Sequence
atgc intronic sequence ATGC exonic sequencegtaatgcattgataggttaaactttctttttctttcaggcttcttctcgcttttctttctggctgctgagttgatgcatttactttgtagACTGAGTAGGTGCACTTCTATAATCACTGGTGAAGATGGACCAATTCCAAGATGCAAGCCTTTTAAGTATACCTATGAAAAGGAGATTGTTATATATCCT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0001g00440.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os02g52470.2 (Oryza sativa), 3'ss of exon 6
gtaatgcattgataggttaaactttctttttctttcaggcttcttctcgcttttctttctggctgctgagttgatgcatttactttgtagACTGAGTAGGTGCACTTCTATAATCACTGGTGAAGATGGACCAATTCCAAGATGCAAGCCTTTTAAGTATACCTATGAAAAGGAGATTGTTATATATCCT
|||| | | ||| || ||| || | | | | | | |||||| || | || || ||| | ||||| || || | ||||| |||||||||||||| ||||| ||||||||||||||||| || || ||||| || ||||||||||||||
---------------gttagtgctgatcattcctttgtcctttttttgggtggttgatgttaatgctgattttctttatata-----tagGTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATCCCAAGATGCAAGCCTTTCAAATACACCTACGAGAAGGAGATTGTTAT-------
upper sequence: Vv18s0001g00440.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os01g41565.1 (Oryza sativa), 3'ss of exon 5
gtaatgcattgataggttaaactttctttttctttcaggcttcttctcgcttttctttctggctgctgagttgatgcatttactttgtagACTGAGTAGGTGCACTTCTATAATCACTGGTGAAGATGGACCAATTCCAAGATGCAAGCCTTTTAAGTATACCTATGAAAAGGAGATTGTTATATATCCT
|||| | | ||| || ||| || | | | | || | |||| || | | ||| | ||||| || || | ||||| ||||| |||||||| ||||| ||||||||||||||||| || || |||||||| |||||||||
---------------gttagtgctgatcattcctttgtccttttttt----tctgtggttgatgttaaggctgattttctttatatatagGTTAAGTAGATGTACCTTTATAACTACTGGCGAAGATGGGCCAATCCCAAGATGCAAGCCTTTCAAATACACCTATGAGAAGGAGATT------------
upper sequence: Vv18s0001g00440.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G402242_T02 (Zea mays), 3'ss of exon 5
--gtaatgcattgataggttaaactttctttttctttcaggcttcttctcgcttttctttctggctgctgagttgatgcatttactttgtagACTGAGTAGGTGCACTTCTATAATCACTGGTGAAGATGGACCAATTCCAAGATGCAAGCCTTTTAAGTATACCTATGAAAAGGAGATTGTTATATATCCT
|| | |||| || || | | ||||| ||| | ||| || | ||| || ||| | | || ||| | ||||| || || | ||||| |||||||||||||| ||||| |||||||||||||| || |||||||||||||| |||||||| |||||
gtatatgttgcttgtaggatatgctgtttccagagttcagtgttcatact--tttggttgactttttatgacgtgttgctcctgcattatagGTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATACCAAGATGCAAGCCCTTCAAGTATACCTATGAGAAGGAGATCGTTAT-------
upper sequence: Vv18s0001g00440.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G402242_T01 (Zea mays), 3'ss of exon 5
--gtaatgcattgataggttaaactttctttttctttcaggcttcttctcgcttttctttctggctgctgagttgatgcatttactttgtagACTGAGTAGGTGCACTTCTATAATCACTGGTGAAGATGGACCAATTCCAAGATGCAAGCCTTTTAAGTATACCTATGAAAAGGAGATTGTTATATATCCT
|| | |||| || || | | ||||| ||| | ||| || | ||| || ||| | | || ||| | ||||| || || | ||||| |||||||||||||| ||||| |||||||||||||| || ||
gtatatgttgcttgtaggatatgctgtttccagagttcagtgttcatact--tttggttgactttttatgacgtgttgctcctgcattatagGTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATACCAAGATGCAAGCCCTTCAA----------------------------------
upper sequence: Vv18s0001g00440.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT2G44270.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaatgcattgataggttaaactttctttttctttcaggcttcttctcgcttttctttctggctgctgagttgatgcatttact-ttgtagACTGAGTAGGTGCACTTCTATAATCACTGGTGAAGATGGACCAATTCCAAGATGCAAGCCTTTTAAGTATACCTATGAAAAGGAGATTGTTATATATCCT
|||| | ||| | | | | || | | | | ||||| | || || || | | ||| |||| |||||| | ||||||||||| || || | |||||||||||||| || ||||||||||| || ||||| |||||||| || |||||||||||||| ||
gtaa-gtatttgttgat--gatttgatggaaaatgaaaaatctgtctcgttcctcaa-ctaattgat-atttgtaacattggtaactgtagATTAAGTAGGTGCACATCGATTACTACTGGTGAAGATGGTCCCATTCCAAGATGTAAACCTTTCAAGTATACATACGAAAAGGAGATTGTCAT-------
upper sequence: Vv18s0001g00440.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G76170.1 (Arabidopsis thaliana), 3'ss of exon 5
----gta-atgcattgataggttaaactttctttttctttcaggcttcttctcgcttttctttct-ggctgctgagttgatgcatttact-ttgtagACTGAGTAGGTGCACTTCTATAATCACTGGTGAAGATGGACCAATTCCAAGATGCAAGCCTTTTAAGTATACCTATGAAAAGGAGATTGTTATATATCCT
|| || | || ||| |||| || | | | | | | || | | || || | || | || || ||||||| ||||||||||||| || || | || || |||||||| |||||||||||||| || ||||| || ||||| || || ||||||||||| ||
gtaaatatatacgtttctagtgatgtttttccttgaatcttggctataatatgtctcatgtcccttaattgattgatttgtaatttggctattgtagATTGAGTAGGTGCACATCAATCACTACAGGCGAAGATGGTCCAATTCCAAGATGTAAACCTTTCAAATATACATACGAGAAGGAGATTGTCAT------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caggcttcttctcgcttttctttctggctgctgagttgatgcatttactttgtagACTGAGTAGGTGCACTTCTATAATCACTGGTGAAGATGGACCAATTCCAAGATGCAAGCCTTTTAAGTATACCTATGAAAAGGAGATTGTTATATATCCT
agttgat putative branch site (score: 5)
tttacttt putative PPT
atttacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgcattgataggttaaactttctttttctttcaggcttcttctcgcttttctttctggctgctgagttgatgcatttactttgtagACTGAGTAGGTGCACTTCTATAATCACTGGTGAAGATGGACCAATTCCAAGATGCAAGCCTTTTAAGTATACCTATGAAAAGGAGATTGTTATATATCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT