Sequence
atgc intronic sequence ATGC exonic sequencegtactaacacataataccttattaacttgtcagacttgtttacattttttctgcttttgaactgtctttaaatcttattctgtttttgtgtgtgtgtgtgttttgaactccagATGCTTTCTTCAAAGGACCTGAACTTTGTGGGCTATACCTACAAGAACTTTGAACTTGTGAACGATCACGATGTCCCCGGCATGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os10g33640.1 (Oryza sativa), 3'ss of exon 10
gtactaacacataataccttattaacttgtcagacttgtttacattttttctgcttttgaactgtctttaaatcttattctgtttttgtgtgtgtgtgtgttttgaactccagATGCTTTCTTCAAAGGACCTGAACTTTGTGGGCTATACCTACAAGAACTTTGAACTTGTGAACGATCACGATGTCCCCGGCATGG
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----tgatcaattattagtcattagctttggaaaatacagtatatgcaaagaatttcc--accttttagaagaaacatgatgactt-acccat-tgtgtcttttg-----cagATGCTGTCTTCAAAGGATTTGAATTTTGTGGGCTACACGTACAAGAACTTCGAACTTGTGAATGATCCTGAAGTACTTGGAATGG
upper sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA13G18670.2 (Glycine max), 3'ss of exon 10
gtactaacacataataccttattaacttgtcagacttgtttacattttttctgcttttgaactgtctttaaatcttattctgtttttgtgtgtgtgtgtgttttga-actccagATGCTTTCTTCAAAGGACCTGAACTTTGTGGGCTATACCTACAAGAACTTTGAACTTGTGAACGATCACGATGTCCCCGGCATGG
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---ctgtcttctaattctctacct-----tcaaatct-tcgatatcttaatttcagttgttcttttcctttatcttagtattcttttgt-----tgtttgtcgagatgttacagATGCTTTCATCTAAGGACTTGAATTTTGTTGGATACACTTACAAGAACTTTGAAATTGTCAATGATTATCAAGTTCCTGGGATAG
upper sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv07s0005g03690.t01 (Vitis vinifera), 3'ss of exon 10
gtactaacacataataccttattaacttgtcagacttgtttacattttttctgcttttgaactgtctttaaatcttattctg--tttttgtgtgtgtgtgtgttttgaactccagATGCTTTCTTCAAAGGACCTGAACTTTGTGGGCTATACCTACAAGAACTTTGAACTTGTGAACGATCACGATGTCCCCGGCATGG
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------------aatatgttaagagtct---aaacttccatctgatgctattttttgttactgtttttttcttctttttccacattttctcatttcagttctctttattatgtagATGCTTTCATCGAAGGACATGAACTTTGTGGGTTATACGTATAAGAACTTTGAAATCATCAATGATTATCAAGTTCCTGGAATGG
upper sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 10
lower sequence: PP1S87_129V6.1 (Physcomitrella patens), 3'ss of exon 10
------------------------------------------------gtactaa-cacataataccttattaacttgtc--agacttgtttacattttttctgcttttgaactgtctttaaatcttattctgtttttgtgtgtgtgtgtgttttgaactccagATGCTTTCTTCAAAGGACCTGAACTTTGTGGGCTATACCTACAAGAACTTTGAACTTGTGAACGATCACGATGTCCCCGGCATGG
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gtatgcagtttcaagtgtcaaatgcgtcatctcaacccagattgccttgagttgttcagcccgtgccttacgaagttcacgcaaacgtatccagaatgtacaggtttttgtaagaggtcactgtgtctgtctgggctcgattgtaacagaaattggg--tgcagATGCTGTCATCAAAGGACGTCAACTTTGTGGGCTATACTTACAAGAATTTCGAGATTGTCCAAGATGTCAATATACCTGGAATTGMapped 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|93015890|gb|EB641410.1|EB641410EST: CGGACGGTAGTAGCGTTCAGGGTTCAGCAAAGGCGGGCCCTTGGAGAAAG ATGCTTTTTTCAAAGGACCTGAACTTTGTGGGCTATACCTACAAGAACTTT
genomic: CGGACGGTAGTAGCGTTCAGGGTTCAGCAAAGGCGGGCCCTTGGAGAAAGgtactaacac ... tgaactccagATGCTTTCTTCAAAGGACCTGAACTTTGTGGGCTATACCTACAAGAACTTT
EST:
gi|9954068|gb|BE640651.1|BE640651EST: CGGACGGTAGTAGCGTTCAGGGTTCAGCGAAGACGGGCCCTTGGAGAAAG ATGCTTTCTTCAAAGGACCTGAACTTTGTGGGCTATACCTACAAGAACTTT
genomic: CGGACGGTAGTAGCGTTCAGGGTTCAGCAAAGGCGGGCCCTTGGAGAAAGgtactaacac ... tgaactccagATGCTTTCTTCAAAGGACCTGAACTTTGTGGGCTATACCTACAAGAACTTT
EST:
gi|6952724|gb|AW424792.1|AW424792EST: CGGACGGTAGTAGCGTTCAGGGTTCAGCAAAGGCGGGCCCTTGGAGAAAG ATGCTTTCTTCAAAGGACCTGAACTTTGTGGGCTATACCTACAAGAACTTT
genomic: CGGACGGTAGTAGCGTTCAGGGTTCAGCAAAGGCGGGCCCTTGGAGAAAGgtactaacac ... tgaactccagATGCTTTCTTCAAAGGACCTGAACTTTGTGGGCTATACCTACAAGAACTTT
EST:
gi|78180424|gb|DV550797.1|DV550797EST: CGGACGGTAGTAGCGTTCAGGGTTCAGCGAAGACGGGCCCTTGGAGAAAG ATGCTTTCTTCAAAGGACCTGAACTTTGTGGGCTATACCTACAAGAACTTT
genomic: CGGACGGTAGTAGCGTTCAGGGTTCAGCAAAGGCGGGCCCTTGGAGAAAGgtactaacac ... tgaactccagATGCTTTCTTCAAAGGACCTGAACTTTGTGGGCTATACCTACAAGAACTTT
EST:
gi|12047061|gb|BF729200.1|BF729200EST: CGGACGGTAGTAGCGTTCAGGGTTCAGCGAAGACGGGCCCTTGGAGAAAG ATGCTTTCTTCAAAGGACCTGAACTTTGTGGGCTATACCTACAAGACCTTT
genomic: CGGACGGTAGTAGCGTTCAGGGTTCAGCAAAGGCGGGCCCTTGGAGAAAGgtactaacac ... tgaactccagATGCTTTCTTCAAAGGACCTGAACTTTGTGGGCTATACCTACAAGAACTTT
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 1 RNA-Seqlibrary.
Block sizes:
45 (upstream exon),
31 (downstream exon)
Score:
6TCCTCGGACGGTAGTAGCGTTCAGGGTTCAGCAAAGGCGGGCCCTTGGAGAAAGgtactaacac ... tgaactccagATGCTTTCTTCAAAGGACCTGAACTTTGTGGGCTATACCTACAAGAACTTTGAACTTGTGAACGATCACGATGTCCCCGGCATGG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaactgtctttaaatcttattctgtttttgtgtgtgtgtgtgttttgaactccagATGCTTTCTTCAAAGGACCTGAACTTTGTGGGCTATACCTACAAGAACTTTGAACTTGTGAACGATCACGATGTCCCCGGCATGG
tttaaatcttattctg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactaacacataataccttattaacttgtcagacttgtttacattttttctgcttttgaactgtctttaaatcttattctgtttttgtgtgtgtgtgtgttttgaactccagATGCTTTCTTCAAAGGACCTGAACTTTGTGGGCTATACCTACAAGAACTTTGAACTTGTGAACGATCACGATGTCCCCGGCATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC