Sequence
atgc intronic sequence ATGC exonic sequencegttcagtttttgatcttttacatgattcaaagttggttactttcgaaatttgcaatgaatggttatattgagatttgtttgtaatttgtggcttttgagcagGAAGTTGAAATAAATCTAATAATTACAGATTACTGTATGCCTGGCATGACTGGTTATGATTTGCTCAAGAAAGTTAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G41310.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G41310.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G31320.2 (Glycine max), 3'ss of exon 2
--------------------------------------------------------gttcagtttttgatcttttacatg-attcaaagttggttactttcgaaatttgcaatgaatggtt-----atattgagatttgtttgtaatttgtggcttttgagcagGAAGTTGAAATAAATCTAATAATTACAGATTACTGTATGCCTGGCATGACTGGTTATGATTTGCTCAAGAAAGTTAAG
|| || | | || | || |||| ||| || | | | | | || | | || || ||||||| ||| |||| || | || | |||| || || | ||||| | || |||||||||||||||||||||||||| || ||||| ||||| |||||| | |||
gtatggtgtgtttttttttgttagatgcataaaggtgtttttagttttaaaattttaaccaacttgttgtgttgtgtttgtgttcagtgtttatttttggccacagat-cagtttctttttctgggattctgagattgtttttggatttttgtgtcttta-tagGAGGTGGAGGTGAATCTTGTTATAACAGATTACTGTATGCCTGGCATGACAGGCTATGACTTGCTTAAGAAAATCAAG
upper sequence: AT2G41310.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G28570.1 (Glycine max), 3'ss of exon 2
------------------------------------------------------------------gttcagtttttgatctttta--catgattcaaagttggttactttcgaaatttgcaatgaatggttatattgagatttgtttgtaatttgtggcttttgagcagGAAGTTGAAATAAATCTAATAATTACAGATTACTGTATGCCTGGCATGACTGGTTATGATTTGCTCAAGAAAGTTAAG
|| || | | || | || || | |||| || | || | | || ||||||| |||| | || | | | | |||| || || | ||||| | || |||||||||||||||||||||||||| || ||||| ||||| |||||| | |||
gtatagtgtgtttttttggttagaatgcataaaaggtgttttttttttttgtaatttaaaaattttaaccaacttgttgtgttgtgttcagtgtttatttttggccacagatcagtttctttttctgggatt---ctgagatt-gtttttggctttttgtgtctttatagGAGGTGGAGGTGAATCTTGTTATAACAGATTACTGTATGCCTGGCATGACAGGCTATGACTTGCTTAAGAAAATCAAG
upper sequence: AT2G41310.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0007g05390.t01 (Vitis vinifera), 3'ss of exon 2
--------------------------------gttcag---tttttgatcttttacatga-----ttcaaagttggttactttcgaaatttgcaatgaatggttatattgagatttgtttgtaatttgtggcttt-tgag----cagGAAGTTGAAATAAATCTAATAATTACAGATTACTGTATGCCTGGCATGACTGGTTATGATTTGCTCAAGAAAGTTAAG
| |||| | | |||||| | | | | || ||| |||| | | | | | ||| ||| | | ||| | |||| ||| |||||||| || | ||||| |||||||| || |||||||||||||| ||||| || |||||||| ||||| ||| | |||
gtatgattcttcttcttttttccattgtcaagggtcaggaatctcaaatctttcttgaggatttccttacattttccctttttttttatttttttttattattctttccgagttttctgaatcttttttcactttgtgaatttacagGAAGTGGAGGTGAATCTTATAATTACTGACTACTGTATGCCTGGAATGACAGGCTATGATTTACTCAAAAAAATCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttgcaatgaatggttatattgagatttgtttgtaatttgtggcttttgagcagGAAGTTGAAATAAATCTAATAATTACAGATTACTGTATGCCTGGCATGACTGGTTATGATTTGCTCAAGAAAGTTAAG
ctttt CT-rich tract
atttgtttgtaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcagtttttgatcttttacatgattcaaagttggttactttcgaaatttgcaatgaatggttatattgagatttgtttgtaatttgtggcttttgagcagGAAGTTGAAATAAATCTAATAATTACAGATTACTGTATGCCTGGCATGACTGGTTATGATTTGCTCAAGAAAGTTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA