Sequence
atgc intronic sequence ATGC exonic sequence...tgtctgaagtggtacattgatgtaaatgatgttagttatcgggggagattgggctgctaaatgtgccacattgcgatgccttgacttgcgattggtgtagAGGAGTTTGTGGCGCATGCGTCCAATGTGAACTGCCTCAAGATTGGGAGGAAGACCTCACGGGTTCTTGTCACCGGAGGAGAGGATCATAAGGTCAATCT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G406553_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g58130.1 (Oryza sativa), 3'ss of exon 1
-tgtctgaagtggtacattgatgtaaatgatgttagttatc-gggggagattgggctgctaaatgtgccacattgcgatgccttgacttgcgattggtgtagAGGAGTTTGTGGCGCATGCGTCCAATGTGAACTGCCTCAAGATTGGGAGGAAGACCTCACGGGTTCTTGTCACCGGAGGAGAGGATCATAAGGTCAATCT
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gtgctt-atgaactgc-ctgaagattgcaacatgatttatttgggggtgattttgtgggtgaacttgcgacattggaatgccttgacttgcgtttggcgtagAGGAGTTTGTGGCGCATTCATCCAATGTCAACTGCCTCAAGATTGGGAGGAAGACTTCACGAGTTCTCGTGACAGGAGGAGATGACCATAAGGTTAATCT
upper sequence: GRMZM2G406553_T04 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA19G00890.1 (Glycine max), 3'ss of exon 2
------------------------------------------------------------------tgtctgaagtggtacattgatgtaaatgatgttagttatcgggggagattgggctgc-taaatgtgccacattgcgatgccttgacttgcgattggtgtagAGGAGTTTGTGGCGCATGCGTCCAATGTGAACTGCCTCAAGATTGGGAGGAAGACCTCACGGGTTCTTGTCACCGGAGGAGAGGATCATAAGGTCAATCT
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gtatccttcatctcttgtctgtctgtgctttacattttgtttgatctatctatgcactcgcccttcattttctatctgcagatctctctctactttgtta-ttatgttagagtctttctttgtgtgtgtgtgtgacttggctg-gccttgacgagttat--gtccagAGGAATTTGTAGCACATGCTTCTACTGTCAATTGCCTCAAGATTGGACGGAAATCATCCAGGGTTCTTGTCACTGGAGGTGAAGATCACAAGGTCAATCT
upper sequence: GRMZM2G406553_T04 (Zea mays), 3'ss of exon 1
lower sequence: Vv10s0071g01150.t01 (Vitis vinifera), 3'ss of exon 1
tgtctgaag-----tggtacattgatg-taaatgatgttagttatcgggggagattgggctgctaaatgtgccacattgcgatgccttgact-tgcgattggtgtagAGGAGTTTGTGGCGCATGCGTCCAATGTGAACTGCCTCAAGATTGGGAGGAAGACCTCACGGGTTCTTGTCACCGGAGGAGAGGATCATAAGGTCAATCT
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--tctgcagatcccttctctacccttgcttcacagcatttgttattttga-attttgaatttttacttct----cgagaaaattccttgaccacggtttttgaacagAGGAATTTGTAGCACACTCTTCCAGTGTAAACTGTCTCAAGATTGGGAGGAAGTCATCCAGGGTTCTTGTCACCGGTGGAGAAGATCACAAGGTGAATCT
upper sequence: GRMZM2G406553_T04 (Zea mays), 3'ss of exon 1
lower sequence: PP1S101_210V6.1 (Physcomitrella patens), 3'ss of exon 1
tgtctgaagtggtacattgatgtaaatgatgttagttatcgggggag--attgggctgctaaatgtgccacattgcgatgccttgacttgcgattggtgtagAGGAGTTTGTGGCGCATGCGTCCAATGTGAACTGCCTCAAGATTGGGAGGAAGACCTCACGGGTTCTTGTCACCGGAGGAGAGGATCATAAGGTCAATCT
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aatcttattagtctaaacactccaaattgt-tgagtcatttacgtgcttattggtgaggatattgtataattcggtttagtccttgactactaccctt-cagAGGAGTTTGTTGCACACTCTTCCAATGTCAACTGCCTCAAGATTGGGAAGAAGTCCTCTAGGGTCTTGGTCACCGGCGGAGAGGATCACAAAGTCAACAT
upper sequence: GRMZM2G406553_T04 (Zea mays), 3'ss of exon 1
lower sequence: PP1S9_241V6.1 (Physcomitrella patens), 3'ss of exon 1
------tgtc-tgaagtggtacattga-tgtaaatgatgttagttatcgggggagattgggctgctaaatgtgccacattgcgatgccttgacttgcgattggtgtagAGGAGTTTGTGGCGCATGCGTCCAATGTGAACTGCCTCAAGATTGGGAGGAAGACCTCACGGGTTCTTGTCACCGGAGGAGAGGATCATAAGGTCAATCT
| || ||| | ||| | | ||| | || ||| | || | ||| | |||| || ||| || | | |||||||| | || |||||| ||||| ||||| |||||| |||| ||||||||||| ||||| | |||| |||| |||| || ||||| || || |||||||| || || || |
gtaaaatatcatgatttcgtatttcaactgtgattgttgtcattt---cgtctcgatgaagttgctg--tggtccagatcatg-ttccttgactactagat--tgcagAGGAATTTGTTGCGCACGCGTCCGATGTCAACTGCCTCAAAATTGGAAAGAAGTCCTCCAGGGTCCTGGTCACGGGCGGGGAGGATCACAAAGTTAACAT
upper sequence: GRMZM2G406553_T04 (Zea mays), 3'ss of exon 1
lower sequence: EFJ05569 (Selaginella moellendorffii), 3'ss of exon 1
tgtctgaagtggtacattgatgtaaatgatgttagttatcgggggagattgggctgctaaatgtgccacattgcgatgccttgacttgcgattggtgtagAGGAGTTTGTGGCGCATGCGTCCAATGTGAACTGCCTCAAGATTGGGAGGAAGACCTCACGGGTTCTTGTCACCGGAGGAGAGGATCATAAGGTCAATCT
|| |||| | ||| | | | | | ||| |||| ||| | |||||||||||| |||||| | ||| | ||||| ||||||||||| |||||||| || || ||||| ||
------------------------------gtgagtttcttcg---catttgatttttttttcagAGCTTTTGGTTGATCTTG--TTGGTGGCAATCCAGAGGAGTTTGTTGCGCATTCTTCCCAGGTGAATTGCCTCAAGATCGGGAGGAAAACATCGCGGGTGCT---------------------------------
upper sequence: GRMZM2G406553_T04 (Zea mays), 3'ss of exon 1
lower sequence: EFJ26184 (Selaginella moellendorffii), 3'ss of exon 1
tgtctgaagtggtacattgatgtaaatgatgttagttatcgggggagattgggctgctaaatgtgccacattgcgatgccttgacttgcgattggtgtagAGGAGTTTGTGGCGCATGCGTCCAATGTGAACTGCCTCAAGATTGGGAGGAAGACCTCACGGGTTCTTGTCACCGGAGGAGAGGATCATAAGGTCAATCT
|| |||| | | || | || | || ||| | | || || |||||||||||| |||||| | ||| | ||||| ||||||||||| |||||||| || || ||||| || |||||||| ||||| ||||| ||||||||| |
------------------------------gtgagtttcttcgcat--tcggttttctttcagagctgttggttgatcttgttggtggcaatc----cagAGGAGTTTGTTGCGCATTCTTCCCAGGTGAATTGCCTCAAGATCGGGAGGAAAACATCGCGGGTGCTCGTCACCGGTGGAGACGATCACAAGGTCAATAT
upper sequence: GRMZM2G406553_T04 (Zea mays), 3'ss of exon 1
lower sequence: EFJ20167 (Selaginella moellendorffii), 3'ss of exon 1
tgtctgaagtggtacattgatgtaaatg---atgttagttatcgggggagattgggctgctaaatgtgccacattgcgatgccttgacttgcgattggtgtagAGGAGTTTGTGGCGCATGCGTCCAATGTGAACTGCCTCAAGATTGGGAGGAAGACCTCACGGGTTCTTGTCACCGGAGGAGAGGATCATAAGGTCAATCT
|||| | | | ||| | | | | | | |||| || | | | | |||| | || || | ||| | |||||| || || || |||| ||| |||| ||||| || || || |||| || |||||||||| |||||||||||||| |||||||| || || || |
-agctgagaaagcagaatgaagcgagcgtacaagctccgtatcctttttttttttttggtttcgctttttctttggcgaagttttcctttaccattagc--agAGGAATTCGTTGCTCATGGATCCGATGTCAACTGTCTTAAAATCGGGAAAAAATCCTCACGGGTGCTTGTCACCGGAGGTGAGGATCACAAAGTGAACAT
upper sequence: GRMZM2G406553_T04 (Zea mays), 3'ss of exon 1
lower sequence: EFJ23110 (Selaginella moellendorffii), 3'ss of exon 1
tgtctgaagtggtacattgatgtaaatgatgttagttatcgggggagattgggctgctaaatgtgccacatt----gcgatgccttgacttgcgattggtgtagAGGAGTTTGTGGCGCATGCGTCCAATGTGAACTGCCTCAAGATTGGGAGGAAGACCTCACGGGTTCTTGTCACCGGAGGAGAGGATCATAAGGTCAATCT
|||| | | | ||| | | | | || | || || | | | || | |||| | || || | ||| | |||||| || || || |||| ||| |||| ||||| || || || |||| || |||||||||| |||||||||||||| |||||||| || || || |
aagctgagaaagcagaatgaagcgagcg-tacaagct-ccgtatccttttttttttttggtttcgctttttctttggcgaagttttcctttaccattagc--agAGGAATTCGTTGCTCATGGATCCGATGTCAACTGTCTTAAAATCGGGAAAAAATCCTCACGGGTGCTTGTCACCGGAGGTGAGGATCACAAAGTGAACAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agattgggctgctaaatgtgccacattgcgatgccttgacttgcgattggtgtagAGGAGTTTGTGGCGCATGCGTCCAATGTGAACTGCCTCAAGATTGGGAGGAAGACCTCACGGGTTCTTGTCACCGGAGGAGAGGATCATAAGGTCAATCT
tgccttgac putative branch site
taaatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtctgaagtggtacattgatgtaaatgatgttagttatcgggggagattgggctgctaaatgtgccacattgcgatgccttgacttgcgattggtgtagAGGAGTTTGTGGCGCATGCGTCCAATGTGAACTGCCTCAAGATTGGGAGGAAGACCTCACGGGTTCTTGTCACCGGAGGAGAGGATCATAAGGTCAATCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT