Sequence
atgc intronic sequence ATGC exonic sequencegcaagtatctcctcacaatgtttcatcccctctccacattctcaacactcatgcggacatcatcaaattctggtaactgcatatgaaaaaaaaaccaaaatcctgacataccggggacttgtttgcagCGTCGGGCGAGCCGCCGCTGGTTCTCGCAGCCTCGGTGCACTGCGCGATGAGGGAGGCCATCAGGGCGGCGAGGAAGGAGTTCTCGGTCAGCACCAGCCC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G141535_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g57690.1 (Oryza sativa), 3'ss of exon 9
gcaagtatctcctcacaatgtttcatcccctctccacattctcaacactcatgcggacatcatcaaattctggtaactgcatatgaaaaaaaaaccaaaatcctgacat-accggggactt-----gtttgcagCGTCGGGCGAGCCGCCGCTGGTTCTCGCAGCCTCGGTGCACTGCGCGATGAGGGAGGCCATCAGGGCGGCGAGGAAGGAGTTCTCGGTCAGCACCAGCCC
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--------------------------------------------------gtgaaaatctcttcttcgtttgctccttttttttttctcaaa--tctgaattctgatattgttgctgtccttcatggcatgcagCGTCCGGTGAGCCGCCGCTGCTGCTGGCGTCGTCGGTGCACTGCGCGATGAGGGAGGCGATCAGGGCGGCCAGGAAGGAGTTCGCCGGCGCCGGAGGCTC
upper sequence: GRMZM2G141535_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g57680.1 (Oryza sativa), 3'ss of exon 9
gcaagtatctcctcacaatgtttcatcccctctccacattctcaacactcatgcggacatcatcaaattctggtaactgcatatgaaaaaaaaaccaaaatcctgacataccg-gggacttgt--ttgcagCGTCGGGCGAGCCGCCGCTGGTTCTCGCAGCCTCGGTGCACTGCGCGATGAGGGAGGCCATCAGGGCGGCGAGGAAGGAGTTCTCGGTCAGCACCAGCCC
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-----------------------------------------------gtgaaatcatcgtcttcttcctttgagcactgaaatcgtgaaggaaatcgaaatctgaaactgttttgtgatccatcgtggcagCGTCCGGTGAGCCGCCGCTGCTGCTGGCGTCGTCGGTGCACTGCGCGATGAGGGAGGCGATCAGGGCGGCCAGGAAGGAGTTCGCCGGCGCCGGCGGCTC
upper sequence: GRMZM2G141535_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os10g04860.1 (Oryza sativa), 3'ss of exon 9
gcaagtatctcctcacaatgtttcatcccctctccacattctcaacactcatgcggacatcatcaaattctggtaactgcatatgaaaaaaaaaccaaaatcctgacataccggggacttgtttgcagCGTCGGGCGAGCCGCCGCTGGTTCTCGCAGCCTCGGTGCACTGCGCGATGAGGGAGGCCATCAGGGCGGCGAGGAAGGAGTTCTCGGTCAGCACCAGCCC
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--------------tcgagattgc-taacctgtgaacaa---caaaccctatacaagc-----tatacattcacaacttta-acactgaaaaatctgaagctgt----tttggcgtatgtcatggcagCGTCCGGTGAGCCGCCGCTGCTGCTGGCGTCGTCCGTGCACTGCGCGATGAGGGAGGCGATCAGGGCGGCGCGGAGAGAGTTCGCCGCTGTCGGCGGCGG
upper sequence: GRMZM2G141535_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g57720.1 (Oryza sativa), 3'ss of exon 2
gcaagtatctcctcacaatgtt-tcatcccctctccacattctcaacactcatgcggacatcatcaaattctggtaactgcatatgaaaaaaaaaccaaaatcctgacataccggggacttgtttgcagCGTCGGGCGA-GCCGCCGCTGGTTCTCGCAGCCTCGGTGCACTGCGCGATGAGGGAGGCCATCA----GGGCGGCGAGGAAGGAGTTCTCGGTCAGCACCAGCCC------------------------------------------------
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--------------gtgaaatcatcgtcttcttcctttgatcctttttctcaaacg--catgagcaat-----gaaatcgtaaaggaactcgaaatctgaaac-tgttttgc--gatccatcttggcagcgtccggtgaagccgccgccgctgctggcgtcgtcggtgcactgcgcgatgagGGAGGCGATCAATCAGGGCGGCCAGGAAGGAGTTCGCCGGCGCCGGCGGCTCGGCGATGACTTTCCAGATGGACGTGCCGGCGACGATGCCGGCCGTCAAMapped 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|44900915|gb|CK827460.1|CK827460EST: TGAGATGTTTAACAGCGCCCCTGACAAGAAGCGTGTCCTATCTTCCAAAG CGTCGGGCGAGCCGCCGCTGGTTCTCGCAGCCTCGGTGCACTGCGCGATGA
genomic: TGAGATGTTTAACAGCGCCCCTGACAAGAAGCGTGTCCTATCTTCCAAAGgcaagtatct ... ttgtttgcagCGTCGGGCGAGCCGCCGCTGGTTCTCGCAGCCTCGGTGCACTGCGCGATGA
EST:
gi|62525891|gb|DN828539.1|DN828539EST: TGAGATGTTTAACAGCGCCCCTGACAAGAAGCGTGTCCTATCTTCCAAAG CGTCGGGCGAGCCGCCGCTGGTTCTCGCAGCCTCGGTGCACTGCGCGATGA
genomic: TGAGATGTTTAACAGCGCCCCTGACAAGAAGCGTGTCCTATCTTCCAAAGgcaagtatct ... ttgtttgcagCGTCGGGCGAGCCGCCGCTGGTTCTCGCAGCCTCGGTGCACTGCGCGATGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taactgcatatgaaaaaaaaaccaaaatcctgacataccggggacttgtttgcagCGTCGGGCGAGCCGCCGCTGGTTCTCGCAGCCTCGGTGCACTGCGCGATGAGGGAGGCCATCAGGGCGGCGAGGAAGGAGTTCTCGGTCAGCACCAGCCC
tcctgac putative branch site (score: 2)
cttgttt putative PPT
atatgaaaaaaaaacc 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 |
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaagtatctcctcacaatgtttcatcccctctccacattctcaacactcatgcggacatcatcaaattctggtaactgcatatgaaaaaaaaaccaaaatcctgacataccggggacttgtttgcagCGTCGGGCGAGCCGCCGCTGGTTCTCGCAGCCTCGGTGCACTGCGCGATGAGGGAGGCCATCAGGGCGGCGAGGAAGGAGTTCTCGGTCAGCACCAGCCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG