Sequence
atgc intronic sequence ATGC exonic sequence...tcagatacatatagcttaacaacgacacagcattttacctgagacacatgtatttccaggctgtttctcatcagtatcatatacttctttcacttctcagCTTCTGTGGGTGAACCTCATAATGGACACACTTGGAGCTCTTGCATTAGCAACCGAGCCTCCAACAGACAACCTTATGAAGAGAAATCCTGTTGGTCGAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G132712_T03 (Zea mays), 3'ss of exon 28
lower sequence: LOC_Os08g40530.1 (Oryza sativa), 3'ss of exon 12
-------------------------------------------------------------------------------------------------tcagat-acatatagcttaacaacgacacagcatttta--cctgagacacatgtatttccaggctgtttctcatcagtatcatatacttctttcacttctcagCTTCTGTGGGTGAACCTCATAATGGACACACTTGGAGCTCTTGCATTAGCAACCGAGCCTCCAACAGACAACCTTATGAAGAGAAATCCTGTTGGTCGAA
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gttggagcaattttcttttattcaattgctatgtaattgctattttgtttgccattgcgaagctacctattgcctattccattgagacactttgttgtgatattgtatgtggatatgctgaaattcttaattctaagctcgacgggcttgtatgctcagttcaactctaat-gctgctctgttcct-ttacacatttcagCTTCTCTGGGTAAATCTAATCATGGATACACTGGGAGCTCTGGCTTTAGCAACTGAACCACCGACGGATAACCTTATGAAGAGACAGCCTGTTGGTCGAA
upper sequence: GRMZM2G132712_T03 (Zea mays), 3'ss of exon 28
lower sequence: EFJ15121 (Selaginella moellendorffii), 3'ss of exon 22
tcagatacatatagcttaacaacgacacagcattttacctgagacacatgtatttccaggctgtttctcatcagtatcatatacttctttcacttctcagCTTCTGTGGGTGAACCTCATAATGGACACACTTGGAGCTCTTGCATTAGCAACCGAGCCTCCAACAGACAACCTTATGAAGAGAAATCCTGTTGGTCGAA
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------------------------------------gtttgaaa---atttact--caatttttttcttacaaccttttgacact--gtttattaatcagTTGCTATGGGTGAACCTGATAATGGACACGCTTGGGGCTTTAGCACTAGCAACAGAGCCTCCAACAGAAGAAATGATGGAAAGAGCTCCTATCGGATTAA
upper sequence: GRMZM2G132712_T03 (Zea mays), 3'ss of exon 28
lower sequence: EFJ08462 (Selaginella moellendorffii), 3'ss of exon 24
tcagatacatatagcttaacaacgacacagcattttacctgagacacatgtatttccaggctgtttctcatcagtatcatatacttctttcacttctcagCTTCTGTGGGTGAACCTCATAATGGACACACTTGGAGCTCTTGCATTAGCAACCGAGCCTCCAACAGACAACCTTATGAAGAGAAATCCTGTTGGTCGAA
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------------------------------------gtttgaaa---atttact--caattgttttcttacaaccttttgacactgttttt--taatcagTTGCTATGGGTGAACCTGATAATGGACACGCTTGGGGCTTTAGCACTAGCAACAGAGCCTCCAACAGAAGAAATGATGGAAAGAGCTCCTATCGGACTAAMapped 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|60340338|gb|DN207311.1|DN207311EST: ATGTGGTTGCTGCTGTGTCCTCTGGTGATGTGCCCCTAAATGCTGTTGAG CTTCTGTGGGTGAACCTCATAATGGACACACTTGGAGCTCTTGCATTAGCA
genomic: ATGTGGTTGCTGCTGTGTCCTCTGGTGATGTGCCCCTAAATGCTGTTGAGgttcggacaa ... cacttctcagCTTCTGTGGGTGAACCTCATAATGGACACACTTGGAGCTCTTGCATTAGCA
EST:
gi|5846827|gb|AI999910.1|AI999910EST: ATGTGGTTGCTGCTGTGTCCTCTGGTGATGTGCCCCTAAATGCTGTTGAG CTTCTGTGGGTGAACCTCATAATGGACACACTTGGAGCTCTTGCATTAGCA
genomic: ATGTGGTTGCTGCTGTGTCCTCTGGTGATGTGCCCCTAAATGCTGTTGAGgttcggacaa ... cacttctcagCTTCTGTGGGTGAACCTCATAATGGACACACTTGGAGCTCTTGCATTAGCA
EST:
gi|5325014|gb|AI783205.1|AI783205EST: ATGTGGTTGCTGCTGAGTCCTCTGGTGATGTGCCCCTAAATGCTGTTGAG CTTCTGTGGGTGAACCTCATAATGGACACACTTGGAGCTCTTGCATTAGCA
genomic: ATGTGGTTGCTGCTGTGTCCTCTGGTGATGTGCCCCTAAATGCTGTTGAGgttcggacaa ... cacttctcagCTTCTGTGGGTGAACCTCATAATGGACACACTTGGAGCTCTTGCATTAGCA
EST:
gi|116821995|gb|EC865361.1|EC865361EST: ATGTTGTTGCTGCTGTGTCCTCTGGTGATGTGCCCCTAAATGCTGTTGAG CTTCCGTGGGTGAACCTCATAATGGACACACTTGGAGCTCTTGCATTAGCA
genomic: ATGTGGTTGCTGCTGTGTCCTCTGGTGATGTGCCCCTAAATGCTGTTGAGgttcggacaa ... cacttctcagCTTCTGTGGGTGAACCTCATAATGGACACACTTGGAGCTCTTGCATTAGCA
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:
48 (upstream exon),
48 (downstream exon)
Score:
73GAAATTCATTCAGTTCCAGCTCACCGTCAATGTTGCTGCACTTGTCATTAATGTGGTTGCTGCTGTGTCCTCTGGTGATGTGCCCCTAAATGCTGTTGAGgttcggacaa ... cacttctcagCTTCTGTGGGTGAACCTCATAATGGACACACTTGGAGCTCTTGCATTAGCAACCGAGCCTCCAACAGACAACCTTATGAAGAGAAATCCTGTTGGTCGAA
Block sizes:
49 (upstream exon),
46 (downstream exon)
Score:
123GAAATTCATTCAGTTCCAGCTCACCGTCAATGTTGCTGCACTTGTCATTAATGTGGTTGCTGCTGTGTCCTCTGGTGATGTGCCCCTAAATGCTGTTGAGgttcggacaa ... cacttctcagCTTCTGTGGGTGAACCTCATAATGGACACACTTGGAGCTCTTGCATTAGCAACCGAGCCTCCAACAGACAACCTTATGAAGAGAAATCCTGTTGGTCGAA
Block sizes:
46 (upstream exon),
49 (downstream exon)
Score:
142GAAATTCATTCAGTTCCAGCTCACCGTCAATGTTGCTGCACTTGTCATTAATGTGGTTGCTGCTGTGTCCTCTGGTGATGTGCCCCTAAATGCTGTTGAGgttcggacaa ... cacttctcagCTTCTGTGGGTGAACCTCATAATGGACACACTTGGAGCTCTTGCATTAGCAACCGAGCCTCCAACAGACAACCTTATGAAGAGAAATCCTGTTGGTCGAA
Block sizes:
45 (upstream exon),
49 (downstream exon)
Score:
54GAAATTCATTCAGTTCCAGCTCACCGTCAATGTTGCTGCACTTGTCATTAATGTGGTTGCTGCTGTGTCCTCTGGTGATGTGCCCCTAAATGCTGTTGAGgttcggacaa ... cacttctcagCTTCTGTGGGTGAACCTCATAATGGACACACTTGGAGCTCTTGCATTAGCAACCGAGCCTCCAACAGACAACCTTATGAAGAGAAATCCTGTTGGTCGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acatgtatttccaggctgtttctcatcagtatcatatacttctttcacttctcagCTTCTGTGGGTGAACCTCATAATGGACACACTTGGAGCTCTTGCATTAGCAACCGAGCCTCCAACAGACAACCTTATGAAGAGAAATCCTGTTGGTCGAA
tacttctttcacttct CT-rich tract
tatcatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcagatacatatagcttaacaacgacacagcattttacctgagacacatgtatttccaggctgtttctcatcagtatcatatacttctttcacttctcagCTTCTGTGGGTGAACCTCATAATGGACACACTTGGAGCTCTTGCATTAGCAACCGAGCCTCCAACAGACAACCTTATGAAGAGAAATCCTGTTGGTCGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA