Sequence
atgc intronic sequence ATGC exonic sequence...aaaaggatggcttttgaacaccaacatgacaattgcttgcaagtaggaggttccaccatatattgaacatccattgttcaatttgtctaattgtgttcagGTCAGCGGAATGCCTACATTTTGTATCCCTGTCCAAGATGGTGGTGTTGGTTTTGATTATCGTCTTCATATGGCTGTCCCAGACAAATGGATTGAACTTC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G073054_T02 (Zea mays), 3'ss of exon 14
lower sequence: AT5G03650.1 (Arabidopsis thaliana), 3'ss of exon 14
-------------------------------------------------------------------aaaaggatggcttttgaacaccaacatgacaattgcttgcaagtaggaggttccac-catatattgaacatccat--tgttcaatttgtctaattgtgttcagGTCAGCGGAATGCCTACATTTTGTATCCCTGTCCAAGATGGTGGTGTTGGTTTTGATTATCGTCTTCATATGGCTGTCCCAGACAAATGGATTGAACTTC
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gtaagttttctgattggctaaataaaaaagtgctctacagaaccataagggatacatattgtgtatcatattaaagatagtccaaaaccaaattagtgtgaactgacaagagaaagttagtatatattttttggtgatctatgctaataaaatcgtttcatt----tcagGTTAGTGGTATGCCAACATTCTGTATTCCTGTCCAAGATGGTGGCGTTGGATTTGACTACCGTTTACACATGGCCATAGCTGATAAGTGGATAGAAATGC
upper sequence: GRMZM2G073054_T02 (Zea mays), 3'ss of exon 14
lower sequence: AT2G36390.1 (Arabidopsis thaliana), 3'ss of exon 14
aaaaggatggcttttgaacaccaacatgacaattgcttgcaagtaggaggtt-ccaccatatattgaacatccattgttcaatttgtc---taattgtgtt-cagGTCAGCGGAATGCCTACATTTTGTATCCCTGTCCAAGATGGTGGTGTTGGTTTTGATTATCGTCTTCATATGGCTGTCCCAGACAAATGGATTGAACTTC
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-----------------------gtaagtcatttgcgcttttgttcagtattactgaagtatttttgatacctctctccggttctctcaattgatttcgttacagGTTAGCGGGATGCCAGCTTTTTGCGTTCCTGTCGAAGACGGTGGTGTGGGTTTTGACTACCGTCTACACATGGCAGTGGCAGATAAATGGATTGAGCTTC
upper sequence: GRMZM2G073054_T02 (Zea mays), 3'ss of exon 14
lower sequence: Vv08s0007g03750.t01 (Vitis vinifera), 3'ss of exon 14
-aaaaggatggcttttgaacaccaacatgacaat-tgcttgcaagtaggaggttccaccatatattgaacatccattgttcaatttgtctaattgtgttcagGTCAGCGGAATGCCTACATTTTGTATCCCTGTCCAAGATGGTGGTGTTGGTTTTGATTATCGTCTTCATATGGCTGTCCCAGACAAATGGATTGAACTTC
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taaaatagtgatttttttctaatgcactaagaatctgtctatggatgctaatccaaggaattggttttctgtttatgatgcaattatttccattttg--cagGTGAGCGGAATGCCAGCATTCTGTATTCCTGTTCAAGATGGTGGTGTGGGATTTGATTATCGCTTACATATGGCCATTGCTGATAAATGGATTGAGCTTCMapped 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|67035192|gb|CO463725.1|CO463725EST: ACGATCTTATTCGTGGGCTTTATCCAGAAGCTGTATCCATTGGCGAAGAT GTCAGCGGAATGCCTACATTTTGTATCCCTGTCCAAGATGGTGGTGTTGGT
genomic: ACGATCTTATTCGTGGGCTTTATCCAGAAGCTGTATCCATTGGCGAAGATgtaagtgctc ... ttgtgttcagGTCAGCGGAATGCCTACATTTTGTATCCCTGTCCAAGATGGTGGTGTTGGT
EST:
gi|101386689|gb|EB815361.1|EB815361EST: ACGATCTTATTCGTGGGCTTTATCCAGAAGCTGTATCCATTGGCGAAGAT GTCAGCGGAATGCCTACATTTTGTATCCCTGTCCAAGATGGTGGTGTTGGT
genomic: ACGATCTTATTCGTGGGCTTTATCCAGAAGCTGTATCCATTGGCGAAGATgtaagtgctc ... ttgtgttcagGTCAGCGGAATGCCTACATTTTGTATCCCTGTCCAAGATGGTGGTGTTGGT
EST:
gi|211410788|gb|FL280482.1|FL280482EST: ACGATCTTATTCGTGGGCTTTATCCAGAAGCTGTATCCATTGGCGAAGAT GTCAGCGGAATGCCTACATTTTGTATCCCTGTCCAAGATGGTGGTGTTGGT
genomic: ACGATCTTATTCGTGGGCTTTATCCAGAAGCTGTATCCATTGGCGAAGATgtaagtgctc ... ttgtgttcagGTCAGCGGAATGCCTACATTTTGTATCCCTGTCCAAGATGGTGGTGTTGGT
EST:
gi|27753880|gb|BM378072.1|BM378072EST: ACGATCTTATTTGTGGGCTTTATCCAGAAGCTGTATCCATTGGCGAAGAT GTCAGCGGAATGCCTACATTTTGTATCCCTGTCCAAGACGGTGGTGTTGGT
genomic: ACGATCTTATTCGTGGGCTTTATCCAGAAGCTGTATCCATTGGCGAAGATgtaagtgctc ... ttgtgttcagGTCAGCGGAATGCCTACATTTTGTATCCCTGTCCAAGATGGTGGTGTTGGT
EST:
gi|211410789|gb|FL280483.1|FL280483EST: ACGATCTTATTCGTGGGCTTTATCCAGAAGCTGTATCCATTGGCGTAGAT GTCAGCGGAATGCCTACATTTTGTATCCCTGTCCAAGATGGTGGTGTTGGT
genomic: ACGATCTTATTCGTGGGCTTTATCCAGAAGCTGTATCCATTGGCGAAGATgtaagtgctc ... ttgtgttcagGTCAGCGGAATGCCTACATTTTGTATCCCTGTCCAAGATGGTGGTGTTGGT
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:
847TTTTGGATTTGCCACTGATGTTGATGCAGTAGTTTACCTAATGCTGGTAAACGATCTTATTCGTGGGCTTTATCCAGAAGCTGTATCCATTGGCGAAGATgtaagtgctc ... ttgtgttcagGTCAGCGGAATGCCTACATTTTGTATCCCTGTCCAAGATGGTGGTGTTGGTTTTGATTATCGTCTTCATATGGCTGTCCCAGACAAATGGATTGAACTTC
Block sizes:
49 (upstream exon),
46 (downstream exon)
Score:
184TTTTGGATTTGCCACTGATGTTGATGCAGTAGTTTACCTAATGCTGGTAAACGATCTTATTCGTGGGCTTTATCCAGAAGCTGTATCCATTGGCGAAGATgtaagtgctc ... ttgtgttcagGTCAGCGGAATGCCTACATTTTGTATCCCTGTCCAAGATGGTGGTGTTGGTTTTGATTATCGTCTTCATATGGCTGTCCCAGACAAATGGATTGAACTTC
Block sizes:
45 (upstream exon),
43 (downstream exon)
Score:
18TTTTGGATTTGCCACTGATGTTGATGCAGTAGTTTACCTAATGCTGGTAAACGATCTTATTCGTGGGCTTTATCCAGAAGCTGTATCCATTGGCGAAGATgtaagtgctc ... ttgtgttcagGTCAGCGGAATGCCTACATTTTGTATCCCTGTCCAAGATGGTGGTGTTGGTTTTGATTATCGTCTTCATATGGCTGTCCCAGACAAATGGATTGAACTTC
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
319TTTTGGATTTGCCACTGATGTTGATGCAGTAGTTTACCTAATGCTGGTAAACGATCTTATTCGTGGGCTTTATCCAGAAGCTGTATCCATTGGCGAAGATgtaagtgctc ... ttgtgttcagGTCAGCGGAATGCCTACATTTTGTATCCCTGTCCAAGATGGTGGTGTTGGTTTTGATTATCGTCTTCATATGGCTGTCCCAGACAAATGGATTGAACTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggaggttccaccatatattgaacatccattgttcaatttgtctaattgtgttcagGTCAGCGGAATGCCTACATTTTGTATCCCTGTCCAAGATGGTGGTGTTGGTTTTGATTATCGTCTTCATATGGCTGTCCCAGACAAATGGATTGAACTTC
gtctaat putative branch site (score: 319)
atatattgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaaaggatggcttttgaacaccaacatgacaattgcttgcaagtaggaggttccaccatatattgaacatccattgttcaatttgtctaattgtgttcagGTCAGCGGAATGCCTACATTTTGTATCCCTGTCCAAGATGGTGGTGTTGGTTTTGATTATCGTCTTCATATGGCTGTCCCAGACAAATGGATTGAACTTC
- - - - -gcttttg
- - - - - - - - - caccaac
- - - - - - - - - - - - - - - - -tgcttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatcca