Sequence
atgc intronic sequence ATGC exonic sequence...caccattgcaacttcatgcatacaagtgtaacatcattatttgaaaaaaaaaaaaaaaaaactttgaaattcattttgttccaactttgatatggactagGTATGGGTTTACAAGAAAACGGCTGAGGAGAGGTTCCCCACTCTGAAGCAATATTCTGATCAGGCTCCTCCAACTGATAAATTTGCCACGCATGAGGTGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv15s0048g00930.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g63920.1 (Oryza sativa), 3'ss of exon 5
-caccattgcaacttcatgcatacaagtgtaacatcattatttga--aaaaaaaaaaaaaaaaactttga---aatt--cattttgttccaactttgatatggactagGTATGGGTTTACAAGAAAACGGCTGAGGAGAGGTTCCCCACTCTGAAGCAATATTCTGATCAGGCTCCTCCAACTGATAAATTTGCCACGCATGAGGTGA
| ||| | || || || | || || | | ||| | | || | || | || || |||| || || | | || || |||| ||||| || |||||||| ||||||||| ||||||||| ||||| | ||||||||| |||||||| ||| |||||||||||| | ||||| || |
gtggggtgttgttttcttaaattcatgtaatgttttttttttcagttagagaaatttatattaattctggttcagtttgcaatttggtctgacgtctttgtgaac-agGTGTGGGTCTATAAGAAAACATCTGAGGAGAAATTCCCCACTTTGAAGAAGTATTCTGATAAGGCTCCTGCAAGTGATAAATTTGCATCTCATGAAGTCA
upper sequence: Vv15s0048g00930.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G137968_T03 (Zea mays), 3'ss of exon 3
-caccat--tgcaa--cttcatgcatacaagtgtaacatcattatttgaaaaaaaaaaaaaaaaaactttgaaattcattttgttccaactttgatatggactagGTATGGGTTTACAAGAAAACGGCTGAGGAGAGGTTCCCCACTCTGAAGCAATATTCTGATCAGGCTCCTCCAACTGATAAATTTGCCACGCATGAGGTGA
| ||| ||||| || || | | | | | ||| | | | | | | | ||| ||| || | || | | | ||||| |||||||| |||||||| |||||||| | ||||||||| ||||| | ||||| || | |||||||||| |||||||||||| | ||||| || |
gcttcattttgcaaggttttttgagactagatttgaggtgattgtgttagcatgtccatatta----cttgcaatcatggctgatataatgcccttgttaa-tagGTGTGGGTTTATAAGAAAACAGCTGAGGAAAAATTCCCCACTTTGAAGAAGTATTCGGACAAAGCTCCTCCAAATGATAAATTTGCTTCTCATGAAGTCA
upper sequence: Vv15s0048g00930.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G137968_T02 (Zea mays), 3'ss of exon 5
---------------------------------------------------------caccattgcaacttcatgcatacaagtgtaacatcattatttgaaaaaaaaaaaaaaaaaactttg-----aaattcattttg-ttccaact----ttgatatgg----------actagGTATGGGTTTACAAGAAAACGGCTGAGGAGAGGTTCCCCACTCTGAAGCAATATTCTGATCAGGCTCCTCCAACTGATAAATTTGCCACGCATGAGGTGA
| ||| || | ||| | | | || || ||||| | | | | | | || | | ||| || || ||| |||||| | ||||| |||||||| |||||||| |||||||| | ||||||||| ||||| | ||||| || | |||||||||| |||||||||||| | ||||| || |
gtaggcccagttcgtttgtcagttatacgctatattccatcatttacagaaatttataataatttaaatcttctgcttc---attttgcaaggttttttgagactagatttgaggtgattgtgttagcatgtccatattacttgcaatcatggctgatataatgcccttgttaatagGTGTGGGTTTATAAGAAAACAGCTGAGGAAAAATTCCCCACTTTGAAGAAGTATTCGGACAAAGCTCCTCCAAATGATAAATTTGCTTCTCATGAAGTCA
upper sequence: Vv15s0048g00930.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G25550.1 (Glycine max), 3'ss of exon 5
--caccattgcaacttcatgcatacaagtgtaacatcattatttgaaaaaaaaaaaaaaaaaactttgaaattcattttgttccaact-ttgatatggactagGTATGGGTTTACAAGAAAACGGCTGAGGAGAGGTTCCCCACTCTGAAGCAATATTCTGATCAGGCTCCTCCAACTGATAAATTTGCCACGCATGAGGTGA
|| | || | || || ||| | | | | | | || |||| || | | || |||| | || | || || | ||||| ||| ||||||||||| |||| |||| || || || ||||| ||||||||||| |||||||||||| |||||||||||| | ||||| || |
cgtacaagtggg---ttatttattcaatttgtcttttaaaaaaaaacattctaagtaaaacaaaacagtattttgttttcatgaaattgttaatgataatcagGTAATGGTATACAAGAAAACAACTGAAGAGAAATTTCCTTCTATGAAGAAATATTCTGATAAGGCTCCTCCAAATGATAAATTTGCTAAACATGAAGTCA
upper sequence: Vv15s0048g00930.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G00970.1 (Glycine max), 3'ss of exon 3
caccattgcaacttcatgcatacaagtgtaacatcattatttgaaaaaaaaaaaaaaaaaactttgaaattcattttgttccaactttgatatggactagGTATGGGTTTACAAGAAAACGGCTGAGGAGAGGTTCCCCACTCTGAAGCAATATTCTGATCAGGCTCCTCCAACTGATAAATTTGCCACGCATGAGGTGA--
|| | || | | ||| || |||| | | |||| |||| ||| | || | | | || | | ||||| || || || | || || | ||||||| ||||||||||| |||||||||||| |||||||| ||| | ||||| || |
------------------gttatttatccaat-ttgtcttttaaataaaacgttcttagtaaaaaaaaatgtatttcgttttcatgaaaatgttaaatgataatcagGT------AAAACAGCAGAAGACAAATTTCCAAGTCTGAAGAAATATTCTGATAAGGCTCCTCCAAATGATAAATATGCTAAACATGAAGTCAAA
upper sequence: Vv15s0048g00930.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G37470.1 (Glycine max), 3'ss of exon 1
cac-cattgcaacttcatgcatacaagtgtaacatcattatttgaaaaaaaaaaaaaaaaaactttgaaattcattttgttccaactttgatatggactagGTATGGGTTTACAAGAAAACGGCTGAGGAGAGGTTCCCCACTCTGAAGCAATATTCTGATCAGGCTCCTCCAACTGATAAATTTGCCACGCATGAGGTGA
|| || ||| | | | | | | |||||| || | | || || || | | | || || | ||||| ||| || |||||||| |||| |||| || || || ||||| ||||||||||| |||||||||||| |||||||||| | ||||| || |
catatgccaacacatcagcaaagtatgggcattttggttatttccaatcattgttagggccttgtttgtataaatataaatg-attgttaatgataatcagGTAATGGTATAGAAGAAAACAACTGAAGAGAAATTTCCTTCTATGAAGAAATATTCTGATAAGGCTCCTCCAAAGGATAAATTTGGTAAACATGAAGTCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaaaaaaaaaaaaaactttgaaattcattttgttccaactttgatatggactagGTATGGGTTTACAAGAAAACGGCTGAGGAGAGGTTCCCCACTCTGAAGCAATATTCTGATCAGGCTCCTCCAACTGATAAATTTGCCACGCATGAGGTGA
ctttgat putative branch site (score: 5)
aaaaaaaaaaactttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caccattgcaacttcatgcatacaagtgtaacatcattatttgaaaaaaaaaaaaaaaaaactttgaaattcattttgttccaactttgatatggactagGTATGGGTTTACAAGAAAACGGCTGAGGAGAGGTTCCCCACTCTGAAGCAATATTCTGATCAGGCTCCTCCAACTGATAAATTTGCCACGCATGAGGTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
caccatt
- - - - - - -tcatgca
- - - - - - - - - - - caagtgt
- - - - - - - - - - - - - - - - - - - - ttgaaaa
- - - - - - - - - - - - - - - - - - - - - -aaaaaaa