Sequence
atgc intronic sequence ATGC exonic sequence...tgacatgctgtcacgatattttatttcttgtgggcttaaggttttgtaattgctgattatgtattgttcttttgactgccattttacctggaacttcaagCTTTGTGTGGGAATTATGTCAATTTTGGCGTATTTGAGCTCTATGGTGACAGAGCACTTGCTGATGCCCTTGATATATCTCTGAAGATGACCCTCTCAGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM5G869993_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g42050.1 (Oryza sativa), 3'ss of exon 22
tgacatgctgtcacgatattttatttcttgtgggcttaaggtt---ttgta-attgctgatt-atgtattgttcttttg-actgccattttacctggaac--ttcaagCTTTGTGTGGGAATTATGTCAATTTTGGCGTATTTGAGCTCTATGGTGACAGAGCACTTGCTGATGCCCTTGATATATCTCTGAAGATGACCCTCTCAGT
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--------tgttcttaaactgtatcttctgggaacctcatctccaattgcagactaaagatttgtatttttttttcttgtactgttattctgactagaaccattgcagCTTTATGTGGAAACTATGTCAACTTTGGTGTATTTGAGCTGTATGGTGACAGAGCACTTGCTGATGCTCTTGATATATCTTTAAAGATGAGCCTCTCAGT
upper sequence: GRMZM5G869993_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv13s0067g01920.t01 (Vitis vinifera), 3'ss of exon 24
---tgacatgctgtcacgatattttatttcttgtgggcttaag-gttttgtaattgctgattatgtattgttcttttgactgccattttacctggaacttcaagCTTTGTGTGGGAATTATGTCAATTTTGGCGTATTTGAGCTCTATGGTGACAGAGCACTTGCTGATGCCCTTGATATATCTCTGAAGATGACCCTCTCAGT
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tagtgtcatttctccgttatatttggtagaatattttctgacctaccataaagatgtaaatcattggctaattttattgttgtc-tttaacc---aaatgacagCTCTTGCTGGAAACTATGTCAACTTTGGTGTGTTTGAACTATATGGTGATAGAGCACTTTCTGATGCCCTTGACATTGCTCTAAAGATGACACTCTCAAT
upper sequence: GRMZM5G869993_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv08s0040g00230.t01 (Vitis vinifera), 3'ss of exon 21
tgacatgctgtcacgatattttatttcttgtgggcttaaggttttgtaattgctgattatgtattgttct-------tttgactgccattttacctggaacttcaagCTTTGTGTGGGAATTATGTCAATTTTGGCGTATTTGAGCTCTATGGTGACAGAGCACTTGCTGATGCCCTTGATATATCTCTGAAGATGACCCTCTCAGT
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-----tactgctgc-atggattctttcaaattgatttactatatttttttcagcatcaatttgttatcatgagccacttttaatgt-agtttactaccatatggcagCACTCACTGGAAACTATGTCAACTTTGGTGTGTTTGAACTGTATGGTGATAGGGCACTTGCTGATGCTCTTGACATTGCTCTAAAAATGATGTTATCCAT
upper sequence: GRMZM5G869993_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ32102 (Selaginella moellendorffii), 3'ss of exon 21
tgacatgctgtcacgatattttatttcttgtgggcttaaggttttgtaattgctgattatgtattgttcttttgactgccattttacctggaacttcaagCTTTGTGTGGGAATTATGTCAATTTTGGCGTATTTGAGCTCTATGGTGACAGAGCACTTGCTGATGCCCTTGATATATCTCTGAAGATGACCCTCTCAGT
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----------------------------------------gtttgctctttgttgcct-tggaagatttgtctgatgaagagtttctttgaca------gCTTTGGGTGGAAATTATGTCAATTTCGGTGTTTTTGAGCTCTACGGCGATCCTGCTCTCGCCGATGCGTTGGACGTAGCTTTGAAGATGTCGTTTTCAATMapped 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|32825983|gb|CD965661.1|CD965661EST: GATCTCACTGACTGTTCTTTCAAGGG CTTTGTGTGGGAATTATGTCAATTTTGGCGTATTTGAGCTCTATGGTGACA
genomic: GATCTCACTGACTGTTCTTTCAAGGGgtgagtaaca ... gaacttcaagCTTTGTGTGGGAATTATGTCAATTTTGGCGTATTTGAGCTCTATGGTGACA
EST:
gi|32824734|gb|CD964456.1|CD964456EST: GATCTCACTGACTGTTCTTTCAAGGG CTTTGTGTGGGAATTATGTCAATTTTGGCGTATTTGAGCTCTATGGTGACA
genomic: GATCTCACTGACTGTTCTTTCAAGGGgtgagtaaca ... gaacttcaagCTTTGTGTGGGAATTATGTCAATTTTGGCGTATTTGAGCTCTATGGTGACA
EST:
gi|32827550|gb|CD967228.1|CD967228EST: GATCTCACTGACTGTTCTTTCAAGGG CTTTGTGTGGGAATTATGTCAATTTTGGCGTATTTGAGCTCTATGGTGACA
genomic: GATCTCACTGACTGTTCTTTCAAGGGgtgagtaaca ... gaacttcaagCTTTGTGTGGGAATTATGTCAATTTTGGCGTATTTGAGCTCTATGGTGACA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtaattgctgattatgtattgttcttttgactgccattttacctggaacttcaagCTTTGTGTGGGAATTATGTCAATTTTGGCGTATTTGAGCTCTATGGTGACAGAGCACTTGCTGATGCCCTTGATATATCTCTGAAGATGACCCTCTCAGT
ttttgac putative branch site (score: 3)
attatgtatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgacatgctgtcacgatattttatttcttgtgggcttaaggttttgtaattgctgattatgtattgttcttttgactgccattttacctggaacttcaagCTTTGTGTGGGAATTATGTCAATTTTGGCGTATTTGAGCTCTATGGTGACAGAGCACTTGCTGATGCCCTTGATATATCTCTGAAGATGACCCTCTCAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG