Sequence
atgc intronic sequence ATGC exonic sequencegtaaaccgaactccaaatcttttttaaacttgaacagattcgaaattgttagattttatagttacaaaacgaactttggttccagGGTCACAGCACTCTGGTGTACGCCGGTGCGGGGATCGTTGAAGGTACAAACCCATCTTTTGAATGGGATGAGCTTGATCTCAAAGCATCTCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G022837_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os09g19734.1 (Oryza sativa), 3'ss of exon 17
----------------------------------gtaaaccgaactccaaatcttttt--taaacttgaacagatt----cgaaattgttagattttat-agttacaaaacgaactttggttccagGGTCACAGCACTCTGGTGTACGCCGGTGCGGGGATCGTTGAAGGTACAAACCCATCTTTTGAATGGGATGAGCTTGATCTCAAAGCATCTCAG
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gtaagaaaaaaatgtagtcagtacgattgatcatataattgggatgtgatgtttttttgtcaaatatgtccatgttgttaccatatcctaagggccaattagttaccaagctgttgtttgttctagGGTCATAGCACTTTAGTTTATGCTGGTGCCGGAATTGTTGAAGGTACAAATCCATCCTTTGAATGGGATGAGCTTGACCTCAAAGCATCTCAG
upper sequence: GRMZM2G022837_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os09g19734.2 (Oryza sativa), 3'ss of exon 17
----------------------------------gtaaaccgaactccaaatctttt--ttaaacttgaacagatt----cgaaattgttagattttat-agttacaaaacgaactttggttccagGGTCACAGCACTCTGGTGTACGCCGGTGCGGGGATCGTTGAAGGTACAAACCCATCTTTTGAATGGGATGAGCTTGATCTCAAAGCATCTCAG-------
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gtaagaaaaaaatgtagtcagtacgattgatcatataattgggatgtgatgtttttttgtcaaatatgtccatgttgttaccatatcctaagggccaattagttaccaagctgttgtttgttctagGGTCATAGCACTTTAGTTTATGCTGGTGCCGGAATTGTTGAAGGTACAAATCCATCCTTTGAATGGGATGAGCTTGACCTCAAAGCATCTCAGGTATTATMapped 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|211419609|gb|FL445141.1|FL445141EST: GAGCTGAGTGCGAGTTCGCTGTCGGGATTAGATCAGCGTTACTTGGAAAA GGTCACAGCACTCTGGTGTACGCCGGTGCGGGGATCGTTGAAGGTACAAAC
genomic: GAGCTGAGTGCGAGTTCGCTGTCGGGATTAGATCAGCGTTACTTGGAAAAgtaaaccgaa ... ttggttccagGGTCACAGCACTCTGGTGTACGCCGGTGCGGGGATCGTTGAAGGTACAAAC
EST:
gi|84977577|gb|DW475999.1|DW475999EST: GAGCTGAGTGCGAGTTCGCTGTCGGGATTAGATCAGCGTTACTTGGAAAA GGTCAC-GACACTCTGGTGTACGCCGGTGCGGGGATCGTTGAAGGTACAAA
genomic: GAGCTGAGTGCGAGTTCGCTGTCGGGATTAGATCAGCGTTACTTGGAAAAgtaaaccgaa ... ttggttccagGGTCACAG-CACTCTGGTGTACGCCGGTGCGGGGATCGTTGAAGGTACAAA
EST:
gi|211331036|gb|FL445935.1|FL445935EST: GAGCTGAGTGCGAGTTCGCTGTCGGGATTAGATCAGCGTTACTTGGAAAA GGTCACAGCACTCTGGTGTACGCCGGTGCGGGGATCGTTGAAGGTACAAAC
genomic: GAGCTGAGTGCGAGTTCGCTGTCGGGATTAGATCAGCGTTACTTGGAAAAgtaaaccgaa ... ttggttccagGGTCACAGCACTCTGGTGTACGCCGGTGCGGGGATCGTTGAAGGTACAAAC
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 3 RNA-Seq libraries.
Block sizes:
49 (upstream exon),
46 (downstream exon)
Score:
81AAATTTTTGACCGTGGAATGTATGCTGGTCCTGTTGGCTGGCTTGGAGGAGCTGAGTGCGAGTTCGCTGTCGGGATTAGATCAGCGTTACTTGGAAAAgtaaaccgaa ... ttggttccagGGTCACAGCACTCTGGTGTACGCCGGTGCGGGGATCGTTGAAGGTACAAACCCATCTTTTGAATGGGATGAGCTTGATCTCAAAGCATCTCAG
Block sizes:
49 (upstream exon),
44 (downstream exon)
Score:
4AAATTTTTGACCGTGGAATGTATGCTGGTCCTGTTGGCTGGCTTGGAGGAGCTGAGTGCGAGTTCGCTGTCGGGATTAGATCAGCGTTACTTGGAAAAgtaaaccgaa ... ttggttccagGGTCACAGCACTCTGGTGTACGCCGGTGCGGGGATCGTTGAAGGTACAAACCCATCTTTTGAATGGGATGAGCTTGATCTCAAAGCATCTCAG
Block sizes:
47 (upstream exon),
40 (downstream exon)
Score:
22AAATTTTTGACCGTGGAATGTATGCTGGTCCTGTTGGCTGGCTTGGAGGAGCTGAGTGCGAGTTCGCTGTCGGGATTAGATCAGCGTTACTTGGAAAAgtaaaccgaa ... ttggttccagGGTCACAGCACTCTGGTGTACGCCGGTGCGGGGATCGTTGAAGGTACAAACCCATCTTTTGAATGGGATGAGCTTGATCTCAAAGCATCTCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaacagattcgaaattgttagattttatagttacaaaacgaactttggttccagGGTCACAGCACTCTGGTGTACGCCGGTGCGGGGATCGTTGAAGGTACAAACCCATCTTTTGAATGGGATGAGCTTGATCTCAAAGCATCTCAG
aaattgttagatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaccgaactccaaatcttttttaaacttgaacagattcgaaattgttagattttatagttacaaaacgaactttggttccagGGTCACAGCACTCTGGTGTACGCCGGTGCGGGGATCGTTGAAGGTACAAACCCATCTTTTGAATGGGATGAGCTTGATCTCAAAGCATCTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT