Sequence
atgc intronic sequence ATGC exonic sequence...ctagattcattagcatctatatgaatgtgggcaatgctagaaagtcttacattgtgaaacggagggagtagtcaaatattgaaattattttagtcgctagTGTATCAGCTGCCATGCATTTTCTCCACTGCAGGTTCATCTTATAGAAGGGATAATTGATGAGGTGGACAGCACAGTTCACGTGTCATGGGTCCAGCCTA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g32800.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g32800.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G868757_T04 (Zea mays), 3'ss of exon 6
ctagattcattagcatctatatgaatgtgggcaatgctagaaagtcttacattgtgaaacggagggagtagtcaaatattgaaattattttagtcgc---tagTGTATCAGCTGCCA------TGCATTTTCTCCACTGCAGGTTCATCTTATAGAAGGGATAATTGATGAGGTGGACAGCACAGTTCACGTGTCATGGGTCCAGCCTA---------------------------------
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----------------------------------------tgagtctttggttttgacgtgtttgtgtt--tccattgtttcatttgactgccttgcgtctggtaatccacttgtaacatttttgctttgtttcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTATCATGGGTCCAGCCTAGAGTGCTTGGAATTCCACAGGTTAAGGCTTTGC
upper sequence: LOC_Os01g32800.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G083076_T01 (Zea mays), 3'ss of exon 5
ctagattcattagcatctatatgaatgtgggcaatgctagaaagtcttacattgtgaaacggagggagtagtcaaatattgaaattattttagtcgctagTGTATCAGCTGCCATGCATTTTCTCCACTGCAGGTTCATCTTATAGAAGGGATAATTGATGAGGTGGACAGCACAGTTCACGTGTCATGGGTCCAGCCTA---------------------------------
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-----------------------------tgtaatcttggtttgacgtgt-ttgtggttccatcatttcatatgactgccctacgtctggcaatc-catttgtaacatttctgctttgttttt--aaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTTTCGTGGGTCCAGCCCAGAGTGCTTGGAATCCCACAGGTTAAGGCTTTGCMapped 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|58681322|gb|CK070009.1|CK070009EST: CTAAGCTTTCTATCAGTGATGTGGAATATCTTCTTATGAAGAGCCTCTCG TGTATCAGCTGCCATGCATTTTCTCCACTGCAGGTTCATCTTATAGAAGGG
genomic: CTAAGCTTTCTATCAGTGATGTGGAATATCTTCTTATGAAGAGCCTCTCGgtaactgcat ... tagtcgctagTGTATCAGCTGCCATGCATTTTCTCCACTGCAGGTTCATCTTATAGAAGGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttacattgtgaaacggagggagtagtcaaatattgaaattattttagtcgctagTGTATCAGCTGCCATGCATTTTCTCCACTGCAGGTTCATCTTATAGAAGGGATAATTGATGAGGTGGACAGCACAGTTCACGTGTCATGGGTCCAGCCTA
gtcttac putative branch site (score: 3)
ttatttt putative PPT
tagtcaaatattgaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctagattcattagcatctatatgaatgtgggcaatgctagaaagtcttacattgtgaaacggagggagtagtcaaatattgaaattattttagtcgctagTGTATCAGCTGCCATGCATTTTCTCCACTGCAGGTTCATCTTATAGAAGGGATAATTGATGAGGTGGACAGCACAGTTCACGTGTCATGGGTCCAGCCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - atgaatg
- - - - - - - - - - - - - - - gcaatgc
- - - - - - - - - - - - - - - - - - - - - - -cttacat