Sequence
atgc intronic sequence ATGC exonic sequencegtatgtatttaccttaattagctgtattcatcacttagttttaatttcaaataattcccataatcccatcccccctttgatacattgatttatttattaagtaatcccatgctgatttgcttgtttgaagGTTGAGGGGGTGAAGCACTCTGGCCCAACCAAAATGGTTCTCTACTTCACTGGGGCTACCAACATTCTCTACACCTTTGGTGGTCATGCTGTCACAGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0001g03540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g14080.1 (Oryza sativa), 3'ss of exon 4
---gtatgtatttaccttaattagctgtattcat-cacttagttttaatttcaaat---aattcccataatcccatcccccctttgatacattgatttatttattaagtaatcccatgctgatttgcttgtttgaagGTTGAGGGGGTGAAGCACTCTGGCCCAACCAAAATGGTTCTCTACTTCACTGGGGCTACCAACATTCTCTACACCTTTGGTGGTCATGCTGTCACAGT
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gtagtaca-acacaaaagcaccatctgttagcatgcagcatgcttgcatttctcgtctgaatagcgaggcgcatgcctgaacattattacattgcgttgtgctgaaaaaacacttgtgttttttgtatgaatatcagGTCGATGGAGTGAAGCACTCGGGCCCTACAAAGATGGTCCTCTACTTCACCGGGGCCACAAACATTCTCTACACCTTCGGTGGGCACGCTGTTACTGT
upper sequence: Vv18s0001g03540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os10g05690.1 (Oryza sativa), 3'ss of exon 2
gtatgtatttaccttaattagctgtattcatcacttagttttaatttcaaataattcccataatcccatcccccctttgatacattgatttatttattaagtaatcccatgctgatttgcttgtttgaagGTTGAGGGGGTGAAGCACTCTGGCCCAACCAAAATGGTTCTCTACTTCACTGGGGCTACCAACATTCTCTACACCTTTGGTGGTCATGCTGTCACAGT
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-------ataagatcaa--agtcccaaacgtcacttatttatgataacaaa--atgatagtaatag-----------tgatagatag--taatt------gtaatagtgcatatattgggaataatgcagGTGGAGGGTGTGGCGCACTCTGGGCCCACAAGCATCGTGCTCTACTTCACGGGGGCCACCAACATCCTCTACACCTTCGGGGGCCACGCTGTCACCGT
upper sequence: Vv18s0001g03540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G045057_T02 (Zea mays), 3'ss of exon 4
gtatgtatttaccttaattagctgtattcatcacttagttttaatttcaaataattcccataatcccatcccccctttgatacattgatttatttattaagtaatcccatgctgatttgcttgtttgaagGTTGAGGGGGTGAAGCACTCTGGCCCAACCAAAATGGTTCTCTACTTCACTGGGGCTACCAACATTCTCTACACCTTTGGTGGTCATGCTGTCACAGT
| ||| | | | | || | || |||| || | || | || ||| | | | || || | || | | |||| || || | || |||| || || |||| |||||| ||||||| ||| ||||| ||||||||||| || || |||||||| |||||||||||||| || ||||||||||| ||
--gtatatatgcgctgagcgtgtgatatgatgcactagtcgattgatcgcctgcttgcgctatgtccagcagatcgt--gtatatggccgtaccaaacat-taat----tgatggacgacaatattatagGTGGAAGGTGTGACGCACTCGGGCCCAAGCAAGATGGTGCTCTACTTCACCGGTGCCACCAACATCCTCTACACCTTTGGAGGCCATGCTGTCACTGT
upper sequence: Vv18s0001g03540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G149481_T03 (Zea mays), 3'ss of exon 5
gtatgtatttaccttaattagctgtattcat-cacttagttttaatttcaaataattcccataatcccatcccc-----cctttgatacattgatttatttattaagtaatcccatgctgatttgcttgtttgaagGTTGAGGGGGTGAAGCACTCTGGCCCAACCAAAATGGTTCTCTACTTCACTGGGGCTACCAACATTCTCTACACCTTTGGTGGTCATGCTGTCACAGT--
||| || | ||| | | | || | | | || | || ||| || | | | | || | ||||| | | |||||| | ||||||| || ||||||||||| || || ||||| ||||| ||||||||||| ||||| || |||||||||||||| || || || || ||||| || ||
-----------------------gtacgcaagcgtagcgttgaagcataatatgcattctgtgggcctgtggcctgtggcctgtgggtgaccggccgagacgatgtgtgtgcttctgctgctctacttgtt-gcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGTGT
upper sequence: Vv18s0001g03540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G149481_T02 (Zea mays), 3'ss of exon 4
gtatgtatttaccttaattagctgtattcat-cacttagttttaatttcaaataattcccataatcccatcccc-----cctttgatacattgatttatttattaagtaatcccatgctgatttgcttgtttgaagGTTGAGGGGGTGAAGCACTCTGGCCCAACCAAAATGGTTCTCTACTTCACTGGGGCTACCAACATTCTCTACACCTTTGGTGGTCATGCTGTCACAGT
||| || | ||| | | | || | | | || | || ||| || | | | | || | ||||| | | |||||| | ||||||| || ||||||||||| || || ||||| ||||| ||||||||||| ||||| || |||||||||||||| || || || || ||||| || ||
-----------------------gtacgcaagcgtagcgttgaagcataatatgcattctgtgggcctgtggcctgtggcctgtgggtgaccggccgagacgatgtgtgtgcttctgctgctctacttgtt-gcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGT
upper sequence: Vv18s0001g03540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA04G43150.2 (Glycine max), 3'ss of exon 5
gtatgtatttaccttaattagctgtattcatcacttagttttaatttcaaataattcccataat--cccatcccccctttgatacattgatt-----tatttattaagtaatcccatgctga-------tttgcttgtttgaagGTTGAGGGGGTGAAGCACTCTGGCCCAACCAAAATGGTTCTCTACTTCACTGGGGCTACCAACATTCTCTACACCTTTGGTGGTCATGCTGTCACAGT
||| | | || |||| | ||| || | | | || || || || || ||||| | | | | ||||| | ||| | ||| || || | | | || || | |||||| ||||||||||| |||| | || ||| ||||| ||||||||||||||||||||||||||||||||||||| || |||||||| |||||||| |||||
gtaaaaagactcgatatttaggagc-ctcagca-tcatcataaaattaaagcaaatcatataatgattgctaacacatgtgatataagtattattgttgccaattttgtgttcttcaattaatattctgtgtgtttctctgaagGCTGAGGGGGTGACGCACACAGGGCCAGCCAAATTGGTTCTCTACTTCACTGGGGCTACCAACATTCTCTATACTTTTGGTGGACATGCTGTTACAGT
upper sequence: Vv18s0001g03540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G11540.1 (Glycine max), 3'ss of exon 5
-------------gtatgtatttacctta--attagc-tgtattca-------tcacttagttttaatttcaaataattcccata-atcccatcccccctttgatacattgatttatttattaagtaatcccatgctgatttgcttgtttgaagGTTGAGGGGGTGAAGCACTCTGGCCCAACCAAAATGGTTCTCTACTTCACTGGGGCTACCAACATTCTCTACACCTTTGGTGGTCATGCTGTCACAGT
||| || ||| | || ||| | | | | ||| || | ||| | || | | ||| | | ||| || | | | || | || |||| || ||| | || || | | |||||||||||||||| |||| | || ||| ||||| |||||||||||||||||||||| |||||||||||||| || |||||||| |||||||| |||||
gtaaaaagactcgatatttaggagcctcaacatcagcataaaattaaagcaaatcaaataacaatgattgctaacacatgtgatataataagtattattgttgctaattatttgtgttcttcaattaat---attctg-tgtgtttctctaaagGTTGAGGGGGTGACGCACACAGGGCCAGCCAAATTGGTTCTCTACTTCACTGGGGCGACCAACATTCTCTATACTTTTGGTGGGCATGCTGTTACAGT
upper sequence: Vv18s0001g03540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G77690.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgtatttaccttaattagctgtattcatcacttagttttaatttcaaataattcccataatcccatcccccctttgatacattgatttatttattaagtaatcccatgctgatttgcttgtttgaagGTTGAGGGGGTGAAGCACTCTGGCCCAACCAAAATGGTTCTCTACTTCACTGGGGCTACCAACATTCTCTACACCTTTGGTGGTCATGCTGTCACAGT
| | |||||| | | || | || || | || | ||| | ||| ||| ||| | || || |||||||| | ||| | |||| ||||| ||||| |||||||| ||||||| |||||| || |||||||| || || |||||||||||||||||||||||||| || || ||||||||
-------gtcattataattaacacaaatcttgttttgattattataagatataga-catatagtcctggtta----ttgttgt-ttaatatatttatt------tttcatataaa-----------aaagGCTGAGGATGTGAAACACTCTGGTCCAACCACAATGGTGCTTTACTTCACCGGAGCCACCAACATTCTCTACACCTTTGGTGGCCACGCCGTCACAGT
upper sequence: Vv18s0001g03540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S213_89V6.1 (Physcomitrella patens), 3'ss of exon 4
gtatgtatttaccttaattagctgtattcatcacttagttttaatttcaaataattcccataatcccatcccccctttgatacattgatttatttattaagtaatcccatgctgatttgcttg------tttgaagGTTGAGGGGGTGAAGCACTCTGGCCCAACCAAAATGGTTCTCTACTTCACTGGGGCTACCAACATTCTCTACACCTTTGGTGGTCATGCTGTCACAGT
|| | | | | | || || | | | ||| | || | |||||||| ||| | || || | ||| || || ||| || || || | |||| |||||| | |||| | |||||||| || || ||||||||||||||||||||||| | || ||||| |||||
-----------gtaaaaccattcaaactttagaaccgactcgcatcctcaaccactttcttaa-cttgcagttgaactggtcgggtgatttatagattgatagattccttcctgcattcctgaatatgttttccagACCTCTGGCGTAACGCACAATGGCCCCGTGTCGAGGGTTTTATACTTCACGGGAGCAACCAACATTCTCTACACCTTTGGAAGCCACGCTGTGACAGT
upper sequence: Vv18s0001g03540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S90_46V6.1 (Physcomitrella patens), 3'ss of exon 4
gtatgtatttaccttaattagctgtattcatcacttagttttaatttcaaataattcccataatccc-atcccccctttgata----cattgatttattta----------ttaagtaatcccatgctgattt---gcttgtttgaag-
||| | ||| | | | | || |||| |||| | || | | || | || | | || ||| ||| || || | | | | | ||| | | || ||| | || || |||| || || |||| ||||| | | ||| | |||||||| || || ||||| ||||| ||||||||||||||||| ||||| || ||
----gtaatggacttcaacgacgtgaattgctacgggttttttatttacaggaagacgagtcatttctattcatctttatatatagccatcaatctaatcaatttctgctttccaacactcctaacgaggttctggacttttatggagccagGTTGCCAATGTTGTTCATTCTGCTCCAACGACCAAGGTCTTGTACTTCACAGGAGCAACCAATATTCTGTACACCTTTGGTGGTCACGCTGTTACTGT
upper sequence: Vv18s0001g03540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ36050 (Selaginella moellendorffii), 3'ss of exon 4
--------------------------------gtatgtatttaccttaattagctgtattcatcacttagttttaatttcaaataattccc--ataatcccatcccccctttgatacat-tgatttatttattaagtaatcccatgctgatttgcttgtttgaagGTTGAGGGGGTGAAGCACTCTGGCCCAACCAAAATGGTTCTCTACTTCACTGGGGCTACCAACATTCTCTACACCTTTGGTGGTCATGCTGTCACAGT
|| || || | | | | | ||| ||| || | | || ||| | ||| ||| || | || || || | || || || || ||| ||| ||| || || ||||| || | ||||| || | || | || |||||||| || |||||||| | |||||||||||||||||||| ||||| ||
gtgagagaagcatctaaaaaagctccactggatgataagcttgtctcgtcaaagtttgctgtagaactagaattatctttcatttatcatgggatagattttaaacttcttacataggcgtggtctaac-atcaataattctcacacttcttcactt--ttgcagGACCCAGGTGTAAAGCATTCGGCCCCAAATAATCTCGTCCAATATTTCACTGGAGCCACCAACATCTTGTACACCTTTGGTGGTCATGCCGTCACTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgatacattgatttatttattaagtaatcccatgctgatttgcttgtttgaagGTTGAGGGGGTGAAGCACTCTGGCCCAACCAAAATGGTTCTCTACTTCACTGGGGCTACCAACATTCTCTACACCTTTGGTGGTCATGCTGTCACAGT
tgctgat putative branch site (score: 3)
tttgctt CT-rich tract
tacattgatttattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtatttaccttaattagctgtattcatcacttagttttaatttcaaataattcccataatcccatcccccctttgatacattgatttatttattaagtaatcccatgctgatttgcttgtttgaagGTTGAGGGGGTGAAGCACTCTGGCCCAACCAAAATGGTTCTCTACTTCACTGGGGCTACCAACATTCTCTACACCTTTGGTGGTCATGCTGTCACAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG