Sequence
atgc intronic sequence ATGC exonic sequencegttagtacttagcaatagcatgaaccctgtacttcatgttgcatgcttgtgtatcggttttgttagaaatttcagttgcatggtgaatattgctgtttcatctattaatggtctggttctagttgtttgtatctaaatgtacccttttgattttttatatccataggtccataacaacagcaaactcttatcacagGTTGAAGTGTTCCAGCGACAGCTCGAACTAGCTAAGGAATTGGAGAGACCTGTTTCTGTTCATTGTGTGCGGGCATTTGGTGATCTTCTGGAAGTATTGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G114131_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g48820.2 (Oryza sativa), 3'ss of exon 4
gttagtacttagcaatagcatgaaccctgtacttcatgttgcatgcttgtgtatcggttttgttagaaatttcagttgcatggtgaatattgctgtttcatctattaatggtctggttctagttgttt-gtatctaaatgtacccttttgattttttatatccataggtccat-aacaacagcaaactcttatcacagGTTGAAGTGTTCCAGCGACAGCTCGAACTAGCTAAGGAATTGGAGAGACCTGTTTCTGTTCATTGTGTGCGGGCATTTGGTGATCTTCTGGAAGTATTGA
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---------------------------------------------------------------------------------------aatcactaggccatataacc----tatgcctcaagtccttttgcatcatgagcaagctttatgcc-------accaataagactatcagaagctaaaaaatatcactgcagGTTGAAGTTTTCCAGCAGCAACTTGAACTTGCTAAGGAGTTGAACAAGCCTGTTTCTGTTCATTGTGTGCGCGCCTTTGGTGATCTTCTGGAGATACTAA
upper sequence: GRMZM2G114131_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT5G17570.1 (Arabidopsis thaliana), 3'ss of exon 4
gttagtacttagcaatagcatgaaccctgtacttcatgttgcatgcttgtgtatcggttttgttagaaatttcagttgcatggtgaatattgctgtttcatctattaatggtctggttctagttgtttgtatctaaatgtacccttttgattttttatatccataggtccataacaacagcaaactcttatcacagGTTGAAGTGTTCCAGCGACAGCTCGAACTAGCTAAGGAATTGGAGAGACCTGTTTCTGTTCATTGTGTGCGGGCATTTGGTGATCTTCTGGAAGTATTGA
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----------------------------------------------------------------------------------------------gtttcaga-attgaaaaacagacc--------ttgtggttaaatggtttatgttc-tcagtgatggcttttgatgc-taaagacatcat-ttttaatttcagGTTACCGTCTTTCGTCAACAGCTTGAACTTGCAAAGGAATTGAAGAAACCTGCGTCAGTTCATTGTGTTCGTGCATTTGGGGATCTACTCGAGATATTAA
upper sequence: GRMZM2G114131_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv15s0024g00050.t01 (Vitis vinifera), 3'ss of exon 5
gttagtacttagcaatagcatgaaccctgtacttcatgttgcatgcttgtgtatcggttttgttagaaatttcagttgcatggtgaatattgctgtttcatctattaatggtctggttctagttgtttgtatctaaatgtacccttttgattttttatatccataggtccataacaacagcaaactcttatcacagGTTGAAGTGTTCCAGCGACAGCTCGAACTAGCTAAGGAATTGGAGAGACCTGTTTCTGTTCATTGTGTGCGGGCATTTGGTGATCTTCTGGAAGTATTGA
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---------------------------------------------------------------------------------------tcctactctcctacttgct-----tctgataatag--aatgctaaagagatgttttccttgaagatgttttgtgaaacagtt--ttatttgtttaattttctgttccagGTTGAAGTTTTCCAGCAACAGCTTGAACTTGCCAAAGAGTTGAAAAGACCAGTTTCTGTCCATTGCGTTCGTGCTTTTGGTGATCTTCTTCAGATAATGCMapped 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|60401013|gb|DN233820.1|DN233820EST: TTGGTCTGGACAAAGGTTCACATGGAAAAACCATCAACTTCGGAGAACAG GTTGAAGTGTTCCAGCGACAACTCGAACTAGCTAAGGAATTGGAGAGACCT
genomic: TTGGTCTGGACAAAGGTTCACATGGAAAAACCATCAACTTCGGAGAACAGgttagtactt ... cttatcacagGTTGAAGTGTTCCAGCGACAGCTCGAACTAGCTAAGGAATTGGAGAGACCT
EST:
gi|74238219|gb|DT646133.1|DT646133EST: TTGGTCTGGACAAAGGTTCACATGGAAAAACCATCAACTTCGGAGAACAG GTTGAAGTGTTCCAGCGACAGCTCGAACTAGCTAAGGAATTGGAGAGACCT
genomic: TTGGTCTGGACAAAGGTTCACATGGAAAAACCATCAACTTCGGAGAACAGgttagtactt ... cttatcacagGTTGAAGTGTTCCAGCGACAGCTCGAACTAGCTAAGGAATTGGAGAGACCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cccttttgattttttatatccataggtccataacaacagcaaactcttatcacagGTTGAAGTGTTCCAGCGACAGCTCGAACTAGCTAAGGAATTGGAGAGACCTGTTTCTGTTCATTGTGTGCGGGCATTTGGTGATCTTCTGGAAGTATTGA
ccataac putative branch site (score: 3)
ctcttatc putative PPT
attttttatatccata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtacttagcaatagcatgaaccctgtacttcatgttgcatgcttgtgtatcggttttgttagaaatttcagttgcatggtgaatattgctgtttcatctattaatggtctggttctagttgtttgtatctaaatgtacccttttgattttttatatccataggtccataacaacagcaaactcttatcacagGTTGAAGTGTTCCAGCGACAGCTCGAACTAGCTAAGGAATTGGAGAGACCTGTTTCTGTTCATTGTGTGCGGGCATTTGGTGATCTTCTGGAAGTATTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG