Sequence
atgc intronic sequence ATGC exonic sequencegtgattataatccttaataaactttagatttgctgccaagtattaagttaaataattggctaatgtttaattgtagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAATATATTAGATTGTCCATGGAAGAAGATGGTGAGGATGCTTCAAATGGAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 11
gtgattataa-tcctta--ataaa-ctttagatttgctgccaagtattaagttaaataattggctaatgttta-attgtagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAATATATTAGATTGTCCATGGAAGAAGATGGTGAGGATGCTTCAAATGGAA
||||| | || | ||| ||||| | | ||| ||| || || | ||| | |||| | || ||| ||| |||||||||||||||||||| |||| |||||||| ||||| ||||||||||| |||||||||||||||||||||||||||||||| ||||||||||||||||
gtgatcacaacttcttgccataaagcagtgaattcactgttaatcatctaaataacaagttggatcatctttttatttcagGAACGTGAAAATCCAACTTTAACCGAGTGGGATCGGTTCGCACATAGAGAGTATATTAGATTGTCCATGGAAGAAGATGGTGAAGATGCTTCAAATGGAA
upper sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA10G32500.1 (Glycine max), 3'ss of exon 11
--------------gtgattata-atccttaa----taaactttagatttgctgccaagtattaagttaaataattggctaatgtttaattgtagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAATATATTAGATTGTCCATGGAAGAAGATGGTGAGGATGCTTCAAATGGAA
| ||| || ||| ||| ||| |||| | | ||||| | | | || || | ||| || ||||||||||| |||||| | | || |||||||| || |||||||||||||| |||||||| | |||||||||||||||||||| ||| ||||||| |
gtaaaaataagattgagatcctatatcactaacaattaaggcttagtaatcttagcaagttctgattacaacaa-----gggtattttgtt-tagGAACGTGAGGATCCAAATTTGACAGAGTGGGATCGTTTTGCACATAGAGAGTATATTAGGCTTTCCATGGAAGAAGATGGTGAAGATATGTCAAATGCCA
upper sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA10G30930.1 (Glycine max), 3'ss of exon 11
----------------------gtgattataatccttaataaactt-tagatttgctgccaagtattaagtta---aataattggc-----taatgtttaattgtagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAATATATTAGATTGTCCATGGAAGAAGATGGTGAGGATGCTTCAAATGGAA
| ||| | || | | | | | || ||| | || | | || ||||||| || | | ||||||||||| || ||||| | || |||||||| || ||||| ||| ||||||||||||| | || ||||||||||||| || ||||| || |||||||
gtgcatgaaatatttgataaaatttattgcattcttgagttagtatgtatgcttggctactgttagtgacttccttggtaattggtatgcatatcttgtgtgaatagGAACGTGAGAACCCAACATTGACAGAGTGGGATCGATTTGCTCATCGAGAATATATTAGGCTTTCAATGGAAGAAGATGTAGAAGATGCCTCTAATGGAA
upper sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 11
-----------------------gtgattataatccttaataaactttagatttgctgccaagtattaagttaaataa--ttggctaatgtttaatt---gtagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAATATATTAGATTGTCCATGGAAGAAGATGGTGAGGATGCTTCAAATGGAA
|| ||| | | | | | | | |||| || | | || | |||| |||| | | |||||||||| ||||| || | || |||||||| || ||||| ||||||||||||||||| | || ||||||||||||| |||||||| || || || |
gtgcatgaatatttgataaaagtgttattgtgctgttgagtcagtat--gattgactattgttggtaagttttgactgccttggtatatgtcttgtgtgaacagGAACGTGAGAATCCTACATTGACAGAGTGGGATCGCTTTGCTCATAGAGAATATATTAGGCTTTCTATGGAAGAAGATGTAGAGGATGCCTCTAACGGTA
upper sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA20G35090.1 (Glycine max), 3'ss of exon 11
--------gtgattataatccttaataa-----actttagatttgctgccaagtattaagttaaataattg-gctaatgtttaattgtagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAATATATTAGATTGTCCATGGAAGAAGATGGTGAGGATGCTTCAAATGGAA
||||| ||||| || | | || || || | | || | || | | ||| || ||||||||||| |||||| | | || |||||||| || |||||||||||||| |||||||| | |||||||||||||||||||| ||| ||||||| |
gtaaaaataagattaagatcctatatcactaacaattaaggcttagtaatgttagtaaattctgattacaacaagggtattttgtt-tagGAACGTGAGGATCCAAATTTGACAGAGTGGGATCGTTTTGCACATAGAGAGTATATTAGGCTTTCCATGGAAGAAGATGGTGAAGATATGTCAAATGCCA
upper sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 11
lower sequence: AT5G28900.1 (Arabidopsis thaliana), 3'ss of exon 11
gtgattataatccttaataaactttagatttgctgccaagtattaa----gttaaataat-tggctaatgtttaattg---tagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAATATATTAGATTGTCCATGGAAGAAGATGGTGAGGATGCTTCAAATGGAA
|| | || ||| |||| || || | || | | | | || |||| | ||||||| || | |||| || || || || || | || || |||||||| |||||||||||||| |||||||| | || ||||||||||||| ||| ||||| || |||||||
gtactaatcatc--taatttaccttgctacttcttcacaccaccacatgcgtcttataacatttctaatgtcaaacggaaacagGAGCGAGAGAACCCTACATTGACAGATTGGGACCGTTTTGCACATAGAGAGTATATTAGGCTATCAATGGAAGAAGATGTTGAAGATGCATCTAATGGAA
upper sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 11
lower sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 10
--gtgattataatcct--taataaactttagatttgctgccaagtattaag--ttaaataat-tggctaatgtttaattg---tagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAATATATTAGATTGTCCATGGAAGAAGATGGTGAGGATGCTTCAAATGGAA
| | | | || | ||| || || | | | | | |||| | | ||||| || |||| || || || || || | || || |||||||| |||||||||||||| |||||| | | || ||||||||||||| ||| ||||| || |||||||
gtactactccacgtttgatattcaaccttgctgttttcttgacacaatgggcctcttataacatttcaaatgtcaaacgaaaacagGAGCGCGAGAACCCGACATTGACAGACTGGGACCGTTTTGCACATAGAGAGTATATTCGGCTATCAATGGAAGAAGATGTTGAAGATGCATCCAATGGAA
upper sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 11
lower sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 10
gtgattataatccttaataaa--ctttagatttgctgccaagtattaagttaaata---attggctaatgtttaattg--------tagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAATATATTAGATTGTCCATGGAAGAAGATGGTGAGGATGCTTCAAATGGAA
|| || | || || |||| | ||| | | | || | | | ||| ||| |||| || |||| ||||| || | |||||| || || |||||||| || ||||| ||||||||||||||||| | || ||||||||||||| || |||||||| |||||||
gt-atcacaaaatatagtaaataccttaaagctagctatacatacttatagagatattcatttctcaatgattgattgctgatacatagGAGCGCGCAAATCCGACATGGACAGAGTGGGATCGTTTTGCTCATAGAGAATATATTAGGCTATCAATGGAAGAAGATGTCGAAGATGCTTCTAATGGAA
upper sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv07s0005g03730.t01 (Vitis vinifera), 3'ss of exon 12
---------------------------gtgattat-aatccttaataaactttagatttgctgccaagtatta-agttaaataattggctaatgtttaatt-gtagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAATATATTAGATTGTCCATGGAAGAAGATGGTGAGGATGCTTCAAATGGAA
| | || |||| || || | || || || |||| ||| |||||| | ||| | ||||||| || |||||||| | || ||||||||||| ||||||||||||||||| ||||| | || ||||||||||||||||| |||| ||||||||||
gtaaattcaacatttttataggtgctcctagtaatcaatcattgccaagttgtattttattcctttagcattatagtattcccattggcatttatttggcaagcagGAACGAGAGGATCCAACTTTGACAGAGTGGGACCGCTTTGCACATAGAGAATACATTAGGCTTTCAATGGAAGAAGATGGTGAAGATGTCTCAAATGGAAMapped 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|23199690|gb|BU582255.1|BU582255EST: TCAACAAGTTCATGGCGTTTGAAACTCGTGATCCGTTCCTCATTCGCCAG GAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAA
genomic: TCAACAAGTTCATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgattataa ... ttaattgtagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAA
EST:
gi|4612853|gb|AI603692.1|AI603692EST: TCATGGC-TTTG-AACTCGTGATCCATTCNTCATTCGCCAG GAACGTGAAAATCCAACTCTAACTGAGTGGGNCCGGTTTGCACATAGAGAA
genomic: TCATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgattataa ... ttaattgtagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAA
EST:
gi|83279222|gb|DV943230.1|DV943230EST: TCAACAAGTTCATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAG GAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAA
genomic: TCAACAAGTTCATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgattataa ... ttaattgtagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAA
EST:
gi|211505070|gb|FK974738.1|FK974738EST: CCTCATTCGCCAG GAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAA
genomic: CCTCATTCGCCAGgtgattataa ... ttaattgtagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAA
EST:
gi|23199745|gb|BU582310.1|BU582310EST: TCAACAAGTTCATGGCGTTTGAAACTCGTGATCCGTTCCTCATTCGCCAG GAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAA
genomic: TCAACAAGTTCATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgattataa ... ttaattgtagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAA
EST:
gi|211372413|gb|FL431585.1|FL431585EST: TCCTCATTCGCCAG GAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAA
genomic: TCCTCATTCGCCAGgtgattataa ... ttaattgtagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAA
EST:
gi|12972292|gb|BG267909.1|BG267909EST: CCATTCCTCATTCGCCAG GAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAA
genomic: CCATTCCTCATTCGCCAGgtgattataa ... ttaattgtagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAA
EST:
gi|26560172|gb|CA832407.1|CA832407EST: TCAACAAGTTCATGGCGTTTGAAACTCGTGATCCGTTCCTCATTCGCCAG GAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAA
genomic: TCAACAAGTTCATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgattataa ... ttaattgtagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAA
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:
48 (upstream exon),
47 (downstream exon)
Score:
159CTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgattataa ... ttaattgtagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAATATATTAGATTGTCCATGGAAGAAGATGGTGAGGATGCTTCAAATGGAA
Block sizes:
49 (upstream exon),
47 (downstream exon)
Score:
142CTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgattataa ... ttaattgtagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAATATATTAGATTGTCCATGGAAGAAGATGGTGAGGATGCTTCAAATGGAA
Block sizes:
49 (upstream exon),
47 (downstream exon)
Score:
144CTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgattataa ... ttaattgtagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAATATATTAGATTGTCCATGGAAGAAGATGGTGAGGATGCTTCAAATGGAA
Block sizes:
49 (upstream exon),
47 (downstream exon)
Score:
113CTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgattataa ... ttaattgtagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAATATATTAGATTGTCCATGGAAGAAGATGGTGAGGATGCTTCAAATGGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttagatttgctgccaagtattaagttaaataattggctaatgtttaattgtagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAATATATTAGATTGTCCATGGAAGAAGATGGTGAGGATGCTTCAAATGGAA
aagtattaagttaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgattataatccttaataaactttagatttgctgccaagtattaagttaaataattggctaatgtttaattgtagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAATATATTAGATTGTCCATGGAAGAAGATGGTGAGGATGCTTCAAATGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG