Sequence
atgc intronic sequence ATGC exonic sequence...tgttggcttttcttcttcccctaaattcaagcaacatcgtttcagttcttcaatttgaatttcgatatttatgatagcctctctgtattctgatgtccagGGTTTCAGAAAAGTTGATCCTGACCGATGGGAATTTGCAAATGAAGGATTTCTTAGAGGCCGAAAACAACTACTGAAGAGTATTGTCAGGAGAAAACCTT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G16820.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G16820.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os03g63750.1 (Oryza sativa), 3'ss of exon 1
tgttggcttttcttcttcccctaaattcaagcaacat-cgtttcagttcttcaatttgaatttcgatatttatgatagcctc-tctgtattctgatgtccagGGTTTCAGAAAAGTTGATCCTGACCGATGGGAATTTGCAAATGAAGGATTTCTTAGAGGCCGAAAACAACTACTGAAGAGTATTGTCAGGAGAAAACCTT
| | | | || | | | | | | | | | | || | || | | | ||| | || || ||| ||||| || || ||||||||||| || | ||||| |||||||| ||||| ||||||||||| | ||| || |||||||||| || ||| || |||||
--atcatataacactcagtcagaagtacttgtaccgggcagatacactgtgccatgtacgttagccggcctctaacgatctcattggtgcacttatgagcagGGATTTAGGAAAGTTGATCCAGATAGGTGGGAGTTTGCAAACGAAGGTTTTCTTAGAGGACAAAAGCATCTACTGAAGACCATCAACAGAAGGAAACCAA
upper sequence: AT5G16820.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G384339_T02 (Zea mays), 3'ss of exon 2
---tgttggcttttcttcttcccctaaattcaagcaacatcgtttcagttcttca-atttgaatttcgatatttatgatagcctctctgtattctgatgtccagGGTTTCAGAAAAGTTGATCCTGACCGATGGGAATTTGCAAATGAAGGATTTCTTAGAGGCCGAAAACAACTACTGAAGAGTATTGTCAGGAGAAAACCTT
| | ||| || | | | || | | || ||| | | | || ||| || | | ||| | || || |||| | |||||| || ||||| |||||||| ||| ||||||||||||||||||| || ||||| ||||| | |||||| || ||||||| ||| ||| || ||||| |
ccttaatttgatttgcactcagctgacaatcgggagagattattttctcagctaacaattatattgcgcc-ctaacgatctcatcggtgccttctta---ccagGGGTTTAGAAAGGTTGATCCAGACAGATGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAAAAACATCTGCTGAAGACTATCAACAGAAGGAAACCAT
upper sequence: AT5G16820.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G115456_T01 (Zea mays), 3'ss of exon 1
---tgt-tggcttttcttcttcccctaaattcaag-caacatcgtttcagttcttcaatttgaatttcgatatttatgatagcctctctgtattctgatgtccagGGTTTCAGAAAAGTTGATCCTGACCGATGGGAATTTGCAAATGAAGGATTTCTTAGAGGCCGAAAACAACTACTGAAGAGTATTGTCAGGAGAAAACCTT
| || | ||| | || | ||| || | |||| |||||| ||| | | | | ||| | ||| || || | | |||||| || ||||| |||||||| ||| ||||||||||||||||||| || ||||| ||||| | || || || ||||||| ||| ||| || ||||| |
tcacatatgatctgcactctactggcaattggaagatgctattttctcagcaaa-caatttatattgc-accctaacgatgtcatctgtgccttttta---ccagGGGTTTAGAAAGGTTGATCCAGACAGATGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAGAAGCATCTGCTGAAGACTATCAACAGAAGGAAACCAT
upper sequence: AT5G16820.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G01190.1 (Glycine max), 3'ss of exon 1
----tgttggcttttcttcttcccctaaattcaagcaacatcgttt---cagttcttcaatttgaatttcgatatttatgatagcctctctgtattctgatgtccagGGTTTCAGAAAAGTTGATCCTGACCGATGGGAATTTGCAAATGAAGGATTTCTTAGAGGCCGAAAACAACTACTGAAGAGTATTGTCAGGAGAAAACCTT
| || || || | | | || |||||| || || |||||| |||| || || || || || | | || ||| |||||||||||||| ||||| || || ||||||||||||||||||||||||||| | ||||| ||||||||| | || ||||| ||| | ||| ||
gcattattagcattacatttagtttta---tcaagctggattagttgtacagttcacacatttttcttctcttaatt-tgttactccttttga---ttgacaaacagGGTTTCAGAAAGGTTGACCCAGATCGATGGGAATTTGCAAATGAAGGATTTTTAAGAGGTGAAAAACAACTTTTAAAAAGTATCAGTAGGCGGAAATCTG
upper sequence: AT5G16820.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G44330.1 (Glycine max), 3'ss of exon 1
----tgttggcttttcttcttcccctaaattcaagcaacatcgttt---cagttcttcaatttgaatttcgatatttatgatagcctctctgtattctgatgtccagGGTTTCAGAAAAGTTGATCCTGACCGATGGGAATTTGCAAATGAAGGATTTCTTAGAGGCCGAAAACAACTACTGAAGAGTATTGTCAGGAGAAAACCTT
|| | || | | | || |||||| || || || ||| |||| || || | || || || | || ||| |||||||| ||||| ||||| || || ||||||||||||||||||||||||||| | ||||| ||||||||| | || ||||| ||| | ||| ||
gcataattaacattacatgtagtttta---tcaagctggattagttgtacaattcacacatttctcttctcttaatc-tgttattctttttga---ttgacaagcagGGTTTTAGAAAGGTTGACCCAGATCGATGGGAATTTGCAAATGAAGGATTTTTAAGAGGTGAAAAACAACTTTTAAAAAGTATCAGTAGGCGGAAATCTG
upper sequence: AT5G16820.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv16s0039g01840.t01 (Vitis vinifera), 3'ss of exon 1
tgttggcttttcttcttcccctaaattcaagcaacatcgtttcagttcttcaatttgaatttcgatatttatga-tagcctctctgt--attctgat-gtccagGGTTTCAGAAAAGTTGATCCTGACCGATGGGAATTTGCAAATGAAGGATTTCTTAGAGGCCGAAAACAACTACTGAAGAGTATTGTCAGGAGAAAACCTT
| ||| || | | | | | | || || | | || || || | | | | | ||| | | | | | | | || ||||| || || || || ||||| ||||| ||||||||||||||||| || ||||| ||||| | |||||| || ||||||||||| ||| ||||| |
-atgcgctattttgttaattgt---cttgaatattatttatttgtgtttgtgatcaaaacttagtttctaaggggtagtttttttcttcactttaatcaaacagGGATTTAGGAAGGTGGATCCAGACCGCTGGGAATTTGCAAATGAGGGTTTTCTAAGAGGTCAAAAACACCTTTTGAAGAGTATTAGTAGGCGAAAATCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttcaatttgaatttcgatatttatgatagcctctctgtattctgatgtccagGGTTTCAGAAAAGTTGATCCTGACCGATGGGAATTTGCAAATGAAGGATTTCTTAGAGGCCGAAAACAACTACTGAAGAGTATTGTCAGGAGAAAACCTT
ttctgat putative branch site (score: 3)
cctctctgtattct CT-rich tract
aatttgaatttcgata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgttggcttttcttcttcccctaaattcaagcaacatcgtttcagttcttcaatttgaatttcgatatttatgatagcctctctgtattctgatgtccagGGTTTCAGAAAAGTTGATCCTGACCGATGGGAATTTGCAAATGAAGGATTTCTTAGAGGCCGAAAACAACTACTGAAGAGTATTGTCAGGAGAAAACCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - -cttcttc
- - - - - - - - - ccctaaa
- - - - - - - - - - - - - -caagcaa