Sequence
atgc intronic sequence ATGC exonic sequence...ttagttcctgtttttgtaaaatataatattgaattagtagagtactagtagaattcattgcattacctgcttgtgtaactgacaaatgataaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCATTGGTGATGGAACAGTGAGCTATGGAATGGATGATGCCGATGACATCTA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G071010_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA10G09280.2 (Glycine max), 3'ss of exon 1
---ttagt-tcctgtttttgtaaaatataatattgaattagtagagtactagtagaattcattgcattacctgcttgtgtaactgacaaatgataaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCATTGGTGATGGAACAGTGAGCTATGGAATGGATGATGCCGATGACATCTA
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ttatcaatatgtcatgcattgatcccacaatggctagtta-cattgtgttattcaaataaaaaagtttgtgt-tttgttaaatatttgtatgttaaa--tgcagTTCCTAGGAACTTCAGATTGCTGGAGGAGCTTGAACGTGGAGAAAAAGGAATTGGAGATGGCACAGTTAGCTATGGAATGGATGATGGTGATGACATTTA
upper sequence: GRMZM2G071010_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA02G35990.1 (Glycine max), 3'ss of exon 1
ttagttcctgtttttgtaaa---atataatattgaattagtagagtactagtagaattcattgcattacctgcttgtgtaactgacaaatgataaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCATTGGTGATGGAACAGTGAGCTATGGAATGGATGATGCCGATGACATCTA
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gtagatattcttgtcatgaattgatcccacaatgg-ctagttacatgttttca-aataaaaaatgtttgtgttctgttaaatatttgtatgtttaaa-tgcagTTCCTAGGAACTTCAGATTGCTGGAGGAGCTTGAACGTGGTGAAAAAGGAATTGGAGATGGCACAGTTAGCTATGGAATGGATGATGGTGATGACATTTA
upper sequence: GRMZM2G071010_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA03G35790.1 (Glycine max), 3'ss of exon 1
ttagttcctgtttttgtaaaatataatattgaattagtagag-tactagtagaattcattgcattacc-tgcttgtgtaactga---caaatg-ataaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCATTGGTGATGGAACAGTGAGCTATGGAATGGATGATGCCGATGACATCTA
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------aatttggttgaaggattacatatgtagccattcttgatatttattgaagatacaatgttagcatgagtatgtagttaaaggcatttgtactttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAATCGGAGATGGAACAGTTAGCTATGGAATGGATGATGGTGACGACATTTA
upper sequence: GRMZM2G071010_T03 (Zea mays), 3'ss of exon 1
lower sequence: AT3G52560.4 (Arabidopsis thaliana), 3'ss of exon 1
ttagttcctgtttttgtaaaatataatattgaattagtagagtactagtaga-attcattg-cattacctgcttgtgtaactgacaaatgataaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCATTGGTGATGGAACAGTGAGCTATGGAATGGATGATGCCGATGACATCTA
|| |||| | | | ||| || | || | || || ||| | || || | || || ||| || | | || ||| |||||| | || || || | || |||||||| || ||||| ||||| || ||||| |||||||| |||||||||||||||||||||| |||||||||||
atatgatatgttctgttctctgctttgattaaaaaaagtgattgcttgttttcatttactgatatgaattgtttttgttac--gcttgttattgcaatatagTTCCGAGGAATTTTCGGTTGTTGGAGGAGCTTGAACGTGGGGAGAAAGGTATTGGGGATGGAACTGTGAGCTATGGAATGGATGATGGAGATGACATCTA
upper sequence: GRMZM2G071010_T03 (Zea mays), 3'ss of exon 1
lower sequence: AT2G36060.3 (Arabidopsis thaliana), 3'ss of exon 1
ttagttcctgtttttgtaaaatataatattgaattagtagagtactagtagaattcattgcattacctgcttgtgtaactgacaaatgataaaaatgca--gTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCATTGGTGATGGAACAGTGAGCTATGGAATGGATGATGCCGATGACATCTA
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-tagattgttttcaagctcagtgctttgcttagaatatagagc-ttatttgtgttagtttccttcactaaaaattgagctgtttgatgttgttaatgtaaagTTCCGAGGAATTTCCGGTTGCTGGAGGAGCTTGAACGTGGAGAGAAAGGTATTGGAGATGGAACTGTGAGCTATGGAATGGATGATGGAGATGACATTTA
upper sequence: GRMZM2G071010_T03 (Zea mays), 3'ss of exon 1
lower sequence: Vv06s0080g01080.t01 (Vitis vinifera), 3'ss of exon 1
ttagttcctgtttttgtaaaatataatattgaatt---agtagagtactagtagaattcattgcattacctgcttgtgtaactgacaaatgataaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCATTGGTGATGGAACAGTGAGCTATGGAATGGATGATGCCGATGACATCTA
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--acaactggagttggaaatgcttggtatcttgtctcaagtgaaactatcttaga-tggaagttacaaggtatgtgtgtttttgtctttatgttatcttgcagTCCCTCGCAACTTCAGATTGCTGGAGGAACTTGAACGTGGGGAGAAGGGTATTGGAGATGGTACTGTGAGTTATGGAATGGATGATGGAGATGACATATA
upper sequence: GRMZM2G071010_T03 (Zea mays), 3'ss of exon 1
lower sequence: Vv08s0007g02580.t01 (Vitis vinifera), 3'ss of exon 1
-----ttagttcctgtttttgtaaaatataatattgaattagtagagtactagtagaattcattgcattacctgcttgtgtaactgacaaatgataaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCATTGGTGATGGAACAGTGAGCTATGGAATGGATGATGCCGATGACATCTA
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tggtctgaagcttagcctttgatatttaaggcgccttattcagacaattttattaattttcaa-gatttgcgcacttttaagtctctgcatttcca----tgcagTCCCTCGAAACTTCAGATTGCTTGAGGAACTTGAACGTGGAGAAAAGGGTATTGGAGATGGTACTGTCAGCTATGGAATGGATGATGGAGATGACATTTAMapped 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|32923039|gb|CF027851.1|CF027851EST: TCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCG TTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCA
genomic: TCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCGgtaagtaacc ... aaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCA
EST:
gi|33095289|gb|CF055283.1|CF055283EST: TCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCG TTCCCCGAAACTTCAGGCTATTATTGGAGCTCGAGCGTGGAGAGAAGGGCA
genomic: TCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCGgtaagtaacc ... aaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCA
EST:
gi|211256805|gb|FL058291.1|FL058291EST: TCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCG TTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAAAAGGGCA
genomic: TCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCGgtaagtaacc ... aaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCA
EST:
gi|71437348|gb|DR818398.1|DR818398EST: TCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCG TTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCA
genomic: TCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCGgtaagtaacc ... aaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCA
EST:
gi|211040687|gb|FL105663.1|FL105663EST: TCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCG TTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTG
genomic: TCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCGgtaagtaacc ... aaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTG
EST:
gi|211055493|gb|FL105750.1|FL105750EST: TCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCG TTCCCCGAAACTTCAGGCTATTA
genomic: TCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCGgtaagtaacc ... aaaaatgcagTTCCCCGAAACTTCAGGCTATTA
EST:
gi|32929652|gb|CF034464.1|CF034464EST: TCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCG TTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCA
genomic: TCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCGgtaagtaacc ... aaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCA
EST:
gi|211437842|gb|FL105651.1|FL105651EST: TCCAGGGGCGATSACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCG TTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCA
genomic: TCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCGgtaagtaacc ... aaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCA
EST:
gi|33104245|gb|CF064205.1|CF064205EST: TCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCGG TTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGC
genomic: TCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTC-Ggtaagtaacc ... aaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGC
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:
517GCGAGGGCGAAACCCACAAACCCTCTCCCTCCCGTACTCCGGCCTACACATCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCGgtaagtaacc ... aaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCATTGGTGATGGAACAGTGAGCTATGGAATGGATGATGCCGATGACATCTA
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
757GCGAGGGCGAAACCCACAAACCCTCTCCCTCCCGTACTCCGGCCTACACATCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCGgtaagtaacc ... aaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCATTGGTGATGGAACAGTGAGCTATGGAATGGATGATGCCGATGACATCTA
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
458GCGAGGGCGAAACCCACAAACCCTCTCCCTCCCGTACTCCGGCCTACACATCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCGgtaagtaacc ... aaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCATTGGTGATGGAACAGTGAGCTATGGAATGGATGATGCCGATGACATCTA
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
341GCGAGGGCGAAACCCACAAACCCTCTCCCTCCCGTACTCCGGCCTACACATCCAGGGGCGATGACGCTGGGTAGCTCCGGCGCCGGATCGAGCGTCGTCGgtaagtaacc ... aaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCATTGGTGATGGAACAGTGAGCTATGGAATGGATGATGCCGATGACATCTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagtagaattcattgcattacctgcttgtgtaactgacaaatgataaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCATTGGTGATGGAACAGTGAGCTATGGAATGGATGATGCCGATGACATCTA
aactgac putative branch site (score: 341)
acaaatgataaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttagttcctgtttttgtaaaatataatattgaattagtagagtactagtagaattcattgcattacctgcttgtgtaactgacaaatgataaaaatgcagTTCCCCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCATTGGTGATGGAACAGTGAGCTATGGAATGGATGATGCCGATGACATCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA