Sequence
atgc intronic sequence ATGC exonic sequence...ccttccctagaccccacccatgcggaagcctctggcaccgggtctgcccttttttcagtaatgtataatctgattgtgagtaatcattttggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 11
-ccttccctagaccccacccatgcggaagcctctggcaccgggtctgcccttttttcagtaatgtataatctgattgtgagtaatcattttggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT
|| | | | | | || || | | | || | | | || | || | | ||||| | | || || ||| ||||| ||||||||||||| ||||||||||| |||||| | || || || || ||||||||||| || | ||||||||||||||| |||| ||||||||||| |||||||| |
ggctacaacatttcttttctttctactaggtaatgttagttg-tttgtcatatcttgaatagtattcaatcttactatgtgtcatctttttgtttggtcagAGCTTAAAGCATAACCCCAATGGAAGATTTGTCGTAGTTTGTGGAGATGGTGAATTCATAATTTATACTGCATTGGCTTGGAGGAATAGGTCATTTGGAT
upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 11
-------ccttccctagaccccacccatgcggaagcctctggcaccgggtctgcccttttttcagtaatgtataatctgattgtgagtaatcattttggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT
|| | || | | | || | | | | |||| | || |||||||| | || || ||| |||| || ||||| || || ||||| |||| |||||||||||||||||||| |||||||| || || ||||| |||| ||||| ||||| |||||||| |
agaagtgagttttaaaataatagtccttattgcgggttcaattatcagcaatatttgttttatgg----gtggtggctgattgt---tgatttcatttattgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTATGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 11
------ccttccctagacccca-cccatgcggaagcctctggcaccgggtctgcccttttttcagtaatgtataatctgattgtgagtaatcattttggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT
| | || | || | | | || | | | || ||||| || | | | ||||| | || || |||| |||| || ||||| || || ||||| |||| |||||||| ||||||||||| |||||||| || || ||||| |||| ||||| ||||| |||||||| |
agaagtgagttttaaaacaatagtccttattgctggttcaattatcaa--caatatttgtttcatgggtg-gtgactt-attgt---tgatttaatttgttgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTGTGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 11
ccttccctagaccccacccatgcggaagcctctggcaccgggtctgcccttttttcagtaatgtataatctgattgtgagtaatcattttggttggtc----agAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT
| | |||||| | | | |||| | | |||||||| |||| | | | | ||| | | |||| || | |||| || | ||| || || ||||| |||| |||||||| ||||||||||| ||||| || || || |||| |||| ||||| |||||||||||||| |
-taaaataataatccacccct-tagttttaattatcaccacttat-ttattttttcatgcatgt-tgactggtgtctgacttgtgatttacttttatactcaagAGTTTAAGGCACAATCCGAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGGGAGTATATTATATACACTGGTTTGGCATGGAGAAATAGATCATTTGGTT
upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 11
ccttccctagaccccacccatgcggaagcctctggcaccgggtctgcccttttttcagtaatgtataatctgat-tgtgagtaatcattttggttggt---cagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT
| | | | | || | | || | |||||| | | | ||| | | ||| | | |||| || | ||||| | | ||| || || ||||| ||||||||||||| ||||||||||| || || || || || ||||| |||| ||||| |||||||||||||| |
agctttaaaataataatctgccccttagttttaattatt---tccactttttttttta-agcatgttgactggtgtctgacttgtgatttacttttattctcagAGTCTAAGGCACAATCCAAATGGGAGGTTCGTTGTTGTTTGTGGAGATGGGGAATATATTATATACACTGCTTTGGCATGGAGAAATAGATCATTTGGTT
upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 11
lower sequence: AT3G15980.5 (Arabidopsis thaliana), 3'ss of exon 11
------------ccttccctagaccccacccatgcggaagcctctggcaccgggtct---gcccttttttcagta-atgtataatctgatt-gtgagtaatcattttggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT
| | |||| | ||| | | | ||| | | | ||| | | ||| || | || ||| | | ||||||||||||||| ||||||||||| |||| || || || || || ||||| ||||||||||| || ||||| |||| |||||
atttgaaatgaagcgttaatagatgataaaaatgaaactctgtttcatatgaagtcccaagagtgtggtccagaataattatgtcttgcctcacatatagCTATTCTAACTC-TCAGAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGA----------------
upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 11
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 15
--ccttccctagaccccacccatgcggaagcctctggcaccgggtctgcc-cttttttcagtaatgtataatctgattgtgagtaatcattttggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT
|| | | ||| || | | || || | || || ||| | ||| | |||| ||||| || ||||||||||||||| ||||||||||| |||| || || || ||||||||||| ||||| || || || |||||| |||| ||| | ||||| |||||||| |
ttactggtattagtaagaaatatgaccttaaatcatttattaattttgtgactacccactgtcatttatgtttctattatt--taatt-ttttgctttttcagAGCTTGAAGCACAACCCTAATGGTAGGTTTGTGGTAGTTTGTGGAGATGGTGAGTATATTATCTACACTGCCTTGGCGTGGCGAAATAGGTCATTTGGCT
upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 11
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
ccttccctagaccccacccatgcggaagcctctggcaccgggtct---gcccttttttcagta-atgtataatctgatt-gtgagtaatcattttggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT
|||| | ||| | | | ||| | | | ||| | | ||| || | || ||| | | ||||||||||||||| ||||||||||| |||| || || || || || ||||| ||||||||||| || ||||| |||| ||||| |||||||| |||||||
----taatagatgataaaaatgaaactctgtttcatatgaagtcccaagagtgtggtccagaataattatgtcttgcctcacatatagctattctaactc-tcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 11
ccttccctagaccccacccatgcggaagcctctggcac---cgggtctgcccttttttcagta-atgtataatctgattgtgagtaatcattttggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT
| | | | | | || || | | || ||| || | | || | | | | |||| || ||||||| | || |||||||| ||||| |||| |||||||| ||||||||||| |||||||| || ||||| || |||| ||||||||||| || ||||| |
----gcattaagctaggatgaatgattgtttccaccatattttaatttattgttatttatgtttacatttatttcttccttttttttttttttttgtgtttcagAGCCTAAAACATAACCCAAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGTGAGTACATTATATATACAGCTTTGGCATGGAGGAATAGGTCTTTTGGTT
upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 11
lower sequence: PP1S61_1V6.1 (Physcomitrella patens), 3'ss of exon 11
--ccttccctagaccccacccatgcggaagcctctggcaccgggtctgcccttttttcagtaatgtataatc-tgattgtgagtaatcat-tttggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT
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gaggtgcttgaggtgtaacctggtcataa----ttattgtctgtgcttgaaacatgtcaattataaatattcatggatgtgtgtgtttgtgtcttgttgtgcagAGCTTGGAGCATAATCCTAATGGCAGATTTGTGGTCGTATGCGGTGATGGAGAGTACATTATTTATACTGCCCTGGCATGGAGGAACAGATCTTTTGGCTMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|26457397|gb|CA828980.1|CA828980EST: GATTACCCTTGGCTGTAAAAGAGTTAGGAAGCTGTGATTTGTACCCACAG AGCTTGAAGCATAACCCTAATGGACGGTTCGTTGT
genomic: GATTACCCTTGGCTGTAAAAGAGTTAGGAAGCTGTGATTTGTACCCACAGgtacttctgg ... ggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGT
EST:
gi|32865242|gb|CF004924.1|CF004924EST: GATTACCCTTGGCTGTAAAAGAGTTAGGAAGCTGTGATTTGTACCCACAG AGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGC
genomic: GATTACCCTTGGCTGTAAAAGAGTTAGGAAGCTGTGATTTGTACCCACAGgtacttctgg ... ggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGC
EST:
gi|31353243|gb|CD437600.1|CD437600EST: GATTACCCTTGGCTGTAAAAGAGTTAGGAAGCTGTGATTTGTACCCACAG AGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGC
genomic: GATTACCCTTGGCTGTAAAAGAGTTAGGAAGCTGTGATTTGTACCCACAGgtacttctgg ... ggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGC
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 4 RNA-Seq libraries.
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
274GCCACAGATGGAGAAAGATTACCCTTGGCTGTAAAAGAGTTAGGAAGCTGTGATTTGTACCCACAGgtacttctgg ... ggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT
Block sizes:
48 (upstream exon),
49 (downstream exon)
Score:
147GCCACAGATGGAGAAAGATTACCCTTGGCTGTAAAAGAGTTAGGAAGCTGTGATTTGTACCCACAGgtacttctgg ... ggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT
Block sizes:
48 (upstream exon),
49 (downstream exon)
Score:
139GCCACAGATGGAGAAAGATTACCCTTGGCTGTAAAAGAGTTAGGAAGCTGTGATTTGTACCCACAGgtacttctgg ... ggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
206GCCACAGATGGAGAAAGATTACCCTTGGCTGTAAAAGAGTTAGGAAGCTGTGATTTGTACCCACAGgtacttctgg ... ggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcccttttttcagtaatgtataatctgattgtgagtaatcattttggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT
atctgat putative branch site (score: 206)
taatgtataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccttccctagaccccacccatgcggaagcctctggcaccgggtctgcccttttttcagtaatgtataatctgattgtgagtaatcattttggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - -ccccacc
- - - - - - - - - catgcgg
- - - - - - - - - - - - - -gcctctg
- - - - - - - - - - - - - - - - - gcaccgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgattg