Sequence
atgc intronic sequence ATGC exonic sequence...gcgggtagcatgaatgcatctatcagaaatgatcttgtgtaggacgaaattttcaagctaatcattcttaaatacttatccttaaatctttgcttttcagTGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM5G814310_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g45770.2 (Oryza sativa), 3'ss of exon 10
------------gcgggtagcatgaatgcatctatcagaaatgatcttgtgtaggacgaaattttcaagctaatcattcttaaatacttatccttaaatctttgcttttcagTGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATG
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catttaacatttgcaactttcaagcatgcat-tatcagaattgttgtcatgcatagcaaa---ttcggtctgtctgaattta----ctgaattttgtgtc----ctttgcagTGTGAGGACATCTATATCAATGCAGTTCTTCCCGCGCTTTTTCTTGCTGTATTTCTTGGTTTTCCACATTTACTTCTTCTCGTACACATATG
upper sequence: GRMZM5G814310_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G19970.1 (Glycine max), 3'ss of exon 11
gcgggtagcatgaatgcatctatcagaaatgatcttgtgtagg-acgaa-attttcaagctaatcattct-taaatacttatccttaaatctt-tgcttttcagTGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATG
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----gttcttttaatatctggaccagtatctattatacattttcatgcacatttgtagggttgtggtccagcgtatgataatacaagtgtattgtaacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTATTTCCTGGTCTTCCACATATATTTCTTCTCTTATGCTTATG
upper sequence: GRMZM5G814310_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA15G05080.1 (Glycine max), 3'ss of exon 11
---gcgggtagcatgaat-gcatctatcagaaatgatcttgtgtaggacgaaattttcaagctaatcattcttaaatacttatccttaaatctttgcttttcagTGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATG
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tcttttaatatctggaccagtatctgttacacattttcatgcacatt-tgtggggttgtggtccagcgtatgataatgagtgtgttca---ttgtaacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTATTTCCTGGTCTTCCACATATATTTCTTCTCTTATGCTTACG
upper sequence: GRMZM5G814310_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT1G60995.1 (Arabidopsis thaliana), 3'ss of exon 12
---------------------------------gcgggtagcatgaa-tgcatctatcagaaatgatcttgtg--taggacgaaattttcaagctaatcattc--ttaaatactta-----tccttaaatctttgcttttcagTGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATG
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gttttggtctcctcttttgcctcagtcacctgtatttccactatgaagctcttttgctcgtgataatctcactgccaagttaaagttttttttgtagctgttcaatggaataataacaaactcttatcctccatatattgcagTGTCAGGACACCAATATCGATGAAGTTCTTCCCGCGTTTCTTCTTGCTGTACTTCTTGGTGTTCCATATTTATTTCTTCTCATATGCATATG
upper sequence: GRMZM5G814310_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S96_202V6.1 (Physcomitrella patens), 3'ss of exon 12
gcgggtagcatgaatgcatctatcagaaatgatcttgtgtaggacgaaattttcaagctaatcattcttaaatacttatccttaaatctt--tgcttttcagTGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATG
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--gaatttttttctgtaagcggttgtttatttcatttggaattataagcttcctttgacggatattgtcacgcgagcaccctttgtacttgccattttgcagCGTGAGGACGCCCCTATCGATGCAGTTCTTTCCTCGCTTCTTTTTTCTCTATTTCATGGCTTTCCACATTTACTTCTTCTCTTATACCTACGMapped 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|211379778|gb|FL404067.1|FL404067EST: CTATTCACGATGATCAG TGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTA
genomic: CTATTCACGATGATCAGgtaatggttt ... tgcttttcagTGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTA
EST:
gi|211054879|gb|FL422556.1|FL422556EST: CTATTCACGATGATCAG TGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTA
genomic: CTATTCACGATGATCAGgtaatggttt ... tgcttttcagTGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTA
EST:
gi|211393234|gb|FL418031.1|FL418031EST: CTATTCACGATGATCAG TGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTA
genomic: CTATTCACGATGATCAGgtaatggttt ... tgcttttcagTGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTA
EST:
gi|67010774|gb|CO439523.1|CO439523EST: TTTCTTGTTTTGACTCTTGTATGGTTATGCGAGCTATTCACGATGATCAG TGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTA
genomic: TTTCTTGTTTTGACTCTTGTATGGTTATGCGAGCTATTCACGATGATCAGgtaatggttt ... tgcttttcagTGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTA
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),
46 (downstream exon)
Score:
169TTGGGATTCTCTTTTTTCTATTTGAGTTCTATGATGATCAATTGCTTGCGTTTCTTGTTTTGACTCTTGTATGGTTATGCGAGCTATTCACGATGATCAGgtaatggttt ... tgcttttcagTGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATG
Block sizes:
48 (upstream exon),
47 (downstream exon)
Score:
205TTGGGATTCTCTTTTTTCTATTTGAGTTCTATGATGATCAATTGCTTGCGTTTCTTGTTTTGACTCTTGTATGGTTATGCGAGCTATTCACGATGATCAGgtaatggttt ... tgcttttcagTGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATG
Block sizes:
48 (upstream exon),
48 (downstream exon)
Score:
226TTGGGATTCTCTTTTTTCTATTTGAGTTCTATGATGATCAATTGCTTGCGTTTCTTGTTTTGACTCTTGTATGGTTATGCGAGCTATTCACGATGATCAGgtaatggttt ... tgcttttcagTGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATG
Block sizes:
49 (upstream exon),
48 (downstream exon)
Score:
248TTGGGATTCTCTTTTTTCTATTTGAGTTCTATGATGATCAATTGCTTGCGTTTCTTGTTTTGACTCTTGTATGGTTATGCGAGCTATTCACGATGATCAGgtaatggttt ... tgcttttcagTGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaattttcaagctaatcattcttaaatacttatccttaaatctttgcttttcagTGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATG
agctaat putative branch site (score: 248)
tctttgcttttc putative PPT
taatcattcttaaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcgggtagcatgaatgcatctatcagaaatgatcttgtgtaggacgaaattttcaagctaatcattcttaaatacttatccttaaatctttgcttttcagTGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATG
- - - - - tgaatgc