Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttctcggtttttcgttttcctgtccgttagtttctgacatcagtctatataattcatctcattctccttgggaatttgcagAGAAACTATCGATTCTTCTTCATGTTTGTCTTCTCCACGACTCTTCTCTGTGTATATGTGTTCGCCTTTTGTTGTGTCTACATAAAGAAGATCAAAGAGT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G41060.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G41060.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA16G26140.2 (Glycine max), 3'ss of exon 3
-------gtaagtttctcggtttttcgttttcctgtccgttagtttctg-acatcagtct---atataattcatctcattctccttgggaattt---gcagAGAAACTATCGATTCTTCTTCATGTTTGTCTTCTCCACGACTCTTCTCTGTGTATATGTGTTCGCCTTTTGTTGTGTCTACATAAAGAAGATCAAAGAGT
|| ||||| | || | ||| | || ||| || | | ||| ||| || | || |||| | | | | | | |||| | || ||||| ||||||||||||||||||||||| || || || || ||| ||||||| ||||| |||||||| ||||| || | | || | |||
attgtatatatatttctggtttggtgacttttcagtt-attatttgatacatgtcactcttgaatgttatgtatctgaatgtgtgcacaattgttatgcagCGTAATTATCGCTTCTTCTTCATGTTTGTCTTCTCAACTACACTACTTTGTATATATGTTTTCGCATTTTGTTGGGTCTATATTAGAAGAATTATGGAGG
upper sequence: AT5G41060.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G07190.1 (Glycine max), 3'ss of exon 3
--------gtaagtttctcggtttttcgttttcctgtccgttagtttctg-acatcagtct---atataattcatctca-ttctccttgggaatt-tgcagAGAAACTATCGATTCTTCTTCATGTTTGTCTTCTCCACGACTCTTCTCTGTGTATATGTGTTCGCCTTTTGTTGTGTCTACATAAAGAAGATCAAAGAGT
|| ||||| | || | ||| | || ||| ||| | | ||| ||| || | || |||| | || | | || ||||| | || ||||| ||||||||||||||||||||||| || || || || ||| ||||||| ||||| |||||||| ||||| || | | || | |||
aattgtatatatatttctggtttggtgacttttcagtt-attattttatacatgtcattcttgaatgttatgtatctgaattgtgcacaattgttatgcagCGTAATTATCGCTTCTTCTTCATGTTTGTCTTCTCAACTACACTACTTTGTATATATGTTTTCGCATTTTGTTGGGTCTATATTAGAAGAATTATGGAGG
upper sequence: AT5G41060.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA19G27160.1 (Glycine max), 3'ss of exon 3
------gtaagtttctcggtttttcgttttcctgtccgttagtttctgacatc----agtctatataattcatctcattctccttgggaattt-----gcagAGAAACTATCGATTCTTCTTCATGTTTGTCTTCTCCACGACTCTTCTCTGTGTATATGTGTTCGCCTTTTGTTGTGTCTACATAAAGAAGATCAAAGAGT
| || |||| |||| || || || || | | || |||| | | | || || |||| | | | | | ||||| |||| | || ||||| ||||||||||||||||||||||| || || || || ||| ||||||| || || ||||| || |||||||| | || | | |
aatggaggaaaattct--gtttacttttcatctatcatttgctatgtgccatccttgaatatgcattatgcatcctaattgcttggataattttttatgcagCGTAATTATCGGTTCTTCTTCATGTTTGTCTTCTCAACTACGCTACTATGTATATATGTTTTTGCATTTTGCTGGGTCTACATTGTAAGAATTATGGCAT
upper sequence: AT5G41060.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA16G05670.2 (Glycine max), 3'ss of exon 3
gtaagtttctcggtttttcgttttcctgtccgttagtttctgacatc-----------agtctatataattcatctcattctccttgggaattt----gcagAGAAACTATCGATTCTTCTTCATGTTTGTCTTCTCCACGACTCTTCTCTGTGTATATGTGTTCGCCTTTTGTTGTGTCTACATAAAGAAGATCAAAGAGT
| | ||| | ||| | |||| | | || |||| | || || | | || || || ||| | | | | |||| |||| | || ||||| ||||||||||||||||||||||| || || || || ||| ||||||| || || ||||| || ||||| || | || | | |
attattttttttgttct--gtttacttttcagttatcatttgctatgcattattattgaatatacattatgtatcctaattgcttgcacgatttttatgcagCGTAATTATCGGTTCTTCTTCATGTTTGTCTTCTCAACTACGCTACTGTGTATATATGTTTTTGCATTTTGCTGGGTCTATATTGTAAGAATTATGGCAT
upper sequence: AT5G41060.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv14s0068g01530.t01 (Vitis vinifera), 3'ss of exon 3
----------gtaagtttctcggtttt--tcgttttcctgtccgt--tagtttctgacatcagtctatataattcatctcattctccttgggaatttgcagAGAAACTATCGATTCTTCTTCATGTTTGTCTTCTCCACGACTCTTCTCTGTGTATATGTGTTCGCCTTTTGTTGTGTCTACATAAAGAAGATCAAAGAGT
|| | ||| | | | | | || || | | | || || | || | | | | | ||| | | | |||| | || |||||||| |||||||||||||||||||| ||||||||||| ||| |||||||||| | || || || ||||| || |||| ||||| || |
ttttccagttgtcatcttcaccaacatgataggaatgatgcatgtgcttgaatttgtgggcaatgcatgaatctgaacactttcacaattctgggt-gcagCGTAATTATCGATTTTTCTTCATGTTTGTCTTCTCGACGACTCTTCTTTGTATATATGTGTTTGGGTTCTGCTGGGTCTATATTAAGAGGATCATGGATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttagtttctgacatcagtctatataattcatctcattctccttgggaatttgcagAGAAACTATCGATTCTTCTTCATGTTTGTCTTCTCCACGACTCTTCTCTGTGTATATGTGTTCGCCTTTTGTTGTGTCTACATAAAGAAGATCAAAGAGT
ttctgac putative branch site (score: 2)
tctatataattcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttctcggtttttcgttttcctgtccgttagtttctgacatcagtctatataattcatctcattctccttgggaatttgcagAGAAACTATCGATTCTTCTTCATGTTTGTCTTCTCCACGACTCTTCTCTGTGTATATGTGTTCGCCTTTTGTTGTGTCTACATAAAGAAGATCAAAGAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA