Sequence
atgc intronic sequence ATGC exonic sequence...attattgtctcagagaaatttatttacaagtccttaatattaaaaaaaaaaactaattatacttgaggaaatggattatagattgatgttattgcaatagGTGCTGCAGAAGAAAGACATTCATATATGGGATGGCAATGCATCCAGAGAGTACCTTGACAGGCAACTACTTGGCTATTGGAATCT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0001g12940.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os11g29390.1 (Oryza sativa), 3'ss of exon 5
--attattgtctcagagaaatttatttacaagtccttaatattaaaaaaaaaaactaattatacttgaggaaatggattatagattgatgttattgcaat-agGTGCTGCAGAAGAAAGACATTCATATATGGGATGGCAATGCATCCAGAGAGTACCTTGACAGGCAACTACTTGGCTATTGGAATCT
|| || | |||| | | | | | | | | | || ||| ||| | ||| || || | | | |||| | || |||||| ||||||||| |||||||||||||| || |||||||| ||||||||
cagcagatgaggcataagtgaatattgttagattttagtttcttcacatgagctcc---catgcttaccactttggtacaatgatacatttttctaccttcagGTTTTACAAGAGAAAGGCATTCATATTTGGGATGGCAATGCTTCGAGAGAGTATCTTGACAG------------------------
upper sequence: Vv18s0001g12940.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G139880_T01 (Zea mays), 3'ss of exon 4
attattgtctcagagaaatttatttacaagtccttaa-tattaaaaaaaaaaactaattatacttgaggaaatggattatagat-tgatgttattgcaatagGTGCTGCAGAAGAAAGACATTCATATATGGGATGGCAATGCATCCAGAGAGTACCTTGACAGGCAACTACTTGGCTATTGGAATCT
| | | | | |||| | | || || | | | | || || ||| || || || | || || ||||| |||| | || | |||||||| |||||||||||||| || |||||||| |||||| |
--tttgataaaaaataaatgtcagaattcttctccaaatcctgagtggattaaactatctcttgaaaggtcctgttttctaaacatgcccttccatttgtagGTTTTGCAAGAAAAGGGTATTCATATCTGGGATGGCAATGCTTCAAGAGAGTATCTTGACCG------------------------
upper sequence: Vv18s0001g12940.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA11G12280.1 (Glycine max), 3'ss of exon 4
-attat-tgtc-tcagagaaatttatttacaagtccttaatattaaaaaaaaaaactaattatacttgaggaaatggattatagattgatgttattgcaatagGTGCTGCAGAAGAAAGACATTCATATATGGGATGGCAATGCATCCAGAGAGTACCTTGACAGGCAACTACTTGGCTATTGGAATCT
|||| ||| | | || ||| ||||| | || | | | | |||| | | ||| | ||| | || ||||||| | ||||||||||| | |||| |||||||||||||||||||||||||||||||||
cattacatgtagtttttgttgttgattcacaagaatgtcttactggttcattagat--attac-tataatgaattttattctggaaacatgttatattgacagGTGCTGCAGGAAAAAGGCATTCATATATGGGATGGCAATGCATCCAGAGA------------------------------------
upper sequence: Vv18s0001g12940.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G01280.1 (Glycine max), 3'ss of exon 5
attattgtctcagagaaatttatttacaagtccttaa-----tattaaaaaaaaaaactaattatacttgaggaaatggattatagattgatgttattgcaatagGTGCTGCAGAAGAAAGACATTCATATATGGGATGGCAATGCATCCAGAGAGTACCTTGACAGGCAACTACTTGGCTATTGGAATCT
| | | | ||||||| ||| | || || | | | ||| || | ||| | ||| | | | | ||| ||||||| ||| | |||| ||||||||| ||||||||||||||||||||||| |||||||| |
---acttgcatgaggtgttttatttttcagttatcaaggaatcttttactggtatgatagattttatcatatgaacttcattctgaaaacaaggtatatt--cagGTGCTACAGGAAAAAGGCATTCATATTTGGGATGGCAATGCATCCAGAGAATACCTTGATGG------------------------
upper sequence: Vv18s0001g12940.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA12G04480.1 (Glycine max), 3'ss of exon 5
-attattgtctcagagaaatttatttacaagt--ccttaatattaaaaaaaaaaac-taattatacttgaggaaatggattatagattgatgttattgcaatagGTGCTGCAGAAGAAAGACATTCATATATGGGATGGCAATGCATCCAGAGAGTACCTTGACAGGCAACTACTTGGCTATTGGAATCT
|| | | ||| ||| ||||| | | || | | | | | | || | | || | ||| | || ||||||| | ||| ||||||| | |||| |||||||||||||||||||||||||||||| ||
ttacatgaagtggttgttattgattcacaagaaggcctcttactggttcattagatatgactacaat----gatttttattctggaagcatgttatattgacagGCGCTGCAGGAAAAAGGCATTCATATATGGGATGGCAATGCATCCAGGGA------------------------------------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaaaaactaattatacttgaggaaatggattatagattgatgttattgcaatagGTGCTGCAGAAGAAAGACATTCATATATGGGATGGCAATGCATCCAGAGAGTACCTTGACAGGCAACTACTTGGCTATTGGAATCT
aactaattatactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attattgtctcagagaaatttatttacaagtccttaatattaaaaaaaaaaactaattatacttgaggaaatggattatagattgatgttattgcaatagGTGCTGCAGAAGAAAGACATTCATATATGGGATGGCAATGCATCCAGAGAGTACCTTGACAGGCAACTACTTGGCTATTGGAATCT
- - - - - -agagaaa
- - - - - - - - - - - - - caagtcc
- - - - - - - - - - - - - - - - - - - attaaaa
- - - - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aggaaat