Sequence
atgc intronic sequence ATGC exonic sequence...ctattactggctcttatcatcgttatgtttgggtatccctaagttcgcattttgtggtattggttctgtggttatctgttcaaagtttcttgatattcagGGTGAGCTGACATATGGGAAAATTGGAGAGTGGCGATTTGACAAGAGATCATACCTACGTGGACCTCCTCCTAGAAACCTTTCCTTGCCGCCTCCAGGGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv13s0084g00830.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os05g32060.1 (Oryza sativa), 3'ss of exon 6
-------------------------ctattactggctc--ttatcatcgttatgtttgggtatccctaagttcgcattttgtggtattggttctgtggttatctgttcaaag---tttcttg----------atattcagGGTGAGCTGACATATGGGAAAATTGGAGAGTGGCGATTTGACAAGAGATCATACCTACGTGGACCTCCTCCTAGAAACCTTTCCTTGCCGCCTCCAGGGG
| | | || |||| ||| || ||| | | | | ||| | | | ||| | |||| ||| ||| | | |||||||||||| || ||||||||||| || || ||||| |||||||| ||||| || || ||| ||| || || ||||| ||| | || || |||||||| |
gtgactactgtttgactttaagtatatgtcatcatatcagttatgtcaattactttgtaaaatctatttatgcattgtcatcaaaattaactttataagcttctcatgaaagagcttttttgtgtcttgtccaaactcagGGTGAGCTAACTTATGGGAAAATAGGGGAATGGCGGTTTGACAAAAGATCTTATCTTCGTTCACCACCGCCAAGAAATCTTACATTACCTCCTCCAGGAG
upper sequence: Vv13s0084g00830.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G035595_T02 (Zea mays), 3'ss of exon 6
----------ctattactggctcttatcatcgttatgtttgggtatc--cctaagttcg----cattttgtg------gtattggttctgtggtta-------tctgttcaaagt-ttcttgatattc-agGGTGAGCTGACATATGGGAAAATTGGAGAGTGGCGATTTGACAAGAGATCATACCTACGTGGACCTCCTCCTAGAAACCTTTCCTTGCCGCCTCCAGGGG
| |||| | | || || ||| | ||| | | | || || ||| ||| ||| || | | ||| | | | ||||| || || || || ||||||| ||||| ||||| ||| |||| || |||||||||||||| ||||||| || | | | || || || ||||| ||| | ||||| ||||| || |
gtattagaatcccaaactgattaatttcttcaatatatctggtttccatacgaaatttaaaaatattgagtgcataaagtagatattttattgttcctgttattttactgaaagtattattaatcttttagGGTGAACTGACCTATGGTAAAGTTGGTGAATGGCGATTTGACAAAAGATCATTCCCAGATAGGCCACCACCAAGAAATCTTACATTGCCCCCTCCTGGAG
upper sequence: Vv13s0084g00830.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT5G13500.1 (Arabidopsis thaliana), 3'ss of exon 7
--------------------------------ctattactggctctta--tcatcgttatgtttgg------gtatccctaagttcgcattttgtggtatt-ggttctgtggttatctgtt--caaagtttcttgat------attcagGGTGAGCTGACATATGGGAAAATTGGAGAGTGGCGATTTGACAAGAGATCATACCTACGTGGACCTCCTCCTAGAAACCTTTCCTTGCCGCCTCCAGGGG
||| ||||| || | | | ||| || | | ||| | || | ||| |||||| | ||| | || ||| ||| || ||||| |||||||||||||| ||||| |||||||||||||| || ||||||||| | | || || |||||||| || ||| | |||||||||||||| || |
gtgattttctgtttgacacgattgtttaattttaatttttggctgataaattaggaacagatttcacatcttgtggtcatttgtttttacttaaggtcattaggttctctttttagtcactactaagttttgctgactgttaaatacagGGGGAGCTGACATATGGCAAAATAGGAGAGTGGCGATTCGATAAGAGATCACATTTGCGGGGTCCTCCTCCAAGGAACATGTCCTTGCCGCCTCCCGGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgcattttgtggtattggttctgtggttatctgttcaaagtttcttgatattcagGGTGAGCTGACATATGGGAAAATTGGAGAGTGGCGATTTGACAAGAGATCATACCTACGTGGACCTCCTCCTAGAAACCTTTCCTTGCCGCCTCCAGGGG
tcttgat putative branch site (score: 4)
tttctt CT-rich tract
ttgatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctattactggctcttatcatcgttatgtttgggtatccctaagttcgcattttgtggtattggttctgtggttatctgttcaaagtttcttgatattcagGGTGAGCTGACATATGGGAAAATTGGAGAGTGGCGATTTGACAAGAGATCATACCTACGTGGACCTCCTCCTAGAAACCTTTCCTTGCCGCCTCCAGGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- -ttactgg
- - - - - - - - - - - - -tgtttgg
- - - - - - - - - - - - - - - - - -tccctaa
- - - - - - - - - - - - - - - - - - - - - - - - - -ttgtggt