Sequence
atgc intronic sequence ATGC exonic sequence...gaaacagcgtcacacagagcaaatggaacacttctaaaagcattcttcttcccctaattgaactttaccttgtggctgaatagaaagcaatttagtgcagGCGTCCATGTTGATACTGTTGTCATGAATCCTCCCTTTGGTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAGGTCAGAACCGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G113640_T05 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g06730.1 (Oryza sativa), 3'ss of exon 5
gaaacagcgtcacacagagcaaatggaacacttctaaa----agcattcttcttcccctaattgaactttaccttgtggctgaatagaaagcaatttagtgcagGCGTCCATGTTGATACTGTTGTCATGAATCCTCCCTTTGGTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAGGTCAGAACCGG
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--tgaatggttattgaaacaaaatcatatatttatacacataagcgtagatgctttcaacattgaaaagcttccc-tgatcttttagctacctgttgaa-gtagGCCTTCTTGTTGACACTGTTGTCATGAATCCTCCCTTTGGGACAAGCAGAAAAGGAGCTGACATGGAATTCATTTCTATGGGCATGAAG-----------
upper sequence: GRMZM2G113640_T05 (Zea mays), 3'ss of exon 5
lower sequence: AT4G28830.1 (Arabidopsis thaliana), 3'ss of exon 5
gaaacagcgtcacacagagcaaatggaacacttctaaaagcattcttcttcccctaattgaactttaccttgtggctgaatagaaagcaatttagtgcagGCGTCCATGTTGATACTGTTGTCATGAATCCTCCCTTTGGTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAGGTCAGAACCGG
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-gtacaatcctcctttcatttcagttcattcaacgaaaagaaga-ttctaccggtaac---atttt----tgtggctccatgaa-------ttgttttagGCCTGATTGTGGATACGGTTGTAATGAACCCTCCATTTGGTACACGGAAGAAAGGAGCTGACATGGAGTTTCTCTCTGCGGCAATGAAG-----------
upper sequence: GRMZM2G113640_T05 (Zea mays), 3'ss of exon 5
lower sequence: Vv11s0016g03520.t01 (Vitis vinifera), 3'ss of exon 5
gaaacagcgt-cacacagagcaaatgga-acacttctaaaagcattcttcttcccctaattgaactttaccttgtggctgaatagaaagcaatttagtgcagGCGTCCATGTTGATACTGTTGTCATGAATCCTCCCTTTGGTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAGGTCAGAACCGG
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-taattgtatatatgttctctgtatacatgctcttcaacatatattactgcacttgtcttttaattttatgtccatgtaacaatgattatctctta-tgtagGTCAAATTGTTGATACTGTTGTAATGAATCCTCCATTTGGAACACGGAAGAAGGGGGCTGACATGGATTTTCTCGCTGTGGCTTTGAAG-----------Mapped 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|211270652|gb|FL248442.1|FL248442EST: CTGGACATCGATTTAGTTTGGTCTGACATAAAGAACTTAAATCTGAWAG GCGTCCATGTTGATACTGTTG
genomic: CTGGACATCGATTTAGTTTGGTCTGACATAAAGAACTTAAATCTGAAAGgtattgttct ... tttagtgcagGCGTCCATGTTGATACTGTTG
EST:
gi|211270651|gb|FL248441.1|FL248441EST: CTGGACATCGATTTAGTTTGGTCTGACATAAAGAACTTAAATCTGAAAG GCGTCCATGTTGATACTGTTGTCATGAATCCTCCCTTTGGTACACGAAGGA
genomic: CTGGACATCGATTTAGTTTGGTCTGACATAAAGAACTTAAATCTGAAAGgtattgttct ... tttagtgcagGCGTCCATGTTGATACTGTTGTCATGAATCCTCCCTTTGGTACACGAAGGA
EST:
gi|211270656|gb|FL248446.1|FL248446EST: CTGGACATCGATTTAGTTTGGTCTGACATAAAGAACTTAAATCTGAAAG GCGTCCATGTTGATAC
genomic: CTGGACATCGATTTAGTTTGGTCTGACATAAAGAACTTAAATCTGAAAGgtattgttct ... tttagtgcagGCGTCCATGTTGATAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttcccctaattgaactttaccttgtggctgaatagaaagcaatttagtgcagGCGTCCATGTTGATACTGTTGTCATGAATCCTCCCTTTGGTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAGGTCAGAACCGG
ccctaat putative branch site (score: 3)
taattgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaaacagcgtcacacagagcaaatggaacacttctaaaagcattcttcttcccctaattgaactttaccttgtggctgaatagaaagcaatttagtgcagGCGTCCATGTTGATACTGTTGTCATGAATCCTCCCTTTGGTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAGGTCAGAACCGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA