Sequence
atgc intronic sequence ATGC exonic sequence...atgggattctcattcgtaggcacacgaacatcagtaatattctttgtacagcatgacatatgaggttgtctaattctctgactgacatttcgttgtgtagTTGTGGAAGATGGTTCGAACTGGAGCATGGGTCAAAGGCAGCTCTTTTGTTTGGGACGTGCACTTCTAAGAAGATGCCGTATCTTAGTTCTTGATGAGGC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G111903_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os06g06440.1 (Oryza sativa), 3'ss of exon 9
-atgggattctcattcgtaggcacacgaacatcagtaatattctttgtacagcatgacata-tgaggttgtctaattct----ctgactgacatttcgttgtgtagTTGTGGAAGATGGTTCGAACTGGAGCATGGGTCAAAGGCAGCTCTTTTGTTTGGGACGTGCACTTCTAAGAAGATGCCGTATCTTAGTTCTTGATGAGGC
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tataccattctt-ttcgtagatat-----cttttgccatactcatattctagcatgatataatgaagctacattattcatatgctaactgtgatattgccatatagTTGTGGAAGATGGGTCGAATTGGAGCATGGGTCAAAGGCAGCTCTTCTGTTTAGGACGAGCACTTTTGAGACGATGCCGTATCTTAGTTCTTGATGAGGC
upper sequence: GRMZM2G111903_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os11g05700.1 (Oryza sativa), 3'ss of exon 8
------atgggattc-tcattcgtaggcacacgaacatcagtaatattctttgtacagcatgacatatgaggttgtctaattct-----ctgactgacatttcgttgtgtagTTGTGGAAGATGGTTCGAACTGGAGCATGGGTCAAAGGCAGCTCTTTTGTTTGGGACGTGCACTTCTAAGAAGATGCCGTATCTTAGTTCTTGATGAGGC
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gtaggggtggtatttaccattctttttgtagatatcttttgtcgtactaatgttgtagcataatacatggagccaccttattcatagtactaattgtgatattgtcatatagTTGTGGAAGATGGGTCGAACTGGAGCATGGGTCAAAGGCAGCTGTTCTGTTTAGGACGTGCACTTTTGAGACGGTGTCGCATCTTAGTTCTTGATGAGGC
upper sequence: GRMZM2G111903_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA16G28900.1 (Glycine max), 3'ss of exon 11
atgggattctcattcgtaggcacacgaacatcagtaatattctttgtacagcatgacatatgaggttgtctaattctctgactgacatttcgttgtgtagTTGTGGAAGATGGTTCGAACTGGAGCATGGGTCAAAGGCAGCTCTTTTGTTTGGGACGTGCACTTCTAAGAAGATGCCGTATCTTAGTTCTTGATGAGGC
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-gtacactttcatcattatggtaacta-tgtcacaagtactttttttcctagttgataaa-----------aact-----agtaatatgttgttacatagTTGTTGAAGATGGATCAAACTGGAGCATGGGACAAAGGCAATTATTTTGTTTGGGGCGTGTTCTTTTAAGGAGAAGTAGGATATTGGTGCTGGATGAAGC
upper sequence: GRMZM2G111903_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA16G28910.1 (Glycine max), 3'ss of exon 11
atgggattctcattcgtaggcacacgaacatcagta-atattctttgtacagcatg-acatatgaggttgtctaattctctgactgacatttcgttgtgtagTTGTGGAAGATGGTTCGAACTGGAGCATGGGTCAAAGGCAGCTCTTTTGTTTGGGACGTGCACTTCTAAGAAGATGCCGTATCTTAGTTCTTGATGAGGC
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-------------------gtaaactttcatcatcatatgataactatgtgacaagtgcttatttcctagttgtaataactag-taacaaattgatgcacagTTGTTGAAGATGGATCAAACTGGAGCATGGGACAAAGGCAATTGTTTTGTTTGGGGCGTGCTCTTTTAAGGAGAAGTAGGATATTGGTGCTGGATGAAGC
upper sequence: GRMZM2G111903_T02 (Zea mays), 3'ss of exon 11
lower sequence: Vv16s0050g02480.t01 (Vitis vinifera), 3'ss of exon 10
atgggattctcattcgtaggcacacgaacatcagtaatattctttgtacagcatgacatatgaggttgtctaattctctgactgacatttcgttgtgtagTTGTGGAAGATGGTTCGAACTGGAGCATGGGTCAAAGGCAGCTCTTTTGTTTGGGACGTGCACTTCTAAGAAGATGCCGTATCTTAGTTCTTGATGAGGC
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gtaagatttcaagctcttagtacacagg-----gtgtccctttttttccattgtagccattaa-------taagggtctgtttg---tttc-------agTTGCGGAAGGTGGATCAAACTGGAGCATGGGGCAGAGGCAGCTCTTCTGTTTGGGGCGTGCCCTCTTGCGAAGAAGCCGGATACTGGTTCTTGATGAAGCMapped 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|32833322|gb|CD973000.1|CD973000EST: TCAGCTTCTTGAAGCTGTCCAGGAGAAGGAGCAGGGATTGGACTCACTTG TTGTGGAAGATGGTTCGAACTGGAGCATGGGTCAAAGGCAGCTCTTTTGTT
genomic: TCAGCTTCTTGAAGCTGTCCAGGAGAAGGAGCAGGGATTGGACTCACTTGgttggatttc ... cgttgtgtagTTGTGGAAGATGGTTCGAACTGGAGCATGGGTCAAAGGCAGCTCTTTTGTT
EST:
gi|32832589|gb|CD972267.1|CD972267EST: TCAGCTTCTTGAAGCTGTCCAGGAGAAGGAGCAGGGATTGGACTCACTTG TTGTGGAAGATGGTTCGAACTGGAGCATGGGTCAAAGGCAGCTCTTTTGTT
genomic: TCAGCTTCTTGAAGCTGTCCAGGAGAAGGAGCAGGGATTGGACTCACTTGgttggatttc ... cgttgtgtagTTGTGGAAGATGGTTCGAACTGGAGCATGGGTCAAAGGCAGCTCTTTTGTT
EST:
gi|61236607|gb|DN586354.1|DN586354EST: TCAGCTTCTTGAAGCTGTCCAGGAGAAGGAGCAGGGATTGGACTCACTTG TTGTGGAAGATGGTTCGAACTGGAGCATGGGTCAAAGGCAGCTCTTTTGTT
genomic: TCAGCTTCTTGAAGCTGTCCAGGAGAAGGAGCAGGGATTGGACTCACTTGgttggatttc ... cgttgtgtagTTGTGGAAGATGGTTCGAACTGGAGCATGGGTCAAAGGCAGCTCTTTTGTT
EST:
gi|76292142|gb|DV031710.1|DV031710EST: TCAGCTTCTTGAAGCTGTCCAGGAGAAGGAGCAGGGATTGGACTCACTTG TTGTGGAAGATGGTTCGAACTGGAGCATGGGTCAAAGGCAGCTCTTTTGTT
genomic: TCAGCTTCTTGAAGCTGTCCAGGAGAAGGAGCAGGGATTGGACTCACTTGgttggatttc ... cgttgtgtagTTGTGGAAGATGGTTCGAACTGGAGCATGGGTCAAAGGCAGCTCTTTTGTT
EST:
gi|18964666|gb|BM661136.1|BM661136EST: TCAGCTTCTTGAAGCTGTCCAGGAGAAGGAGCAGGGATTGGACTCACTTG TTGTGGAAGATGGTTCGAACTGGAGCATGGGTCAAAGGCAGCTCTTTGGTT
genomic: TCAGCTTCTTGAAGCTGTCCAGGAGAAGGAGCAGGGATTGGACTCACTTGgttggatttc ... cgttgtgtagTTGTGGAAGATGGTTCGAACTGGAGCATGGGTCAAAGGCAGCTCTTTTGTT
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:
45 (upstream exon),
49 (downstream exon)
Score:
74GTTCTAGGCAAATGTCAGCTTCTTGAAGCTGTCCAGGAGAAGGAGCAGGGATTGGACTCACTTGgttggatttc ... cgttgtgtagTTGTGGAAGATGGTTCGAACTGGAGCATGGGTCAAAGGCAGCTCTTTTGTTTGGGACGTGCACTTCTAAGAAGATGCCGTATCTTAGTTCTTGATGAGGC
Block sizes:
47 (upstream exon),
49 (downstream exon)
Score:
132GTTCTAGGCAAATGTCAGCTTCTTGAAGCTGTCCAGGAGAAGGAGCAGGGATTGGACTCACTTGgttggatttc ... cgttgtgtagTTGTGGAAGATGGTTCGAACTGGAGCATGGGTCAAAGGCAGCTCTTTTGTTTGGGACGTGCACTTCTAAGAAGATGCCGTATCTTAGTTCTTGATGAGGC
Block sizes:
47 (upstream exon),
49 (downstream exon)
Score:
409GTTCTAGGCAAATGTCAGCTTCTTGAAGCTGTCCAGGAGAAGGAGCAGGGATTGGACTCACTTGgttggatttc ... cgttgtgtagTTGTGGAAGATGGTTCGAACTGGAGCATGGGTCAAAGGCAGCTCTTTTGTTTGGGACGTGCACTTCTAAGAAGATGCCGTATCTTAGTTCTTGATGAGGC
Block sizes:
48 (upstream exon),
49 (downstream exon)
Score:
177GTTCTAGGCAAATGTCAGCTTCTTGAAGCTGTCCAGGAGAAGGAGCAGGGATTGGACTCACTTGgttggatttc ... cgttgtgtagTTGTGGAAGATGGTTCGAACTGGAGCATGGGTCAAAGGCAGCTCTTTTGTTTGGGACGTGCACTTCTAAGAAGATGCCGTATCTTAGTTCTTGATGAGGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtacagcatgacatatgaggttgtctaattctctgactgacatttcgttgtgtagTTGTGGAAGATGGTTCGAACTGGAGCATGGGTCAAAGGCAGCTCTTTTGTTTGGGACGTGCACTTCTAAGAAGATGCCGTATCTTAGTTCTTGATGAGGC
gactgac putative branch site (score: 177)
tttcgtt CT-rich tract
tctaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgggattctcattcgtaggcacacgaacatcagtaatattctttgtacagcatgacatatgaggttgtctaattctctgactgacatttcgttgtgtagTTGTGGAAGATGGTTCGAACTGGAGCATGGGTCAAAGGCAGCTCTTTTGTTTGGGACGTGCACTTCTAAGAAGATGCCGTATCTTAGTTCTTGATGAGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - -gcacacg
- - - - - - - - - - - - - aacatca
- - - - - - - - - - - - - - - - - - - - - - - - cagcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgacatt