Sequence
atgc intronic sequence ATGC exonic sequence...aatcaaatgacatccatatccaaaataattgggtgtgcctttgtgcttttgtattattgtcacagtttcgtaatgtggatctttgtgtttccattttcagAGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os12g04990.3 (Oryza sativa), 3'ss of exon 15
---------------------------------------aatcaaatgacatccatatccaaaataattgggtg-tgcctttgtgcttttgtattattgt------cacagtttcgtaatgtggatctttgtgtttccatttt-cagAGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGG
|| || | | | || | ||||| || |||| || | ||||| ||| || | ||| | || | ||||| ||||| ||||| | ||||| ||||||||||||||||||||||| || ||||| ||| |||| ||||||||||||||||| |||||||| ||||||| |||||| ||
gtaagatctgtgtttgggtttaactagacttggttggataaataacttgtccttttgttcacagtaattcctcactgttattgtttttgtacattatcacttctcacactcttccataacgcaaattct---gtttctatttttcagAGATTAAACTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATGAACCATATCCTCGTGGAGAAATCTGTGTTAGGGGACCTACGATATTCTGTGG
upper sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os11g04980.2 (Oryza sativa), 3'ss of exon 16
---aatcaaatgacatccatatccaaaataattgggtgtgcctttgtgcttttgtat-tattgtcacagtttcgtaatgtggatctttgtgtttccatttt-cagAGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGG
| | || | || | | | | | | |||| |||| | | | ||||| | || |||||| ||| | ||| ||||||| ||||| | || || ||||||||||||||||||||||| || ||||| |||||||| |||||||||||||||||||||||||| ||| ||| ||||| ||
ttaaccccaaataagtctaggtttcatct--tcaactaaaatattgtttttttttgcgtgctatcacactctcataatgtaaatcct---gttgccatttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAACCATATCCTCGTGGAGAAATTTGTGTTAGGGGAACTACGATATTTTTTGG
upper sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA15G34650.1 (Glycine max), 3'ss of exon 4
----------aatcaaatgacatccatatccaaaataattgggt-gtgcctttgtgc-ttttgtattattgtcacagtttcgt--aatgtggatctttgtgtttccattttcagAGG--TGAAACTTGTG-GATGTCCCAGAA---------ATGAATTATACATCTGATGAT--CAACCTTATC----CTCGTGGAGAAATTTGTGTTAGAGGACCTATA-ATATTCCAGGG------------------------
| ||| | | | || | | | || || | || | | ||| | | | |||| | ||| | | | || | || || || | |||| | || ||| | ||| || | || | ||| ||| ||||||| | ||| | | | |||| || | || | | || ||||||
gttttcaacaagataaaaaagaagcttagaggacgagttcgagttatggcattaggtgcctcacatttatcacccgatttcatggaattttggaagatttgccttggttgtcggatgactgaaggatatgcaatgacggagagtcttgtgttataagTTGCATTGATGAGGATGACAACCTTGTTGGCTCTCCTAATGTAGCCTGTGATATAAAACTTGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAG
upper sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA20G28200.1 (Glycine max), 3'ss of exon 16
--aatcaaatgacatccatatccaaaat--aattgggtgtgcctttgtgcttttgtattattgtcacagtttcgtaatgtggatctttgtgtttccat-tttcagAGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGG
| |||| | || | || || |||| || | || | |||| |||| | | || || | || |||| | |||||||| | ||||| |||||||| ||||||||||| ||||||||||||||||| || |||| ||||| ||||||||||| || || || | | || | ||
ctccttttatgaaaga-atttaaaagatgaaattatgtttaatttatgtcagctgtagctttgttatg----cctagtgccaacagttttgttcttttgtttcagAGATAAAACTAGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAGCCCAATCCCCGTGGTGAAATTTGTGTCAGGGGTCCCCTTGTTTTTCGAGG
upper sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA10G39540.1 (Glycine max), 3'ss of exon 16
---aatcaaatgacatccatatccaaaataattgggtgtgcctttgtgcttttgtattattgtcacagtttcgtaatgtggatctttgtgtttccattttcagAGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGG
| | || || | | || | | || | | |||| || | | | | || || ||||| || ||| ||||| | |||||||||||||| ||||||||||| ||||||||||||||||| || |||| ||||| ||||||||||| || || || || | || | |||
cactttttatggaagaatttaaaagatgaagttatatttaatttatgtcatctgtagctttcttat-gcctagtgcca-agagttttgttcttttgttt-cagAGATAAAACTTGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAGCCCAATCCCCGTGGTGAAATTTGTGTCAGGGGTCCCATTGTTTTTCGGGG
upper sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT5G27600.1 (Arabidopsis thaliana), 3'ss of exon 16
aatcaaatgacatccatatccaaaataattgggtgtgcc----tttgtgcttttgtattattgtcacagtttcgtaatgtggatctt-----tgtgtttccattttcagAGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGG
|| | | | ||| | || | | | | ||||||||| | | | | || | || ||| ||| | || | |||||| |||||||||||||| || ||||||||||| ||||| || |||||||| || || ||||| ||||| ||||| |||||||| || || ||| | ||
--gtaagcaatgtgttattttaaagacagtgtatatatcagaatccaaacttttgtatccaaattgtatgactggtttttgtgttttgaaaatgttttttctttcttagAGGTAAAACTTGTGGATGTTCCCGAAATGAATTACACATCAGACGATCAACCATACCCACGTGGTGAAATCTGTGTAAGAGGACCAATCATCTTCAAAGG
upper sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT3G05970.1 (Arabidopsis thaliana), 3'ss of exon 16
--aatcaaatgacatccatatccaaaataattgggtgtgcc-tttgtgcttttgtattattgtcaca--gtttcgtaatgtggatctttgtgtttccat-tttcagAGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGG
| | | || | | | | | || || | | | |||| | ||| | | | | | || | || | | || |||| || ||||||| || || ||||||||||||||||||||||| |||||||| | ||||| || |||| ||||| ||||| |||||||| || ||||| || || ||
gtgagctttttac-tgactctgcgatatgataagtagagtaatttggaactaaatatccattttaaattgctttgggatttaa---tatgcatttctatatttcagAAGTAAAGCTTGTGGATGTCCCAGAAATGAACTATACATCAGCGGATCAGCCCCATCCCCGTGGCGAAATATGTGTTAGGGGTCCTATCATTTTTACAGG
upper sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv14s0128g00720.t01 (Vitis vinifera), 3'ss of exon 16
aatcaaatgacatccatatccaaaataattgggtgtgcctttgtgcttttgtattattgtcacagtttcgtaatg-tggatctttgtg--tttccattttcagAGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGG
|| || | | | || | ||| | | | | | | | || | | || | | || || ||||| ||||||| | || ||||||||||| || ||||||||||| || ||||| ||||| || |||||||| || ||||| ||||| || || || | | ||||| ||
---taattgccggatgtctttaagaaaatggtattcacaactaatgaactaattcactgagttgtgtggattctggttgctccctgcccttttcctctttcagAAATAAAGCTTGTGGATGTTCCTGAAATGAATTACACCTCTGAGGATCAGCCCTATCCTCGCGGTGAAATATGTGTCAGGGGTCCCGTTCTCTTCCAAGG
upper sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 16
aatcaaatgacatccatatccaaaataattgggtgtgcctttgtgcttttgtat-tattgtcacagtttcgta-atgtggatctttgtgtttccattttcagAGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGG
| ||| | || ||| | || | | |||| | | || | | || | ||| | | | | || || | | ||| ||||||| ||||| ||||||||||| || |||||||| || |||||||| ||||| || ||||||||||| ||||| |||||| | || || || | || | ||
-aacaagaaaaatgtggctcctgagtacaacaat-tttctttccattgtggtctgtgctgctctattttgggataaatttatgttaatttgtcctctttcagAAGTGAAGCTTGTGGATGTTCCGGAAATGAACTACACATCTGAGGATCAGCCCTATCCTCGTGGTGAAATCTGTGTTCGGGGTCCCATTCTTTTTCTAGG
upper sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S12_178V6.1 (Physcomitrella patens), 3'ss of exon 19
---------------------------------------------------aatcaaatgacatccatatcca-----aaataat----tgggtgtgcctttgtgcttttgtattattgtcacagtttcgtaatgtggatctttgtgtttccat-tttcagAGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGG
||||| | || || || | |||| | | || | | | | | | || |||| | | | | | || ||| || | ||||||||||| |||| || || || || ||| | || ||| | |||| | ||||||||||| ||||| |||||||| |||||||| ||| ||||| | ||
gtaagtttcccgaaggattaatctgttttagtgatttttcgctattattaagatcaactaacttctatgatgacttgcaaatgtccttgtagatgaagatcagcacactgttctaatattcact-tctaggattaaatgaattggtggccttatgtctcagAGGTGAAGCTTGCTGACGTTCCCGAGATGGAGTACACAGATAATGACAAGCCTTATCCTCGAGGAGAGATTTGTGTGAGAGGACCCATATTATTCAAAGGMapped 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|67023162|gb|CO451911.1|CO451911EST: TATTGGTGACAGATCAATTGGTCATGTTGGATCCCCAACTGCATCTTGTG AGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACATCTGATGATCAAC
genomic: TATTGGTGACAGATCAATTGGTCATGTTGGATCCCCAACTGCATCTTGTGgtaagctccg ... ccattttcagAGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACATCTGATGATCAAC
EST:
gi|211216805|gb|FL024790.1|FL024790EST: TATTGGTGACAGATCAATTGGTCATGTTGGATCCCCAACTGCATCTTGTG AGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACATCTGATGATCAAC
genomic: TATTGGTGACAGATCAATTGGTCATGTTGGATCCCCAACTGCATCTTGTGgtaagctccg ... ccattttcagAGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACATCTGATGATCAAC
EST:
gi|211216803|gb|FL024788.1|FL024788EST: TATTGGTGACAGATCAATTGGTCATGTTGGATCCCCAACTGCATCTTGTG AGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACATCTGATGATCAAC
genomic: TATTGGTGACAGATCAATTGGTCATGTTGGATCCCCAACTGCATCTTGTGgtaagctccg ... ccattttcagAGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACATCTGATGATCAAC
EST:
gi|211216806|gb|FL024791.1|FL024791EST: TATTGGTGACAGATCAATTGGTCATGTTGGATCCCCAACTGCATCTTGTG AGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACATCTGATGATCAAC
genomic: TATTGGTGACAGATCAATTGGTCATGTTGGATCCCCAACTGCATCTTGTGgtaagctccg ... ccattttcagAGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACATCTGATGATCAAC
EST:
gi|211216802|gb|FL024787.1|FL024787EST: TATTGGTGACAGATCAATTGGTCATGTTGGATCCCCAACTGCATCTTGTG AGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACATCTGATGATCAAC
genomic: TATTGGTGACAGATCAATTGGTCATGTTGGATCCCCAACTGCATCTTGTGgtaagctccg ... ccattttcagAGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACATCTGATGATCAAC
EST:
gi|91873018|gb|EB402975.1|EB402975EST: TATTGGTGACAGATCAATTGGTCATGTTGGATCCCCAACTGCATCTTGTG AGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACCATCTGATGATCAA
genomic: TATTGGTGACAGATCAATTGGTCATGTTGGATCCCCAACTGCATCTTGTGgtaagctccg ... ccattttcagAGGTGAAACTTGTGGATGTCCCAGAAATGAATTATAC-ATCTGATGATCAA
EST:
gi|50335868|gb|CO530994.1|CO530994EST: TATTGGTGACAGATCAATTGGTCATGTTGGATCCCCAACTGCATCTTGTG AGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACATCTGATGATCAAC
genomic: TATTGGTGACAGATCAATTGGTCATGTTGGATCCCCAACTGCATCTTGTGgtaagctccg ... ccattttcagAGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACATCTGATGATCAAC
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),
45 (downstream exon)
Score:
60CTTGAAGGCTATGGAATGACGGAGACATCCTGTATCATATCTGCAATGGATATTGGTGACAGATCAATTGGTCATGTTGGATCCCCAACTGCATCTTGTGgtaagctccg ... ccattttcagAGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
263CTTGAAGGCTATGGAATGACGGAGACATCCTGTATCATATCTGCAATGGATATTGGTGACAGATCAATTGGTCATGTTGGATCCCCAACTGCATCTTGTGgtaagctccg ... ccattttcagAGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
260CTTGAAGGCTATGGAATGACGGAGACATCCTGTATCATATCTGCAATGGATATTGGTGACAGATCAATTGGTCATGTTGGATCCCCAACTGCATCTTGTGgtaagctccg ... ccattttcagAGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGG
Block sizes:
48 (upstream exon),
49 (downstream exon)
Score:
126CTTGAAGGCTATGGAATGACGGAGACATCCTGTATCATATCTGCAATGGATATTGGTGACAGATCAATTGGTCATGTTGGATCCCCAACTGCATCTTGTGgtaagctccg ... ccattttcagAGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttgtattattgtcacagtttcgtaatgtggatctttgtgtttccattttcagAGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGG
tttccattttc CT-rich tract
tattattgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatcaaatgacatccatatccaaaataattgggtgtgcctttgtgcttttgtattattgtcacagtttcgtaatgtggatctttgtgtttccattttcagAGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
aatcaaa
- - - - -acatcca
- - - - - - - - - - -aaaataa
- - - - - - - - - - - - - - - - - -tgccttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtggatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgttt