Sequence
atgc intronic sequence ATGC exonic sequence...tcatataatgatttgttgtgttttgcattactatttcttggtctgcagttttacaattttttattctaagaactcacagaattttgcttcaacattccagAGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGAATCTTCTGGTGTCTTTACAACGACTGATAAAGCATCAGCACACTTAAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G051004_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g07490.1 (Oryza sativa), 3'ss of exon 6
tcatataatgatttgttgtgttttgcattactatttcttggtctgcagtt-ttacaattttttattctaagaactcacagaattttgcttcaacatt--ccagAGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGAATCTTCTGGTGTCTTTACAACGACTGATAAAGCATCAGCACACTTAAAG
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---ccgtgcccctgctctcgatacacaattatgtttctgtgactacattaatttctgttagttcttgcatttgcacctaagaatttgcccccttcttttccagAGATCCAGCAGATATTCCTTGGGGTAACTTTGGAGCTGAGTATGTTGTTGAATCTTCAGGTGTTTTTACAACAACTGAAAAGGCATCGGCACATTTGAAG
upper sequence: GRMZM2G051004_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA03G22790.1 (Glycine max), 3'ss of exon 6
---tcatataatgatttgttgtgttttgcattactatttc-------ttggtctgca--gttttacaattttttattctaagaactcaca-----gaattttgcttcaacattccagAGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGAATCTTCTGGTGTCTTTACAACGACTGATAAAGCATCAGCACACTTAAAG
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gtatcatgagttgggctcttataattacaatagatgttacaaatgtactggtttacaaagtgttaaagagttctaaacaacagattaacatgtgcaaattttgttcatgtattc-agAGATCCTGCAGAGATCCCATGGAGTGATTTTGGGGCTGATTATGTCATTGAGTCTTCAGGAGTTTTTACAACAGTGGAGAAAGCTTCATCACATTTGAAG
upper sequence: GRMZM2G051004_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA16G09020.1 (Glycine max), 3'ss of exon 6
----------------tcatataatgatttgttgtgttttgcat-tactatttcttggtctgcagttttacaattttttattctaag--aactcacagaattttgcttcaacattccagAGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGAATCTTCTGGTGTCTTTACAACGACTGATAAAGCATCAGCACACTTAAAG
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gtatcatgagttgagctcttataattaaaagggatgttatgtgtgtactagattacaaagtg---ttaaagagttctaaacaatagattaacatgcacacatttattttatgtattcagAGATCCTGCAGAGATCCCATGGAGTGATTTTGGGGCTGAATATGTCATTGAGTCTTCTGGAGTTTTTACAACAGTGGAGAAAGCTTCATCACATTTGAAGMapped 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|67025324|gb|CO454073.1|CO454073EST: GGGAAGAAGGTCACAATTACAAGCAAAAG AGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGA
genomic: GGGAAGAAGGTCACAATTACAAGCAAAAGgtaatgttga ... aacattccagAGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGA
EST:
gi|31611887|gb|CD568509.1|CD568509EST: GATTCAACCCTGGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAG AGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGA
genomic: GATTCAACCCTGGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAGgtaatgttga ... aacattccagAGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGA
EST:
gi|31612121|gb|CD568743.1|CD568743EST: GATTCAACCCTGGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAG AGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGA
genomic: GATTCAACCCTGGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAGgtaatgttga ... aacattccagAGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGA
EST:
gi|166449651|gb|EG092831.1|EG092831EST: CAATTACAAGCAAAAG AGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGA
genomic: CAATTACAAGCAAAAGgtaatgttga ... aacattccagAGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGA
EST:
gi|31664252|gb|CD572977.1|CD572977EST: GATTCAACCCTGGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAG AGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGA
genomic: GATTCAACCCTGGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAGgtaatgttga ... aacattccagAGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGA
EST:
gi|29946974|gb|CB816419.1|CB816419EST: GATTCAACCCTGGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAG AGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGA
genomic: GATTCAACCCTGGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAGgtaatgttga ... aacattccagAGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGA
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:
400AGTATGACTCTACTCATGGCCCGTTTAAAGGTTCTATTTGTGTTGTGGATGATTCAACCCTGGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAGgtaatgttga ... aacattccagAGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGAATCTTCTGGTGTCTTTACAACGACTGATAAAGCATCAGCACACTTAAAG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
170AGTATGACTCTACTCATGGCCCGTTTAAAGGTTCTATTTGTGTTGTGGATGATTCAACCCTGGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAGgtaatgttga ... aacattccagAGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGAATCTTCTGGTGTCTTTACAACGACTGATAAAGCATCAGCACACTTAAAG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
221AGTATGACTCTACTCATGGCCCGTTTAAAGGTTCTATTTGTGTTGTGGATGATTCAACCCTGGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAGgtaatgttga ... aacattccagAGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGAATCTTCTGGTGTCTTTACAACGACTGATAAAGCATCAGCACACTTAAAG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
666AGTATGACTCTACTCATGGCCCGTTTAAAGGTTCTATTTGTGTTGTGGATGATTCAACCCTGGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAGgtaatgttga ... aacattccagAGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGAATCTTCTGGTGTCTTTACAACGACTGATAAAGCATCAGCACACTTAAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagttttacaattttttattctaagaactcacagaattttgcttcaacattccagAGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGAATCTTCTGGTGTCTTTACAACGACTGATAAAGCATCAGCACACTTAAAG
aactcac putative branch site (score: 666)
ttacaattttttattc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcatataatgatttgttgtgttttgcattactatttcttggtctgcagttttacaattttttattctaagaactcacagaattttgcttcaacattccagAGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGAATCTTCTGGTGTCTTTACAACGACTGATAAAGCATCAGCACACTTAAAG
- - - - - -tttgttg
- - - - - - - - - - - ttgcatt
- - - - - - - - - - - - - - - - -tttcttg
- - - - - - - - - - - - - - - - - - - - -tctgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttttgct