Sequence
atgc intronic sequence ATGC exonic sequencegtaggattcttttccccgtcctttgattcctctgcatcatccatctatcttgcttgaagttataataatattgtaatgacacacagGATGATGCAAGCAAAACTCCAGCTTCTGCGCGCCATAAACGTGGCTGCAACTGCAAGAAATCAAACTGTCTGAAGAAATACTGTGAATGCTATCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G14770.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G14770.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os07g07974.1 (Oryza sativa), 3'ss of exon 6
gtagg-attcttttccccgtcctttgattcctctgcatcatccatctatcttgcttgaagttataataatattgtaatgacacacagGATGATGCAAGCAAAACTCCAGCTTCTGCGCGCCATAAACGTGGCTGCAACTGCAAGAAATCAAACTGTCTGAAGAAATACTGTGAATGCTATCAG
||||| | ||| | | | || | | | ||| | || || || | | |||| | ||| | ||||| ||| | | ||| ||||||||||| || || ||||| | || ||||| |||||||| |||| |||||| ||||||||||||||||||||||||
gtaggcgctttttgctggatagtctgtactacttctagccctcatttccatt-tatgtggtgctga-aatacttcaataaattgcagGAAGATCCTAACAACACTCCAGCTTCAGCTCGACATAAGAGAGGATGCAATTGCAAGAAGTCAAGCTGTCTTAAGAAATACTGTGAATGCTATCAG
upper sequence: AT4G14770.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os03g43730.1 (Oryza sativa), 3'ss of exon 9
gtaggattcttttccccgtcctttgattcctctgcatcatccatctatcttgcttgaagttataataatattgtaatgacacacagGATGATGCAAGCAAAACTCCAGCTTCTGCGCGCCATAAACGTGGCTGCAACTGCAAGAAATCAAACTGTCTGAAGAAATACTGTGAATGCTATCAG
||| || |||| | |||| || | | |||| ||| | | | ||| | || | ||| || | ||| || | | |||||| ||||| | || |||||| | || ||||| ||||||| |||| | ||| ||||||||||||||||||||| ||||
gtaagagcacattccttttgcttt---tcttttctgtcat-----tattgctcataacgttct-------ttttcatggcata--gGAAGACTCTAATGCAACTCCTGCTTCATCTCGTCATAAAAGAGGTTGCAATTGCAAGAGATCATATTGTGTGAAGAAATACTGTGAATGCTTTCAG
upper sequence: AT4G14770.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G153754_T01 (Zea mays), 3'ss of exon 6
-------gtaggattcttttccccgtccttt-gattcctctgcatcatccatctatcttgcttgaagttataata-----atattgtaatgaca-cacagGATGATGCAAGCAAAACTCCAGCTTCTGCGCGCCATAAACGTGGCTGCAACTGCAAGAAATCAAACTGTCTGAAGAAATACTGTGAATGCTATCAG
|| | | ||| | | || ||| | | | | | || | | | | || | ||||| | | ||||| ||| | | ||| ||||| ||||| || || || || | || ||||| || ||||| |||| |||||| |||||||||||||||||||| |||
gtatggcgttgcgtacttctgttggagattgagatgtatgtacgtgtgttggccatttactcccagaccgtggtgcttacattctacaatgaaatcgcagGAAGATCCTAACAACACTCCGGCTTCGGCTCGTCACAAGAGAGGATGCAATTGTAAGAAGTCAAGCTGTCTCAAGAAATACTGTGAATGCTACCAG
upper sequence: AT4G14770.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G00920.1 (Glycine max), 3'ss of exon 8
gtaggattcttttccccgtcctttgattcctctgcatcatccatctatcttgcttgaagttataataatattgtaatgacacacagGATGATGCAAGCAAAACTCCAGCTTCTGCGCGCCATAAACGTGGCTGCAACTGCAAGAAATCAAACTGTCTGAAGAAATACTGTGAATGCTATCAG
|| || | | | | |||| || || | ||||| || || ||| | | |||| | | ||||||| ||| |||||||||||||| || || || ||| | || ||||||||||| ||||||| ||| || |||||||| |||||||| ||||||
gttagaaaataaactcgacttagtttttcccctaagcaattgaaacatctt--ttataggtatta-attattatctt--tttgtagGATGACCCAAATAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAACTGCAAAAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
upper sequence: AT4G14770.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G39080.1 (Glycine max), 3'ss of exon 12
----gtaggattcttttccccgtcctttgattcctctgcatcatccatctatcttgcttgaagttataataatattgtaatgacacacagGATGATGCAAGCAAAACTCCAGCTTCTGCGCGCCATAAACGTGGCTGCAACTGCAAGAAATCAAACTGTCTGAAGAAATACTGTGAATGCTATCAG
| | | | || | | ||| | || | | | | | || || || | ||| | | |||| | | | |||||||| | | ||||||||||||||| || || || ||| | || || || ||||||||||||| ||| || |||||||| |||||||| ||||||
gtcagcaaattaatatttaactttattttctcactttctaattttaaaccatttttttttcatatatta-attatttt--ttccttgcagGATGACCCTAACAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGTAATTGCAAGAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
upper sequence: AT4G14770.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G28740.2 (Glycine max), 3'ss of exon 4
-gtaggattcttttccccgtcctttgattcctctgcatcatccatctatcttgcttgaagttataataatattgtaatgacacacagGATGATGCAAGCAAAACTCCAGCTTCTGCGCGCCATAAACGTGGCTGCAACTGCAAGAAATCAAACTGTCTGAAGAAATACTGTGAATGCTATCAG
|| | | | | || || | || | || | | | || || |||| |||| | | | | |||||||| | |||||||||||| || || || || ||| | || || || ||||||||||||| ||| || |||||||| |||||||||||||||
gtcagcaaattaatatttaactttatttttcactttctaatttaa--accatgttttttcatatattaattcttttttt-cttgcagGATGACCTTAACAAAACTCCAGCCTCAGCACGACACAAAAGAGGATGTAATTGCAAGAAATCAAGCTGCCTAAAGAAATATTGTGAATGCTATCAG
upper sequence: AT4G14770.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G44670.2 (Glycine max), 3'ss of exon 6
gtaggattcttttccccgtcctttgattcctctgcatcatccatctatcttgcttgaagttataataatattgtaatgacacacagGATGATGCAAGCAAAACTCCAGCTTCTGCGCGCCATAAACGTGGCTGCAACTGCAAGAAATCAAACTGTCTGAAGAAATACTGTGAATGCTATCAG
|| || | | | ||| | || | | | | || |||| |||| | | |||||||| ||| ||||| |||||||| || || || || | || ||||||||||| ||||||| ||| || |||||||| |||||||| ||||||
gttagaaaataaacttgacttagtttttcacgtaagcaattgaaaccaccttttatgggtattaat--tattatctt--tttgcagGATGACCCAAATAAAACACCAGCTTCAGCACGACACAAGAGAGGATGCAACTGCAAAAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
upper sequence: AT4G14770.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv05s0020g03880.t01 (Vitis vinifera), 3'ss of exon 7
gtaggattcttttccccgtcctttgattcctctgcatcatccatctatcttgcttgaagttataataa-tattgtaatgacacacagGATGATGCAAGCAAAACTCCAGCTTCTGCGCGCCATAAACGTGGCTGCAACTGCAAGAAATCAAACTGTCTGAAGAAATACTGTGAATGCTATCAG
|| | | | | | | | || | | | |||| |||| | | ||| | || | | |||||||| | ||||||||||||||||| || || || ||| | || ||||||||||||||||||| || || |||||||| || ||||||||||||
gttaggacataattcttgccttgtg-----tttatacagaaaatctgaactgctagttaccctgttaagtgaggttttctcttgcagGATGAACCTAGCAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAACTGCAAGAAATCAAGTTGCCTAAAGAAATATTGCGAATGCTATCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgcatcatccatctatcttgcttgaagttataataatattgtaatgacacacagGATGATGCAAGCAAAACTCCAGCTTCTGCGCGCCATAAACGTGGCTGCAACTGCAAGAAATCAAACTGTCTGAAGAAATACTGTGAATGCTATCAG
ttgaagttataataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggattcttttccccgtcctttgattcctctgcatcatccatctatcttgcttgaagttataataatattgtaatgacacacagGATGATGCAAGCAAAACTCCAGCTTCTGCGCGCCATAAACGTGGCTGCAACTGCAAGAAATCAAACTGTCTGAAGAAATACTGTGAATGCTATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA