Sequence
atgc intronic sequence ATGC exonic sequencegtgagttcatacacttcgttagaaaagcgaatttttacttgtttgttgtcttcattctgccgcttagtgctcccaatattgttcagctagatcagcacaacacatttcaatttcattttctcatgaagtttgctcaacctgtaacaatgtttttttattattttagCTTGATGAAGAAGATTTTAAGGAGGAACAGAACTCTGTAGCACGTCTCATTCACATGTTGCACAATGATGAGCCTGAAGAGATGTTGAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM5G825524_T02 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os03g58700.1 (Oryza sativa), 3'ss of exon 13
gtgagttcatacacttcgttagaaaagcgaatttttacttgtttgttgtcttcattctgccgcttagtgctcccaatattgttcagctagatcagcacaacacatttcaatttcattttctcatgaagtttgctcaacctgtaacaatgtttttttattattttagCTTGATGAAGAAGATTTTAAGGAGGAACAGAACTCTGTAGCACGTCTCATTCACATGTTGCACAATGATGAGCCTGAAGAGATGTTGAAG
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-----------------gtaatatacacg---cttcattctacaattttctttggcttgtta--tattgtttctgctgctgttcaactgaatcagcgca-cacaat---attctattttcttatcaagttt-----acctgttatattgctt------------agCTTGATGATGAGGATTTTAAGGAGGAACAGAATTCTGTGGCGCGTCTTATTCACATGTTGCACAATGATGACCATGAAGAGATGTTGAAG
upper sequence: GRMZM5G825524_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA14G40270.1 (Glycine max), 3'ss of exon 13
--gtgagttcatacacttcgttagaaaagcgaattttta----cttgtttgttgtcttcattctgccgctt----agtgctc--ccaatattgttcagctagatcagcacaacacat--ttcaatttcattttct-------catgaagtttgctcaa------cctgtaacaa-tgtttttttattattt---tagCTTGATGAAGAAGATTTTAAGGAGGAACAGAACTCTGTAGCACGTCTCATTCACATGTTGCACAATGATGAGCCTGAAGAGATGTTGAAG
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gtgtgcctgagtatttattatcttgggattttgtttataaagatatgattgttctctgtgacctgttatttttgaattatttatttaacatttcttta-tatgtcaaagcaataaataatctattattattccctacataaatataatattttctcaagatcatcctattttaaatatttttccatcttatacacagGTTGATGAAGAAGATTTCAATGAGGAGCAAAACTCTGTTGCTCGCCTCATACACATGTTTCATAATGATGAATCAGAGGAAATGTTTAAG
upper sequence: GRMZM5G825524_T02 (Zea mays), 3'ss of exon 13
lower sequence: AT2G17790.1 (Arabidopsis thaliana), 3'ss of exon 12
gtgagttcatacacttcgttagaaaagcgaatttttacttgtttgttgtcttcattctgccgcttagtgctcccaatattgttcagctagatcagcacaacacatttcaatttcattttctcatgaagtttgctcaacctgtaacaatgtttttttattattttagCTTGATGAAGAAGATTTTAAGGAGGAACAGAACTCTGTAGCACGTCTCATTCACATGTTGCACAATGATGAGCCTGAAGAGATGTTGAAG
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-----------------------------------------gttgttataagcattttg-----agatactttctatcttgtact-taatatcctctcaatcacttgtgaccccaatattaagttgtattt---tgacttctgtacatatttttctacgctcttagGTTGATGAAGATGATTTTCAGGAGGAGCAGAATTCTGTTGCGCTTCTCATTCATATGTTATATAATGATGACCCAGAAGAGATGTTTAAG
upper sequence: GRMZM5G825524_T02 (Zea mays), 3'ss of exon 13
lower sequence: Vv18s0001g14680.t01 (Vitis vinifera), 3'ss of exon 13
gtgagttcatacacttcgttagaaaagcgaatttttacttgtttgttgtcttcattctgccgcttagtg-ctcccaatattgttcagctagatcagcacaacacatttcaatttcattttctcatgaagtttgctcaacctgtaacaatgtttttttattattttagCTTGATGAAGAAGATTTTAAGGAGGAACAGAACTCTGTAGCACGTCTCATTCACATGTTGCACAATGATGAGCCTGAAGAGATGTTGAAG
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-------------------------------------------ttttattttattttttccttttactttcttcttgaattatcactgtagattggtatag---ataacaatctttgtttttcttg---tttacttta--tgcaacaat----------------agCTTGATGAGGAGGATTTCAAGGATGAACAAAATTCTGTCGCTCGTCTCATACACATGTTCTACAATGATGACCCCGAAGAAATGTTGAAGMapped 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|211321313|gb|FL043262.1|FL043262EST: TTTAATTAAGGGGGCTGATAAAGGATATGGATGGGGCTCAAGATGATGAA CTTGATGAAGAAGATTTTAAGGAGGAACAGAACTCTGTAGCACGTCTCATT
genomic: TTTAATTAA-GGGGCTGATAAAGGATATGGATGGGGCTCAAGATGATGAAgtgagttcat ... attattttagCTTGATGAAGAAGATTTTAAGGAGGAACAGAACTCTGTAGCACGTCTCATT
EST:
gi|31356431|gb|CD440788.1|CD440788EST: ATTTAATTAAGGGGCTGATAAAGGATATGGATGGGGCTCAAGATGATGAA CTTGACGAAGAAGATTTTAAGGAGGAACAGAACTCTGTAGCACGTCTCATT
genomic: ATTTAATTAAGGGGCTGATAAAGGATATGGATGGGGCTCAAGATGATGAAgtgagttcat ... attattttagCTTGATGAAGAAGATTTTAAGGAGGAACAGAACTCTGTAGCACGTCTCATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcattttctcatgaagtttgctcaacctgtaacaatgtttttttattattttagCTTGATGAAGAAGATTTTAAGGAGGAACAGAACTCTGTAGCACGTCTCATTCACATGTTGCACAATGATGAGCCTGAAGAGATGTTGAAG
ctgtaac putative branch site (score: 3)
tttttttattatttt putative PPT
tgtaacaatgtttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttcatacacttcgttagaaaagcgaatttttacttgtttgttgtcttcattctgccgcttagtgctcccaatattgttcagctagatcagcacaacacatttcaatttcattttctcatgaagtttgctcaacctgtaacaatgtttttttattattttagCTTGATGAAGAAGATTTTAAGGAGGAACAGAACTCTGTAGCACGTCTCATTCACATGTTGCACAATGATGAGCCTGAAGAGATGTTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG