Sequence
atgc intronic sequence ATGC exonic sequencegtacgctcttaacactctgctaattcattttatgttcaacatgaggaaagaaaaaatatatatagcgagccaagtgtctgaccactccattctacctgctacctcagGACTGTTGTTTAATCCCGGAGTCACCCTTCTACCTCGAAGGGAAGGGAGGACTCCTCGAGTTCGTCGAGAGGCGGCTCAAGGACAACGGCCACATGGTCA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G080375_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g09570.1 (Oryza sativa), 3'ss of exon 8
gtacgctcttaacactctgctaattcattttat-gttcaacatgaggaaagaaaaaatatatatagcgagccaagtgtctgaccactccattctacctgctacctcagGACTGTTGTTTAATCCCGGAGTCACCCTTCTACCTCGAAGGGAAGGGAGGACTCCTCGAGTTCGTCGAGAGGCGGCTCAAGGACAACGGCCACATGGTCA
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gtatgttttaatcattctacttgttcattgcattgatcaatctagggtaa------------atgctgaattatatggttgatc--tacttttt------tacttcagGATTGTTGCTTAATCCCAGAGTCTCCATTCTATCTAGAAGGAAAAGGTGGACTCCTTGAATTCATCGAGAAACGGCTCAAGGACAATGGCCATATGGTCA
upper sequence: GRMZM2G080375_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 8
-------------------------------------gtacgctcttaacactctgctaattcattttatgttcaacatgaggaaagaaaaaatatatatag---cgagccaagtgtctgaccactccattctacctgctacctcagGACTGTTGTTTAATCCCGGAGTCACCCTTCTACCTCGAAGGGAAGGGAGGACTCCTCGAGTTCGTCGAGAGGCGGCTCAAGGACAACGGCCACATGGTCA
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taacaattgtaagtgtattttatcgtctaagtgcaccagttgcttttgaggatctg--gatctttttcttttcctgtgttatgatgaatactatgactgcagGTTTTATTGCAATGTATG-CCACTCT-TGCTAGCAGAGATGT--GGACTGTTGCTTGATTCCAGAGTCACCCTTCTACCTTGAAGGAAAGGGTGGACTTTTTGA-----------------------------------------Mapped 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|116813643|gb|EC856113.1|EC856113EST: GTTTTATCGCGATGTACGCAACTCTAGCTAGCCGTGATGTG GACTGTTGTTTAATCCCGGAGTCACCCTTCTACCTCGAAGGGAAGG
genomic: GTTTTATCGCGATGTACGCGACTCTAGCTAGCCGTGATGTGgtacgctctt ... gctacctcagGACTGTTGTTTAATCCCGGAGTCACCCTTCTACCTCGAAGGGAAGG
EST:
gi|211450005|gb|FL281917.1|FL281917EST: GTTTTATCGCGATGTACGCGACTCTAGCTAGCCGTGATGTG GACTGTTGTTTAATCCCGGAGTCACC
genomic: GTTTTATCGCGATGTACGCGACTCTAGCTAGCCGTGATGTGgtacgctctt ... gctacctcagGACTGTTGTTTAATCCCGGAGTCACC
EST:
gi|211450006|gb|FL281918.1|FL281918EST: GTTTTATCGCGATGTACGCGACTCTAGCTAGCCGTGATGTG GACTGTTGTTTAATCCCGGAGTCACCCTTCTACCTCGAAGGGAAGGGAGGA
genomic: GTTTTATCGCGATGTACGCGACTCTAGCTAGCCGTGATGTGgtacgctctt ... gctacctcagGACTGTTGTTTAATCCCGGAGTCACCCTTCTACCTCGAAGGGAAGGGAGGA
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:
40 (upstream exon),
41 (downstream exon)
Score:
42GTTTTATCGCGATGTACGCGACTCTAGCTAGCCGTGATGTGgtacgctctt ... gctacctcagGACTGTTGTTTAATCCCGGAGTCACCCTTCTACCTCGAAGGGAAGGGAGGACTCCTCGAGTTCGTCGAGAGGCGGCTCAAGGACAACGGCCACATGGTCA
Block sizes:
40 (upstream exon),
47 (downstream exon)
Score:
393GTTTTATCGCGATGTACGCGACTCTAGCTAGCCGTGATGTGgtacgctctt ... gctacctcagGACTGTTGTTTAATCCCGGAGTCACCCTTCTACCTCGAAGGGAAGGGAGGACTCCTCGAGTTCGTCGAGAGGCGGCTCAAGGACAACGGCCACATGGTCA
Block sizes:
40 (upstream exon),
47 (downstream exon)
Score:
276GTTTTATCGCGATGTACGCGACTCTAGCTAGCCGTGATGTGgtacgctctt ... gctacctcagGACTGTTGTTTAATCCCGGAGTCACCCTTCTACCTCGAAGGGAAGGGAGGACTCCTCGAGTTCGTCGAGAGGCGGCTCAAGGACAACGGCCACATGGTCA
Block sizes:
40 (upstream exon),
47 (downstream exon)
Score:
149GTTTTATCGCGATGTACGCGACTCTAGCTAGCCGTGATGTGgtacgctctt ... gctacctcagGACTGTTGTTTAATCCCGGAGTCACCCTTCTACCTCGAAGGGAAGGGAGGACTCCTCGAGTTCGTCGAGAGGCGGCTCAAGGACAACGGCCACATGGTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaatatatatagcgagccaagtgtctgaccactccattctacctgctacctcagGACTGTTGTTTAATCCCGGAGTCACCCTTCTACCTCGAAGGGAAGGGAGGACTCCTCGAGTTCGTCGAGAGGCGGCTCAAGGACAACGGCCACATGGTCA
gtctgac putative branch site (score: 149)
ctacctc putative PPT
atatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgctcttaacactctgctaattcattttatgttcaacatgaggaaagaaaaaatatatatagcgagccaagtgtctgaccactccattctacctgctacctcagGACTGTTGTTTAATCCCGGAGTCACCCTTCTACCTCGAAGGGAAGGGAGGACTCCTCGAGTTCGTCGAGAGGCGGCTCAAGGACAACGGCCACATGGTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
