Sequence
atgc intronic sequence ATGC exonic sequence...tcatttcataacttagcttgttacctatttccctctcaagtcaaaatggaaattttcttacccgtttgtttttcccccttccaaatatgcatatatgcagATGAAAGACTCAATGATATTGTTGGAAGTGCATACTATGTTGCACCTGAAGTTCTCCATAGATCCTATTATCTGGAAGCAGATATTTGGAGTGTTGGCGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv15s0048g02840.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os06g50030.1 (Oryza sativa), 3'ss of exon 5
tcatttcataacttagcttgttacctatttccctctcaagtcaaaatggaaattttcttacccgtttg----tttttcccccttccaaatatgc-atata-tgcagATGAAAGACTCAATGATATTGTTGGAAGTGCATACTATGTTGCACCTGAAGTTCTCCATAGATCCTATTATCTGGAAGCAGATATTTGGAGTGTTGGCGT
|| || | | | | || |||||| |||| | | | | |||| ||| | | || | | | ||| ||||| |||||||||||| || ||||||||||||||||||||||| |||||||| || || ||| | || ||||| ||| | |||||||||| ||||||||| | || ||
----ttaatgaact--ttggctaactatttttctcttcactgttgcttggtatttcattagctgaccagacaccttgttctttgtattttgtgctatataatgcagATGAAAGGCTTAATGATATTGTTGGAAGTGCATATTATGTTGCCCCAGAGGTTTTACACAGATCATATAGTATGGAAGCAGACATTTGGAGTATAGGTGT
upper sequence: Vv15s0048g02840.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os10g36710.1 (Oryza sativa), 3'ss of exon 5
---------------------------------------------------------------tcatttcat----aacttagcttgttacc-------tatttccctctcaagtcaaaatggaaattttcttacccgttt-----------gtttttcccccttccaaatatgcatatatgcagATGAAAGACTCAATGATATTGTTGGAAGTGCATACTATGTTGCACCTGAAGTTCTCCATAGATCCTATTATCTGGAAGCAGATATTTGGAGTGTTGGCGT
| | | || || || | || | || | | | || |||| | || | || | |||| | ||| | ||| | | ||||||||||| | |||||||||||||| ||||||||||||||||| || ||||| || ||||| || ||| ||||||||| || |||||| |||| ||
gtatttccccccaaaagaattatgcccttccaaagaacttgtgtttcatcttatgttttttttttactctattatgaatttgtcctgacatggtgaaaatactgttttttgaaaccaaatagtgaaaatactcaagtgttttgatgacacacatatttatgattggtcaatgccttcttttacagATGAAAGATTAAATGATATTGTTGGTAGTGCATACTATGTTGCTCCAGAAGTCCTACATAGGTCATATAGCACGGAAGCAGACATGTGGAGTATTGGTGT
upper sequence: Vv15s0048g02840.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G115518_T01 (Zea mays), 3'ss of exon 5
-tcatttcataactta-gcttgttacctatttccctctcaagtcaaaatggaaattttcttacccgtttgtttttcccccttccaaa-tatgcatatatgcagATGAAAGACTCAATGATATTGTTGGAAGTGCATACTATGTTGCACCTGAAGTTCTCCATAGATCCTATTATCTGGAAGCAGATATTTGGAGTGTTGGCGT
| | || | | || || | | | ||| | || | | || |||| ||| | |||||| ||||||||||||| ||||||||||||||||||||||| || |||||||| || || ||||| || ||||| || | |||||||||| ||||||||| | || ||
tggaatacactatcaacatttacagttaatattttttttcagttcactcattaactaaatcttatacttaattttgtgtgttctgcactatgca---atgcagATGAAAGGCTCAATGATATTGTTGGAAGTGCTTATTATGTTGCTCCAGAGGTTCTACACAGATCATACAGTATGGAAGCAGACATTTGGAGTATAGGTGT
upper sequence: Vv15s0048g02840.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G173928_T01 (Zea mays), 3'ss of exon 5
-------tcatt-tcataacttagcttgttacctatttccctctcaagtcaaaatggaaattttcttacccgtttgtttttcccccttccaaatatgcatatatgcagATGAAAGACTCAATGATATTGTTGGAAGTGCATACTATGTTGCACCTGAAGTTCTCCATAGATCCTATTATCTGGAAGCAGATATTTGGAGTGTTGGCGT
|| | |||| | ||| |||| | ||||| | | | | | | ||||| | || | || ||| | ||||| |||||||||||| |||||||||||||||||||| ||||| ||||| || || || ||||| || ||||| || | |||||||||| ||||||||| | || ||
ttggaagacactatcattattta--cagttaaccatttcttttgctcattca--ttaactcaatcttatac--ttaatcttatatgttctgtgc-tacatat-tgcagATGAAAGGCTCAATGATATTGTTGGAAGCGCATATTATGTCGCTCCAGAGGTTCTACACAGATCGTACAGTATGGAAGCAGACATTTGGAGTATAGGTGT
upper sequence: Vv15s0048g02840.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G031893_T01 (Zea mays), 3'ss of exon 5
------------------------------------------tcatttcataacttagcttgttacctatttccctctca--agtcaaaatggaaattttcttacccgtttgtttttccccct-----tccaaata-----tgcatatatgcagATGAAAGACTCAATGATATTGTTGGAAGTGCATACTATGTTGCACCTGAAGTTCTCCATAGATCCTATTATCTGGAAGCAGATATTTGGAGTGTTGGCGT
||| | || | | | | | ||| | | | | || || | || || |||| | | ||| ||| || | | | | |||||||||| || ||||| |||||||||||||||||||||||||| || ||||| | ||||| || ||| |||||||| || ||||| |||| ||
gtattacatacctccgcacaagggccatccaattgtaaagttctgttttacaaatatgttagaagtccattgacataaaatgaaacatgatatgaccttcctccaaaaaatgttctaacgcctgatgctcctgatgccttttccccctttacagATGAAAGGCTTAATGACATTGTTGGAAGTGCATACTATGTTGCTCCAGAAGTCTTGCATAGGTCATATAGCACAGAAGCAGACATGTGGAGCATTGGTGT
upper sequence: Vv15s0048g02840.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G100560_T01 (Zea mays), 3'ss of exon 5
------------------------------------------tcatttcataacttagcttgttacctatttccctctca--agtcaaaatggaaattttcttacccgtttgtttttccccct-----tccaaata-----tgcatatatgcagATGAAAGACTCAATGATATTGTTGGAAGTGCATACTATGTTGCACCTGAAGTTCTCCATAGATCCTATTATCTGGAAGCAGATATTTGGAGTGTTGGCGT
||| | || | | | | | ||| || | | | || || | || || |||| | ||| ||| || | | | | |||||||||| || ||||| |||||||||||||||||||||||||| || ||||| | ||||| || ||| |||||||| || ||||| |||| ||
gtattacatacctccacacaagggccatccaattgtaaagttctgttttacaaatatgttagaagtccattgccataaaatgaaacatgatatgaccttcctccaaaaaatgttctaatgcctgatgctcctgatgctttttccccctttacagATGAAAGGCTTAATGACATTGTTGGAAGTGCATACTATGTTGCTCCAGAAGTCTTGCATAGGTCATATAGCACAGAAGCAGACATGTGGAGAATTGGTGT
upper sequence: Vv15s0048g02840.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G138245_T01 (Zea mays), 3'ss of exon 5
---------------------------------------------tcatttcataacttagcttgttacctatttccctc--tcaagtcaaaatggaaattttcttacccgtttgtttt---------tcccccttccaaatatgcatatatgcagATGAAAGACTCAATGATATTGTTGGAAGTGCATACTATGTTGCACCTGAAGTTCTCCATAGATCCTATTATCTGGAAGCAGATATTTGGAGTGTTGGCGT
|||| | || | | | | | ||| | | | | || || | || || |||||| | | ||| | | |||||||||| || ||||| |||||||||||||||||||| ||||| || ||||| | ||||| || ||| |||||||| || |||||| |||| ||
gtattacatacctccacacaaggatcatccattcctaatggagttctattttacaaatatgttagaagtccattgacataaaacgaaacatgatatgagcttcctctaaaagatgttttaaagcctgatgctcctgatgcctcctccccctcacagATGAAAGGCTTAATGACATTGTTGGAAGTGCATACTACGTTGCTCCAGAAGTCTTGCATAGGTCATATAGCACAGAAGCAGACATGTGGAGTATTGGTGT
upper sequence: Vv15s0048g02840.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA16G02340.1 (Glycine max), 3'ss of exon 6
tcatttcataacttagcttgttacctatttccctctcaagtcaaa-atggaaattttcttacccgtttgtttttcccccttccaaatatgcatatatgcagATGAAAGACTCAATGATATTGTTGGAAGTGCATACTATGTTGCACCTGAAGTTCTCCATAGATCCTATTATCTGGAAGCAGATATTTGGAGTGTTGGCGT
| | | | | || | ||| | | | | | | ||||| || | | || | | ||| |||||| | || || | |||||||| |||| ||||| ||||| || |||||||| |||||||||||||| || || || || || ||| ||||||||||||||| |||||| |||| ||
tagtctgttccatgtactcataacccaagacattgttgggatatttatggatataaggtcatccctcttaatttttcccttc-gtgtgtgttgatttacagATGAACGACTGAATGACATTGTCGGGAGTGCATATTATGTTGCACCTGAGGTCCTTCACAGGTCATATAGTCTGGAAGCAGATATATGGAGTATTGGTGT
upper sequence: Vv15s0048g02840.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA07G05750.1 (Glycine max), 3'ss of exon 5
tcatttcataacttagcttgttacctatttccctctcaagtcaaa-atggaaattttcttacccgtttgtttttcccccttccaaatatgcatatatgcagATGAAAGACTCAATGATATTGTTGGAAGTGCATACTATGTTGCACCTGAAGTTCTCCATAGATCCTATTATCTGGAAGCAGATATTTGGAGTGTTGGCGT
| | | | | || | ||| | | | | | | ||||| || | || | | ||| |||||| | | || || | ||||||| |||| ||||| |||||||| ||||| || |||||||||||||| || || || || || ||| ||||||||||||||| |||||| |||| ||
tagtctgttccatgtactcataacccaagacattgttgggatatttatggatataaggccatccctcttaatttttcccttc-atgtgtgttgatttacagATGAGCGACTGAATGACATTGTTGGGAGTGCGTATTATGTTGCACCTGAGGTCCTTCACAGGTCATATAGTCTGGAAGCAGATATATGGAGTATTGGTGT
upper sequence: Vv15s0048g02840.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT2G46700.2 (Arabidopsis thaliana), 3'ss of exon 4
tcatttcataacttagcttgttacctatttccctctcaagtcaaa--atggaaattttcttac--ccgtttgtttttcccccttccaaatatgcatatatgcagATGAAAGACTCAATGATATTGTTGGAAGTGCATACTATGTTGCACCTGAAGTTCTCCATAGATCCTATTATCTGGAAGCAGATATTTGGAGTGTTGGCGT
| || | | || ||| | | | | ||| |||| | | | | | || || | | |||||||||||||||| |||||||| ||||||||||| |||||||| || ||||||||| | || || || ||| || || || ||||| |||||| |||| ||
-----------------gtaagacttttcattctttcaggccttgtcactatactttccttatagctgcctactagtgaaatttgattgaattcctcaatgcagATGAAAGACTGAATGATATAGTTGGAAGTGCCTACTATGTCGCGCCTGAAGTTTTACACAGGTCATATAGCCTTGAGGCTGATATATGGAGTATTGGAGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atggaaattttcttacccgtttgtttttcccccttccaaatatgcatatatgcagATGAAAGACTCAATGATATTGTTGGAAGTGCATACTATGTTGCACCTGAAGTTCTCCATAGATCCTATTATCTGGAAGCAGATATTTGGAGTGTTGGCGT
ttcttac putative branch site (score: 2)
aaatatgcatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcatttcataacttagcttgttacctatttccctctcaagtcaaaatggaaattttcttacccgtttgtttttcccccttccaaatatgcatatatgcagATGAAAGACTCAATGATATTGTTGGAAGTGCATACTATGTTGCACCTGAAGTTCTCCATAGATCCTATTATCTGGAAGCAGATATTTGGAGTGTTGGCGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - tgttacc
- - - - - - - - - - - - - - - ccctctc
- - - - - - - - - - - - - - - - - - - - tcaaaat