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttcccattgagctatcatcgttcctttttatttttgtttgttagctagatgtcttcttattcttaacttctgagcagGTGTTACACGAATTTTTGCAAGTGGAAGCTTTTGCTAAATTGAGCAATGCAATTGGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG