Sequence
atgc intronic sequence ATGC exonic sequencegtaaggctgtagtgataagcttccaagaatagtttgtggtaatggataactgattatgtgttgctccttgtaatttgtagGGGAAGGTAGGCCAGTTATGGACTGGGCAACACGTGTTAAGGTTGCTGCTGGTGCAGCTCGTGGAATAGCTTATCTTCATGAAGACT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv01s0011g02460.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os05g01040.1 (Oryza sativa), 3'ss of exon 2
------------gtaaggctgtagtgataagcttccaagaatagtttgtggtaatggataactgattatgtgttg---ctccttgtaatttgtagGGGAAGGTAGGCCAGTTATGGACTGGGCAACACGTGTTAAGGTTGCTGCTGGTGCAGCTCGTGGAATAGCTTATCTTCATGAAGACT
| ||| | || || ||| || || | | || | | |||| ||| | | |||||| ||| | || ||||| ||| | || ||| | | | ||||| ||||||| ||||| |||||||||||||| ||||| |||||||| |
gtatggtttaacctcttgctacattg-tacatggccatttcgttcttctgcaagtagaaactgaaacatgtattgaatcaacctgtaatc-acagGACAGGGGAGGCCTGTTCTAGATTGGTCGGCTAGGGTTAAAATTGCTGCAGGTGCTGCTCGTGGAATAGCGTATCTACATGAAGATT
upper sequence: Vv01s0011g02460.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA16G19520.1 (Glycine max), 3'ss of exon 3
--------------------------------------------------gtaaggctgt-agtga-taagcttccaagaatagtttgtggtaatggataactgattatgtgt------tgctccttgtaa-----tttgtagGGGAAGGTAGGCCAGTTATGGACTGGGCAACACGTGTTAAGGTTGCTGCTGGTGCAGCTCGTGGAATAGCTTATCTTCATGAAGACT
||| ||| ||||| | | | |||| | ||| || | |||||| | | |||| || || |||| |||||||||||||||||| |||||||| ||| ||||||||| |||| ||||| ||||| | |||||||||||||| ||||||||||
gtaaagctagttcagagggctagctgaatgattgtttcatgatattttgattaaatgtgtcagtgaatgtgttcaaaagagtgtattgctaacatttctctttgattaaatttaatctgtgctaactgaaagtgaatttgaagGGGAAGGTAGGCCAGTGCTGGACTGGACAAAACGTGTTAAAATTGCGGCTGGGGCAGCCAGAGGAATAGCTTATCTCCATGAAGACT
upper sequence: Vv01s0011g02460.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G14310.1 (Glycine max), 3'ss of exon 2
gtaaggctgt-----agtgataagcttccaagaatagtttgtggtaatggataactgattatgtgttgct--ccttgtaatttgtagGGGAAGGTAGGCCAGTTATGGACTGGGCAACACGTGTTAAGGTTGCTGCTGGTGCAGCTCGTGGAATAGCTTATCTTCATGAAGACT
|||| || |||||||| ||||| | | || || ||||| | | | || |||||||||| ||||||||| ||| || | || ||||||| |||||||| |||| ||||||||||| || ||| |||||||||| ||||||||||
gtaaaactacatctgagtgataatagattgttt-cagtttattttgattgact-ttgattgtat-taactgatattgtaatttgcagGGGAAGGCCAGCCTGTGCTAGAATGGGCAAACCGTGTTAAAATTGCAGCTGGTGCAGCCCGAGGACTAGCTTATCTCCATGAAGACT
upper sequence: Vv01s0011g02460.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G68690.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaaggctgtagtgataagcttccaaga--atagtttgtggtaatggataactgattatg--tgttgctccttgtaa---tttgtagGGGAAGGTAGGCCAGTTATGGACTGGGCAACACGTGTTAAGGTTGCTGCTGGTGCAGCTCGTGGAATAGCTTATCTTCATGAAGACT
|||| | || ||||||| | | ||| | || | | | | | || || | | | | | | || | | ||| | |||||||||||||||||||| |||| ||||| |||||||||||| ||||||||||||||||||| |
gtaaagaaaaagca-----tctccaagattacattttatatatatacacacaccactgggactgacactatctacatgtctcttaaacagGAGAAAAATCTGTTCTAGACTGGGCAACACGTGTTAAAATTGCGGCTGGGGCAGCTCGTGGACTAGCTTATCTTCATGAAGATT
upper sequence: Vv01s0011g02460.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G26150.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaaggctgtagtgataagcttccaagaatagtttgtggtaatggataactgattatgtgttgctccttgtaatttgtagGGGAAGGTAGGCCAGTTATGGACTGGGCAACACGTGTTAAGGTTGCTGCTGGTGCAGCTCGTGGAATAGCTTATCTTCATGAAGACT
||||| | | | || | | ||| | | || | | | |||| | || | | | ||| | ||| | || | | | |||||||||||||||||||| ||||||||||||| ||||||||| |||||||||| |||||||| |
gtaagtaag-atttctagacataaaagcacaaacc----caaaccacatttacttattactatctttccatggtctttagCCGCAGGAACTCCGGGTCTAGACTGGGCAACACGTGTTAAAATTGCTGCTGGTGCGGCTCGTGGACTAGCTTATCTCCATGAAGATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agaatagtttgtggtaatggataactgattatgtgttgctccttgtaatttgtagGGGAAGGTAGGCCAGTTATGGACTGGGCAACACGTGTTAAGGTTGCTGCTGGTGCAGCTCGTGGAATAGCTTATCTTCATGAAGACT
aactgat putative branch site (score: 3)
ctccttgt putative PPT
ttgtaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggctgtagtgataagcttccaagaatagtttgtggtaatggataactgattatgtgttgctccttgtaatttgtagGGGAAGGTAGGCCAGTTATGGACTGGGCAACACGTGTTAAGGTTGCTGCTGGTGCAGCTCGTGGAATAGCTTATCTTCATGAAGACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA