Sequence
atgc intronic sequence ATGC exonic sequence...ttgacttgttgtagagaaatgctaaaggttgaatctttaggcttagatcagtagttctttagtttcatgtgtgaagttttgaaagttcttttttgtgtagCGTTATGTAGCTTTGAAAGTTCAGAAGAGTGCTCAACATTATACAGAGGCAGCAATGGATGAGATAAAGATTTTGAAACAGATAGCTGAAGGTGACTCGG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G44850.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G44850.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os03g53720.2 (Oryza sativa), 3'ss of exon 1
-ttgacttgttgtagagaaatgctaaaggttgaatctttaggcttagatcagtagttctttagt-ttcatgtgtgaagttttgaaagttcttttttgtgtagCGTTATGTAGCTTTGAAAGTTCAGAAGAGTGCTCAACATTATACAGAGGCAGCAATGGATGAGATAAAGATTTTGAAACAGATAGCTGAAGGTGACTCGG
| | || | ||| | | || | ||| || || | || || ||| | |||| ||| | | | || || | ||||| || |||| || ||||||||||| || || || |||||||| || ||||||||||| ||||| ||||| ||||| || || ||||| | |
agtactgttttattcgttaatcccaccatcatcatacacgaaat-gtatctgttcttatataccctttgtgtttctgaatttgttggttatatat-atgcagAGATATGTGGCGCTGAAGGTGCAGAAGAGTGCACAGCACTACACAGAGGCGGCCATGGATGAGATCAAGATCTTGAAGCAGATTGCCGATGGTGATCCTG
upper sequence: AT3G44850.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA12G08900.1 (Glycine max), 3'ss of exon 1
ttgacttgttgtagagaaatgctaaaggttgaatctt--taggcttagatcagtagttctttagttt---catgtgtgaagttttgaaagttcttttttgt--gtagCGTTATGTAGCTTTGAAAGTTCAGAAGAGTGCTCAACATTATACAGAGGCAGCAATGGATGAGATAAAGATTTTGAAACAGATAGCTGAAGGTGACTCGG
| | | | | | | || | |||||| | | | ||||| || | | |||| | ||| |||| | ||| ||||||||| | ||| ||||||||||||| || || ||||| || || || |||||||| ||||||||| | ||||| |||||||| || ||| |||
-------aaaccaaacatccaccatgtttcacttgttactgtttttagattttaaactttgaagtttgtacacacttaataaagggaaaactttttcttgtttgcagCATTATGTAGCCCTTAAAATTCAGAAGAGTGCACAGCACTATACTGAAGCCGCGATGGATGAAATAAAGATTCTCAAACAAATAGCTGAGGGGGACCCGG
upper sequence: AT3G44850.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA12G30440.1 (Glycine max), 3'ss of exon 1
--ttgacttgttgtagagaaatgctaaaggttg--aatctttaggcttagatcagtagttctttagtttcatgtgtgaagttttgaaagttcttttttgtgtagCGTTATGTAGCTTTGAAAGTTCAGAAGAGTGCTCAACATTATACAGAGGCAGCAATGGATGAGATAAAGATTTTGAAACAGATAGCTGAAGGTGACTCGG
|| || | | | | | | || || | | || ||| ||||| | | || | |||| | ||| || ||| ||| | |||| ||||| || || ||| |||| ||||||||||| ||||| || || || ||||||||||| ||||||||| | ||||| || ||||| || || | |
gcccatgttatttttcattctttcaataccatgctaacgtacatgcggcaatctatagtt-tggaactttgttagtgatgctttaaattgtctgttt---gcagCGATATGTTGCCTTAAAAATTCAAAAGAGTGCTCAGCATTACACTGAAGCGGCAATGGATGAAATAAAGATTCTTAAACAAATTGCTGACGGGGATCCAG
upper sequence: AT3G44850.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA17G05480.1 (Glycine max), 3'ss of exon 1
--ttgacttgttgtagagaaatgctaaaggttg--aatctttaggcttagatcagtagttctttagtttcatgtgtgaagttttgaaagttcttttttgtgtagCGTTATGTAGCTTTGAAAGTTCAGAAGAGTGCTCAACATTATACAGAGGCAGCAATGGATGAGATAAAGATTTTGAAACAGATAGCTGAAGGTGACTCGG
| || || | | | | | ||| || | | || ||| ||||| | | || | |||| ||||| || | ||| | || |||| | ||| || || ||| |||| ||||||||||| ||||| || || || ||||||||||| ||||||||| | ||||| || ||||| || || | |
gcctatgttattcttcattcttttaataccttgctaacatacatgcggcaatctttagtt-tggaactttgttagtgatgttttaaa---ttgtttgtttgcagCGATTTGTTGCCTTAAAAATTCAAAAGAGTGCTCAGCATTACACTGAAGCGGCAATGGATGAAATAAAGATTCTTAAACAAATTGCTGACGGGGATCCAG
upper sequence: AT3G44850.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv06s0061g01050.t01 (Vitis vinifera), 3'ss of exon 1
ttgacttgttgtagagaaatgctaaaggttgaatctt-taggcttagatcagtagttctttagtt--tcatgtgtgaagttttgaaagttcttttttgtgtagCGTTATGTAGCTTTGAAAGTTCAGAAGAGTGCTCAACATTATACAGAGGCAGCAATGGATGAGATAAAGATTTTGAAACAGATAGCTGAAGGTGACTCGG
| || | | ||| || | || | || | || | | |||| | |||| | | || || | | || ||||| || || |||||||||||||| ||||||||| | |||||||| |||||||| ||||||||||||| || |||||||||| ||||| || ||| | |
---gttccttttttccatatgtcaagcactatattatgtatttccatatgtttccatttttaactgttcatcgttttgataatgcaaaaccctaattctgtagAAATACGTCGCTTTGAAAGTTCAAAAGAGTGCTAAGCATTATACTGAGGCAGCCATGGATGAGATAACCATACTGAAACAGATTGCTGAGGGAGACCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatcagtagttctttagtttcatgtgtgaagttttgaaagttcttttttgtgtagCGTTATGTAGCTTTGAAAGTTCAGAAGAGTGCTCAACATTATACAGAGGCAGCAATGGATGAGATAAAGATTTTGAAACAGATAGCTGAAGGTGACTCGG
ttcttttttgt CT-rich tract
ttctttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgacttgttgtagagaaatgctaaaggttgaatctttaggcttagatcagtagttctttagtttcatgtgtgaagttttgaaagttcttttttgtgtagCGTTATGTAGCTTTGAAAGTTCAGAAGAGTGCTCAACATTATACAGAGGCAGCAATGGATGAGATAAAGATTTTGAAACAGATAGCTGAAGGTGACTCGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - agagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttttga