Sequence
atgc intronic sequence ATGC exonic sequencegttagttcccttctcaatgtaccaactagtatatttatatttcaaatactgatggtccactatttaaacagAGAGGAACTATTGTTGAGAAACTCACTGAGGAAACTCTGAGAGACTGGAACCATCTAATAGAGCTCCTTTCCCTATGCGAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0023g03060.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os08g43400.4 (Oryza sativa), 3'ss of exon 4
-----------------------------------------gttagttcccttctcaatgtaccaactagtatatttatatttcaaatactgatggt-ccact--attt--aaacagAGAGGAACTATTGTTGAGAAACTCACTGAGGAAACTCTGAGAGACTGGAACCATCTAATAGAGCTCCTTTCCCTATGCGAAG
| | | | | ||||| ||||| | | | | | | ||| | ||| | |||| ||||||| |||||||| || |||||||||||||||||||| |||| ||| | | ||||| | | || ||| | | || ||||
gtacactcactgttctccttttactagcttgaacttactacataatctgtttgtgttttcctccaacctgtatact-gttctcgagttgttcatgtttccatttgatttcaaaacagAAAGGAACTACCGTAGAGAAACTCACTGAGGAAACCTTGAGGGACAAGGATCATCTTAGGAACCTTCTTGCTGTGTGTGAAG
upper sequence: Vv04s0023g03060.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G05650.1 (Glycine max), 3'ss of exon 4
gttagttcccttctcaatgtacc------aactagtatatttatatttcaaatactgatggtccactatttaaacagAGAGGAACTATTGTTGAGAAACTCACTGAGGAAACTCTGAGAGACTGGAACCATCTAATAGAGCTCCTTTCCCTATGCGAAG
|| | | | || ||| ||| | || || | || |||| | || | || | ||||||||||| ||| || ||||||||| |||||| ||||||||| | || |||||||||||| | ||| || |||| | |||||||
gtaaatatctttatcagtgtttttcaaaaagctggtgcttctacattttactta---acagtttgcaatttaaacagAAAGGGACAGTTGTTGAGAGACTCACAGAGGAAACTTTAAGGGACTGGAACCATTTTCAAGAACTTATTTCATTCTGCGAAG
upper sequence: Vv04s0023g03060.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA01G37340.1 (Glycine max), 3'ss of exon 4
gttagttcccttctcaatgtacc-aactagtatatttatatttcaaatactgatggtccactatttaaacagAGAGGAACTATTGTTGAGAAACTCACTGAGGAAACTCTGAGAGACTGGAACCATCTAATAGAGCTCCTTTCCCTATGCGAAG------------------
|| | || | ||| ||||||||| | | |||| |||| | || || || |||||||||| || ||||||||| ||| |||||||||||| | ||||| ||||||||| | | ||| || |||| | || ||||
-gtatacgtcatcattttctacagaactagtatttgtgcattt----tacttacagtttgttaatttaacagAGAGGGACAGTTGTTGAGAGACTGACTGAGGAAACTTTAAGAGATTGGAACCATTTTACAGAACTTATTTCTTTCTGTGAAGGTAAGAAGCGTTTTAATG
upper sequence: Vv04s0023g03060.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G66310.1 (Arabidopsis thaliana), 3'ss of exon 6
--------gttagttcccttctcaatgtaccaactagtatatttata-tttcaaatactgatggtccactatttaaacagAGAGGAACTATTGTTGAGAAACTCACTGAGGAAACTCTGAGAGACTGGAACCATCTAATAGAGCTCCTTTCCCTATGCGAAG
| || || | || |||| |||| | | ||| | |||| || ||| | || ||| | |||| ||| || |||||||||||||||| |||||||||||| |||||||||| ||| | | |||||||| || | ||| |||
gtaaatatgatactttcttttattttgtag-aactgatctttttgcaatttctcatgctgggctttttctttttga-cagAAAGGGACAGTTGTTGAGAAACTCACAGAGGAAACTCTGCGAGACTGGAATCATTTCAAGGAGCTCCTATCTGTCTGCAAAG
upper sequence: Vv04s0023g03060.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G51150.2 (Arabidopsis thaliana), 3'ss of exon 6
------gttag--ttcccttctcaatgtaccaactagtatatttatatttcaaatactgatggtccactatttaaacagAGAGGAACTATTGTTGAGAAACTCACTGAGGAAACTCTGAGAGACTGGAACCATCTAATAGAGCTCCTTTCCCTATGCGAAG
||| | | | ||| | | | | ||| | | || ||||| | | ||| || ||||| |||||| |||| ||||||||||| |||||||||||| | |||||||| ||| | | ||||| | || | || ||
gtaaaagttgggactggcatcttatggaattggtatgcataatctcactt----tactggtcatttact-ttgggacagAAAGGAACAGTTGTCGAGAAACTCACGGAGGAAACTCTGCGGGACTGGAATCATTTTAAGGAGCTTTTATCAATCTGTATAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgtaccaactagtatatttatatttcaaatactgatggtccactatttaaacagAGAGGAACTATTGTTGAGAAACTCACTGAGGAAACTCTGAGAGACTGGAACCATCTAATAGAGCTCCTTTCCCTATGCGAAG
tactgat putative branch site (score: 2)
aactagtatatttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagttcccttctcaatgtaccaactagtatatttatatttcaaatactgatggtccactatttaaacagAGAGGAACTATTGTTGAGAAACTCACTGAGGAAACTCTGAGAGACTGGAACCATCTAATAGAGCTCCTTTCCCTATGCGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT