Sequence
atgc intronic sequence ATGC exonic sequencegttagtcgacgcatctaaatctcacgtgatttcttcttagagattgaatataattttcttgtctaattaggacctctatgatttggtaaaaaccttggactttgttctatgtagGTCATTAATCTTTATATGGTATTGCTGAAAGAAAGGGAAGCTAGAGAACCAAAGAAGTTTCTTAAATGTCATTTTTTCAATACATTTTTCTTCACTAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G06910.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G06910.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G03010.2 (Glycine max), 3'ss of exon 3
-----------------gttagtcgacgcatctaaatctcacgtgatttcttcttagagattga-atataattttcttgtctaattaggacctctatgatttgg----taaaaaccttggactttgttctatgtagGTCATTAATCTTTATATGGTATTGCTGAAAGAAAGGGAAGCTAGAGAACCAAAGAAGTTTCTTAAATGTCATTTTTTCAATACATTTTTCTTCACTAAG
|| | | | || | | | | ||| |||| | || | | | || | | | || | | |||| || ||| | || |||| || ||| | || | | |||||||||||| ||||| ||||||||| ||||||||| || ||||||||||||||||| ||||||| || |||
gttaaacttgttcgcttattgtttgtttaacctttgttgaatgctgtggaagagaagaagttgatacctagctataatcgtggtttgaaattgttgcactgtgaaatccagtgatcttgtaccttgcctt-tgcagGTAATAAATATGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAACCACTGAAGTTTCTGAACTGTCATTTTTTCAATACCTTTTTCTACAAAAAG
upper sequence: AT3G06910.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G15890.1 (Glycine max), 3'ss of exon 4
-------------------gttagtcgacgcatctaaatctcacgtgatttctt--cttagagattgaatataattttcttgtctaattaggacctctatgatttggtaa-aaaccttggactttgttctatgtagGTCATTAATCTTTATATGGTATTGCTGAAAGAAAGGGAAGCTAGAGAACCAAAGAAGTTTCTTAAATGTCATTTTTTCAATACATTTTTCTTCACTAAG
||||| || | | | | | || | |||| | | | || | || | || | | ||| || | | | || || || | | || |||| || ||| | || ||| |||||| || || ||||| ||||||||| ||| ||||| |||||||||||||||||||| ||||||| || |||
gtaaacttgtttgctgattattagtttacccctttgttgttgagttgctgaagaaatttagtacctaactgtatcatgatttgacatttttacaccttgaaattcagtgatggatcatgtacctt-tattgtgcagGTTATAAATTTGTACCTGGAATTGCTTAAGGAGAGGGAGCAAAGAGAACCACTGAAATTTCTGAAATGTCATTTTTTCAATACCTTTTTCTACAAAAAG
upper sequence: AT3G06910.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G37640.4 (Glycine max), 3'ss of exon 3
gttagtcgacgcatctaaatctcacgtgatttcttcttagagattga--atataattttcttgtctaattaggacc----tctatgatt------tggtaaaaaccttggactttgt------tctatgtagGTCATTAATCTTTATATGGTATTGCTGAAAGAAAGGGAAGCTAGAGAACCAAAGAAGTTTCTTAAATGTCATTTTTTCAATACATTTTTCTTCACTAAG
|||| || | | | | | | | | |||| | || || | ||| || | | | | ||| || ||| || || || | || || |||| || ||| | || | | |||||||||||| ||||| ||||| ||| |||||||||| || ||||||||||||| ||| ||||||| || | |
gttaccttgtttgcttattgtttatttaacctttgttgaattgttgaggaagaaaagttgatacctagctataatcatggtttgaaattgttgcaccgtgaaatccagtgatcttataccttacctttgcagGTAATAAATGTGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAGCCACAGAAGTTTCTGAACTGTCATTTTTTCAGTACCTTTTTCTACAAGAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtctaattaggacctctatgatttggtaaaaaccttggactttgttctatgtagGTCATTAATCTTTATATGGTATTGCTGAAAGAAAGGGAAGCTAGAGAACCAAAGAAGTTTCTTAAATGTCATTTTTTCAATACATTTTTCTTCACTAAG
gtctaat putative branch site (score: 3)
ctttgttct putative PPT
tatgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtcgacgcatctaaatctcacgtgatttcttcttagagattgaatataattttcttgtctaattaggacctctatgatttggtaaaaaccttggactttgttctatgtagGTCATTAATCTTTATATGGTATTGCTGAAAGAAAGGGAAGCTAGAGAACCAAAGAAGTTTCTTAAATGTCATTTTTTCAATACATTTTTCTTCACTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT