Sequence
atgc intronic sequence ATGC exonic sequencegtaacagtatgatcattttatccattagtttcaaggcattccttaataactttcctctattttcttagAGGTATATGCTGCAAGAGAGAAGAATGGGATTTATATTCCAAAAGACCGCTACATTCAAGAAGAGGCTGAGAAAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G45850.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G45850.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os05g02670.3 (Oryza sativa), 3'ss of exon 8
----------------------gtaacagtat-gatcattttatc--cattagtttcaaggcattccttaataac-tttcctctattttcttagAGGTATATGCTGCAAGAGAGAAGAATGGGATTTATATTCCAAAAGACCGCTACATTCAAGAAGAGGCTGAGAAAAAG
| | | || |||| | | | | | | | | || | | | |||| ||| | | |||||| | ||||||||||||||||||||| || || ||||||| ||| |||||| | ||||| || || |||||||||
gtttgtcttcatgattattattattcttttgtagagcattgaagcggtaggaatcatacagtgtgtattcaccccgtctcctttatgtcttcagAGGTGTTTGCTGCAAGAGAGAAGAATGGTATATACATTCCAAGAGAACGCTACCTCCAAGAGGAAGCCGAGAAAAAG
upper sequence: AT3G45850.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G024576_T01 (Zea mays), 3'ss of exon 7
---------gtaacagtatgatcattttatccattagtttcaaggcattccttaataac----tttcctctattttcttagAGGTATATGCTGCAAGAGAGAAGAATGGGATTTATATTCCAAAAGACCGCTACATTCAAGAAGAGGCTGAGAAAAAG
| | || | | ||| || ||| ||| || | | | |||| ||| | |||||| | |||||||||||||||||| || || |||||||||| ||| |||||| | |||||||| ||||||||||||
gttgttcttgcttttttttgtaactcggaatcataagaatcaca-catcttgtattcatctggtctcctgtatatctccagAGGTGTTTGCTGCAAGAGAGAAGAACGGTATCTATATTCCAAGAGAGCGCTACCTCCAAGAAGAAGCTGAGAAAAAG
upper sequence: AT3G45850.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA15G04830.1 (Glycine max), 3'ss of exon 7
-----------------------------------------------------------------------------------------------gtaacagtatgatcattttatccattagtttcaagg--cattccttaa---taactttcctctattt---tcttagAGGTATATGCTGCAAGAGAGAAGAATGGGATTTATATTCCAAAAGACCGCTACATTCAAGAAGAGGCTGAGAAAAAG
|| || | ||| ||| || || | || || | || || || | ||||||| | |||||| ||||| |||||||||||||||||||| ||||| ||| || |||||| |||| ||||| || ||||| |||
gttgttgactgttcccatattaatgtagtttccgtccctttgttttttcctttgtgctctttttttctctaaatagagagaaaaatagtatgttggttacttctttctcactttctcacactccttgatggttcagtgctgaaatgtagtacttttctatttatgttacagAGGTGTATGCAGCAAGAGAGAAGAATGGGATCTATATACCACGTGATCGCTACCTTCATGAAGAAGCAGAGAAGAAG
upper sequence: AT3G45850.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA11G15520.2 (Glycine max), 3'ss of exon 7
---------------------------------------gtaacagtatgatcattttatccatta-gtttcaaggc---attccttaataacttt-cctctatt-ttcttagAGGTATATGCTGCAAGAGAGAAGAATGGGATTTATATTCCAAAAGACCGCTACATTCAAGAAGAGGCTGAGAAAAAG
| | || | ||||| | ||| |||| || | | | ||| ||| | | | | || |||||| ||||||||||||||||| ||||| |||||||| || || || || |||| ||||| || |||||||||
gttgtttaatgcttttgtattctaaaagaaaatagcaccatgttaata-aactatttttccttttacagttcagtgctggaatgttgaatttttttacgtatgtggtttgcagAGGTGTATGCTGCAAGAGAGAAAAATGGAATTTATATACCGCGGGATCGTTATCTTCATGAAGAAGCAGAGAAAAAG
upper sequence: AT3G45850.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA12G07910.1 (Glycine max), 3'ss of exon 7
---------------------------------------------------------------------------------------------gtaacagtatgatcattttatccatta-gtttcaaggc---attccttaataactttcc-tctattttct-tagAGGTATATGCTGCAAGAGAGAAGAATGGGATTTATATTCCAAAAGACCGCTACATTCAAGAAGAGGCTGAGAAAAAG
| | || | ||||| | | | |||| || | | | ||| |||||| | | | | | |||||| ||||||||||||||||| ||||| |||||||| || || || || |||| ||||| | ||||| |||
gttgttcactgtttacatatttgtaaaatagtttctgttagtcacttcgcattttccctctttcagttttctctaaacaaagaaaatagcaccatgctaata-aactatttttcctttcacagttcagtgctgaaatgttgaatttctttccatgtgtggtttgcagAGGTGTATGCTGCAAGAGAGAAAAATGGAATTTATATACCGCGGGATCGTTATCTTCATGAAGAAGGGGAGAAGAAG
upper sequence: AT3G45850.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv06s0004g03810.t01 (Vitis vinifera), 3'ss of exon 8
---------------------------------------------------gtaacagtatgatcattttatccattagtttcaaggc----attccttaataactt-----tcctctattttcttagAGGTATATGCTGCAAGAGAGAAGAATGGGATTTATATTCCAAAAGACCGCTACATTCAAGAAGAGGCTGAGAAAAAG
|| ||| || ||| | | ||| || | ||| || | ||| | | | ||| | |||||| ||||||||||||||||||||||| || ||||| || ||| || || || | ||||| || |||||||||
gttgttaatgctttttatatataatcttatgcatggtcagatagatgaatcatatagttattattattagacaattgagtggtaaagagtaaattatgcaacatcttgatgtttttatctttaatcagAGGTCTATGCTGCAAGAGAGAAGAATGGTATCTATATACCTCGAGATCGTTATCTTAATGAAGAAGCAGAGAAAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cattttatccattagtttcaaggcattccttaataactttcctctattttcttagAGGTATATGCTGCAAGAGAGAAGAATGGGATTTATATTCCAAAAGACCGCTACATTCAAGAAGAGGCTGAGAAAAAG
taataac putative branch site (score: 1)
ctttcctctattttct CT-rich tract
ttaataacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacagtatgatcattttatccattagtttcaaggcattccttaataactttcctctattttcttagAGGTATATGCTGCAAGAGAGAAGAATGGGATTTATATTCCAAAAGACCGCTACATTCAAGAAGAGGCTGAGAAAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG