Sequence
atgc intronic sequence ATGC exonic sequencegtacgcaagcgtagcgttgaagcataatatgcattctgtgggcctgtggcctgtggcctgtgggtgaccggccgagacgatgtgtgtgcttctgctgctctacttgttgcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G149481_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g14080.1 (Oryza sativa), 3'ss of exon 4
--------gtacgcaagcgtagc--gttgaagcataatatgcattc--tgtgggcctgtggcctgtggcctgtgggtgaccggc----cgagacgatgtgt-------gtgcttctgctgctc-tacttgttgcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGT
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gtagtacaacacaaaagcaccatctgttagcatgcagcatgcttgcatttctcgtctgaatagcgaggcgcatgcctgaacattattacattgcgttgtgctgaaaaaacacttgtgttttttgtatgaatatcagGTCGATGGAGTGAAGCACTCGGGCCCTACAAAGATGGTCCTCTACTTCACCGGGGCCACAAACATTCTCTACACCTTCGGTGGGCACGCTGTTACTGT
upper sequence: GRMZM2G149481_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA11G11310.1 (Glycine max), 3'ss of exon 4
-------------------gtacgcaagcgtagcgttgaagcataatatgcatt-ctgtgggcctgtggcctgtggcctgtgg--gtgaccggccgagacgatgtg-tgtgcttctgctgctctacttgt-tgcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGT
|| | |||| | | || || ||| ||| | | | || || | || | || | ||||| | | | | || | || | || || || ||||| || || |||||||| |||| || || || || ||||||||||||||||||||||| ||||| || || |||||||| ||
gtaacaataataaatttacaaacagatacgtactactacattattattattattactgatattcaattattaattatatgcaattgtaattaatttagtagtaatgctatgcttttccgattgttattatgcttagATGGAAGGAGTTAAGCATTCGGGTCCGACCAAATTGGTTCTATATTTTACGGGGGCCACAAACATTCTCTACACATTCGGGGGACATGCTGTTACTGT
upper sequence: GRMZM2G149481_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA06G11540.1 (Glycine max), 3'ss of exon 5
---------------------------gtacgcaagcgtagcgttgaagcataatatgcattctgtgggcctgtggcctgtggcctg-tgggtg--accggccgagacgatgtgtgtgcttc---tgctgctctacttgttgc-----agGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGT
|| ||| || || ||||| | | | || | |||| | | || | | | || ||||| |||| | | ||| |||| | ||||||| || |||| |||| | ||||| |||| |||| ||||||||||| ||||| || ||||||||||| ||||| || ||||| |||||||| ||
gtaaaaagactcgatatttaggagcctcaacatcagcataaaattaaagcaaatcaaataacaatgattgctaacacatgtgatataataagtattattgttgctaattatttgtgttcttcaattaatattctgtgtgtttctctaaagGTTGAGGGGGTGACGCACACAGGGCCAGCCAAATTGGTTCTCTACTTCACTGGGGCGACCAACATTCTCTATACTTTTGGTGGGCATGCTGTTACAGT
upper sequence: GRMZM2G149481_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA12G03490.1 (Glycine max), 3'ss of exon 4
---------------gtacgcaagcgtagcgttgaagcataatatgcattctgtgggcctgtggcctgtggcctgtgggtgaccggccgagacgatgt-gtgtgcttctgctgctctacttgttgc-------agGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGT
|| | || | | || || ||| | | | | | | | | || | | | || || | || | || | ||||| || | || || || ||||| || || |||||||| |||| || || || || ||||||||||||||||||||||| ||||| || || |||||||| ||
gtgacaacaatattcataaattaagttacaaataatttattattattattatttcatacattaaattattaatgatatgaaactgtcattaatatagtagtaatgctatgtttttccaattgttattatgcttagATGGAAGGAGTTAAGCATTCGGGTCCGACCAAATTGGTTCTATATTTTACGGGGGCCACAAACATTCTCTACACATTCGGGGGACATGCTGTTACTGT
upper sequence: GRMZM2G149481_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA04G43150.2 (Glycine max), 3'ss of exon 5
---------------------------gtacgcaagcgtagcgttgaagcataatatgcattctgtgggcctgtggcctgtggcctgtgggtgaccggccgagacgatgtgtg-tgcttctgctgctctacttgttgc-----agGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGT
| | | || || ||||| | || | | || || | |||| | | | | | | ||||| | | | | ||| |||| | ||| ||| || |||| |||| | ||||| |||| |||| ||||||||||| ||||| || ||||||||||| ||||| || || || |||||||| ||
gtaaaaagactcgatatttaggagcctcagcatcatcataaaattaaagcaaatcatataatgattg---ctaacacatgtgatataagtattattgttgccaattttgtgttcttcaattaatattctgtgtgtttctctgaagGCTGAGGGGGTGACGCACACAGGGCCAGCCAAATTGGTTCTCTACTTCACTGGGGCTACCAACATTCTCTATACTTTTGGTGGACATGCTGTTACAGT
upper sequence: GRMZM2G149481_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT2G21050.1 (Arabidopsis thaliana), 3'ss of exon 4
gtacgcaagcgtagcgttgaagcataatatgcattctgtgggcctgtggcctgtggcctgtgggtgaccggccgagacgatgtg-tgtgcttctgctgctctacttgttgcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGT
|| | || | |||| | ||| | ||| | | | | | | | |||| ||| | || || || | |||| || || |||||||| || || || | |||| |||| | |||||||| ||||||||||||||||| ||||| ||||| || || |||||||| ||
----------ttaatgcataaatgttatatac---ttgtagagttgtagataattgaattttcttatagaaggagaataatgtaatgtaccaatgttggaataataaaaatagGTAGAAGGAGTGAAGCATTCAGGACCAAGCAAGCTGGTTTTATACTTCACAGGGGCCACAAACATTCTTTACACATTCGGTGGACATGCTGTTACTGT
upper sequence: GRMZM2G149481_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT1G77690.1 (Arabidopsis thaliana), 3'ss of exon 4
gtacgcaagcgtagcgttgaagcataatatgcattctgtgggcctgtggcctgtggcctgtgggtgaccggccgagacgatg--tgtgtgcttctgctgctctacttgttgca--gGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGT
| || | ||| | || ||| || | | | | | | | | || ||| | | | | | | | | | || ||| | ||||| ||||| || || |||| |||||||| ||||||||||| ||||| |||||||||||||| || || || ||||| || || ||
------------gtcattataat-taacacaaatcttgt---tttgattattataagatatagacatatagtcctggttattgttgtttaatatatttatttttcatataaaaaagGCTGAGGATGTGAAACACTCTGGTCCAACCACAATGGTGCTTTACTTCACCGGAGCCACCAACATTCTCTACACCTTTGGTGGCCACGCCGTCACAGT
upper sequence: GRMZM2G149481_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 4
gtacgcaagcgtagcgttgaagcataatatgcattctgtgggcctgtggcctgtggcctgtgggtgaccggccgagacgatgtgtgtgcttctgctgctctacttgtt-----gcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGT
||| | | || || || | | | | || | | | || || | | | || | | || ||||| |||| | || || ||||| ||||| || || ||||| ||||||| |||||||| ||||| ||||||||||||||||| ||||| || || ||||| || ||
----------gtactatacatatatctcattcaa-ccaaatatccaaaacatatgatattaaaattagtaaatgattttatttatttattt--atttatttatttgttaatgggcagATGGAAGGAGTGAAACACTCAGGTCCATCCAAGCTGGTGCTATACTTCACAGGGGCTACAAACATTCTCTACACATTCGGGGGACATGCTGTGACTGT
upper sequence: GRMZM2G149481_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv18s0001g03540.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------gtacgcaagcgtagcgttgaagcataatatgcattctgtgggcctgtggcctgtggcctgtgggtgaccggccgagacgatgtgtgtgcttctgctgctctacttgtt-gcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGT
||| || | ||| | | | || | | | || | || ||| || | | | | || | ||||| | | |||||| | ||||||| || ||||||||||| || || ||||| ||||| ||||||||||| ||||| || |||||||||||||| || || || || ||||| || ||
gtatgtatttaccttaattagctgtattcat-cacttagttttaatttcaaataattcccataatcccatcccc-----cctttgatacattgatttatttattaagtaatcccatgctgatttgcttgtttgaagGTTGAGGGGGTGAAGCACTCTGGCCCAACCAAAATGGTTCTCTACTTCACTGGGGCTACCAACATTCTCTACACCTTTGGTGGTCATGCTGTCACAGT
upper sequence: GRMZM2G149481_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ34222 (Selaginella moellendorffii), 3'ss of exon 4
gtacgcaagcgtagcgttgaagcataatatgcattctgtgggcctgtggcctgtggcctgtgggtgaccggccgagacgatgtgtgtgcttctgctgctctacttgttgcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGT
| || | || | | | | ||| || ||| || |||| | | || || |||| | || ||| || | || ||| || || |||||| | || ||| ||| |||||||||||||||| || ||||||||||| ||||| || || ||||| || || || || ||
--gtgtgagtggagggaggggggcgagtata-gtttcgtgagct------ctgtcactatcacgaga---gctctttcgatctttgctaatctcttggaactcctgccatagGCGGACAATGTCAAGCACACTGGAGCGAGCAAACTGGTGCTCTACTTCACTGGAGCCACAAACATACTCTATACATTTGGAGGCCATGCGGTGACTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgtgggtgaccggccgagacgatgtgtgtgcttctgctgctctacttgttgcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGT
ctctactt CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgcaagcgtagcgttgaagcataatatgcattctgtgggcctgtggcctgtggcctgtgggtgaccggccgagacgatgtgtgtgcttctgctgctctacttgttgcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT