Sequence
atgc intronic sequence ATGC exonic sequencegtacatgactatttgcttgacacatattcctgaacctcttcatgacattacatctgacacttttccgaagctctctactttacactacttctgacactctgcatttcatctttcagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTTGGGATGGAAGAAATACGGAGAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G068755_T03 (Zea mays), 3'ss of exon 44
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 45
gtacatgactatttgcttgacacatattcctgaacctcttcatgacattacatctgacacttttccgaagctctctactttacactacttctgacactctgcatttcatctttcagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTTGGGATGGAAGAAATACGGAGAAG
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---------------------------------------gtatgtggtta--tttgctagctat--ggatgtgcatg-tatacaggatatccgcctgatgtcacattgtctttcagGTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGCATTCATATTTATTTGCAAGAACTAGGGATGGAAGAGATTCGGAGAAG
upper sequence: GRMZM2G068755_T03 (Zea mays), 3'ss of exon 44
lower sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 47
gtacatgactatttgcttgacacatattcctgaacctcttcatgacattacatctgacacttttccgaagctctctactttacactacttctgacactctgcatttcat-ctttcagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTTGGGATGGAAGAAATACGGAGAAG
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----------attgtcaagaagcagagt--tgaaa----ttgccaaattctatcttgatatgttttgttcattaaaattttgt-tcagtattaacatttatttttttgtgcttgcagGTTCTTCAGAGCACTATCTATGATGTTGACCTTGATCGCATACTTCAAAGCATCCATTTGTACCTGCAAGACTTGGGAATGGAGGAAATTAGGAGAAG
upper sequence: GRMZM2G068755_T03 (Zea mays), 3'ss of exon 44
lower sequence: GLYMA10G35140.1 (Glycine max), 3'ss of exon 48
gtacatgactatttgcttgacacatattcctgaacctcttcatgacattacatctgacacttttccgaagctctctactttacactacttctgacactctgcatttcatctttcagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTTGGGATGGAAGAAATACGGAGAAG
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-----------ctttgtcaagaagcagagttagaattgc---caaattctctcttgatatgtttt--attcattaaaattttgttcagtattaacatgtatttgtttgtgctgcagGTTCTTCAGAGCACTATCTATGATGTTGACCTTGATCGCATACTTCAAAGCATCCATTTGTACCTGCAAGACTTGGGAATGGAGGAAATTAGGAGAAG
upper sequence: GRMZM2G068755_T03 (Zea mays), 3'ss of exon 44
lower sequence: AT2G35630.1 (Arabidopsis thaliana), 3'ss of exon 47
---------------------gtacatgact-atttgcttgacacatat--tcctgaacctcttcatg--aca-ttacatctgacacttttccgaagctc----tctactt------tacactacttctgacactctgcatttcatctttcagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTTGGGATGGAAGAAATACGGAGAAG
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gtattttaggacaatcattgttcacataactcaagtagttgttacgtacagccctactgtctattatgcaacacttgcctttcctacttgctacaatcacagtgtcaaattgtttagtattgtatatctgataat-tgcttgtccttgttaagCTCCTCCAAAGCACCATATATGAAGTTGATCTTGATAGACTTCTTCAGAGTATCCATGTATATCTGCAAGATCTGGGAATGGAAGAGATACGTAGGAG
upper sequence: GRMZM2G068755_T03 (Zea mays), 3'ss of exon 44
lower sequence: PP1S66_170V6.1 (Physcomitrella patens), 3'ss of exon 46
gtacatgactatttgcttgacacatattcctgaacctcttcatgacatt-acatctgacacttttccgaagctctctactttacactacttctgacactctgcatttcatcttt---cagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTTGGGATGGAAGAAATACGGAGAAG
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--------------gtttggaactgattttctcatattctcttgaaattgatttgtgtttctttttctgacttttgtactacgtgtgggttgttaacgtgtgaagctgtttttatggcagGTTCTTGGTTCAACTTTGCTTGAAGTAGACCTTGATCGAATTCTTCAAAGCATTCACGAGTATTTTGAAGAGCTGGGAATGGCAGAAATACGGAAACGMapped 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|93014606|gb|EB640126.1|EB640126EST: CAAATGTTTAATTAAGTTGACGAAG GTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGC
genomic: CAAATGTTTAATTAAGTTGACGAAGgtacatgact ... catctttcagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGC
EST:
gi|67021414|gb|CO450163.1|CO450163EST: ATCAGAAGTTTTCAGACTTAGTTGTCAAATGTTTAATTAAGTTGACGAAG GTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGC
genomic: ATCAGAAGTTTTCAGACTTAGTTGTCAAATGTTTAATTAAGTTGACGAAGgtacatgact ... catctttcagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGC
EST:
gi|67015335|gb|CO444084.1|CO444084EST: ATCAGAAGTTTTCAGACTTAGTTGTCAAATGTTTAATTAAGTTGACGAAG GTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGC
genomic: ATCAGAAGTTTTCAGACTTAGTTGTCAAATGTTTAATTAAGTTGACGAAGgtacatgact ... catctttcagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGC
EST:
gi|71317537|gb|DR795494.1|DR795494EST: ATCAGAAGTTTTCAGACTTAGTTGTCAAATGTTTAATTAAGTTGACGAAG GTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGC
genomic: ATCAGAAGTTTTCAGACTTAGTTGTCAAATGTTTAATTAAGTTGACGAAGgtacatgact ... catctttcagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGC
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:
107CCCTTCAAGATGGCCATCGCCTACACCAACGGAGTCTCTTGCTGTAAAAAATCAGAAGTTTTCAGACTTAGTTGTCAAATGTTTAATTAAGTTGACGAAGgtacatgact ... catctttcagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTTGGGATGGAAGAAATACGGAGAAG
Block sizes:
49 (upstream exon),
46 (downstream exon)
Score:
22CCCTTCAAGATGGCCATCGCCTACACCAACGGAGTCTCTTGCTGTAAAAAATCAGAAGTTTTCAGACTTAGTTGTCAAATGTTTAATTAAGTTGACGAAGgtacatgact ... catctttcagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTTGGGATGGAAGAAATACGGAGAAG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
55CCCTTCAAGATGGCCATCGCCTACACCAACGGAGTCTCTTGCTGTAAAAAATCAGAAGTTTTCAGACTTAGTTGTCAAATGTTTAATTAAGTTGACGAAGgtacatgact ... catctttcagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTTGGGATGGAAGAAATACGGAGAAG
Block sizes:
49 (upstream exon),
48 (downstream exon)
Score:
51CCCTTCAAGATGGCCATCGCCTACACCAACGGAGTCTCTTGCTGTAAAAAATCAGAAGTTTTCAGACTTAGTTGTCAAATGTTTAATTAAGTTGACGAAGgtacatgact ... catctttcagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTTGGGATGGAAGAAATACGGAGAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttccgaagctctctactttacactacttctgacactctgcatttcatctttcagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTTGGGATGGAAGAAATACGGAGAAG
ttctgac putative branch site (score: 51)
tttcatctttc putative PPT
tacttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacatgactatttgcttgacacatattcctgaacctcttcatgacattacatctgacacttttccgaagctctctactttacactacttctgacactctgcatttcatctttcagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTTGGGATGGAAGAAATACGGAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA