Sequence
atgc intronic sequence ATGC exonic sequencegtttgatccctgccctctcatcttcatttcctcagctcttgcttcaaatggttgttacctgactgtcatcccacctccattttctgctcagATTGGTGATCTTGGACTATCAAAGGTGAAGCAGCACACTTTGGTGTCTGGCGGTGTTAGAGGAACCTTACCATGGATGGCACCAGAGCTTCTGAGTGGGA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g54510.3 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g54510.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G039106_T03 (Zea mays), 3'ss of exon 4
gtttgatccct------gccctctcat------cttcatttcctcag----ctcttgcttcaaa--tggttgtta---cctgactgtcatcccacctccattttctgctcagATTGGTGATCTTGGACTATCAAAGGTGAAGCAGCACACTTTGGTGTCTGGCGGTGTTAGAGGAACCTTACCATGGATGGCACCAGAGCTTCTGAGTGGGA
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gtttgatcccttccccagcctttccctacgccgctttatctttctggggaattcttgtcgcaatgctggatatcttctcctgacttctccccaacacaaatactctgatcagATCGGTGATCTCGGGCTATCAAAGGTTAAACAGCATACTTTGGTATCTGGTGGTGTTAGAGGAACCTTACCGTGGATGGCACCAGAGCTTCTGAGTGGGA
upper sequence: LOC_Os02g54510.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G052658_T01 (Zea mays), 3'ss of exon 5
gtttgatccctgccctctcat-------cttcatttcctcagctcttgct-tca-aatggttgttacctgactgtcatcccacctc---cattttctgctcagATTGGTGATCTTGGACTATCAAAGGTGAAGCAGCACACTTTGGTGTCTGGCGGTGTTAGAGGAACCTTACCATGGATGGCACCAGAGCTTCTGAGTGGGA
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gtttgatccccagcctttccctctgctgctttatctttctggaaattgttgtcacaatggtggat-cctgact-tgtcccaaactcaaatactctctgatcagATCGGTGATCTTGGACTGTCAAAGGTTAAACAGCATACTTTGGTATCTGGTGGTGTTAGAGGAACCTTACCATGGATGGCACCAGAGCTTCTGAGTGGGA
upper sequence: LOC_Os02g54510.2 (Oryza sativa), 3'ss of exon 6
lower sequence: PP1S131_116V6.1 (Physcomitrella patens), 3'ss of exon 6
----------------------------------------------------------------gtttgatccc-tgccctct----catcttcatttcctcagctcttgcttcaaatggttgttacctgactgtcatcccacctccattt--tctgctcagATTGGTGATCTTGGACTATCAAAGGTGAAGCAGCACACTTTGGTGTCTGGCGGTGTTAGAGGAACCTTACCATGGATGGCACCAGAGCTTCTGAGTGGGA
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gtatgactccaacaagataccagaatccgtatagattatgagctacagttgttgcaggatactagttttctactgtgtcctccatagcgaaaacatgctttctgtactgaatctatatgac-aaaattcggtggcggttttattcttttttattctctccagGTTGGGGACTTAGGACTGTCAAAAGTGAAACATCAAACCATGGTGTCAGGTGGTGTCAGAGGGACTCTACCATGGATGGCACCAGAGCTGTTGAATGGAAMapped 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|396941216|gb|HO188425.1|HO188425EST: GGTCAACATGAGGGATCCACAACGACCAATCTGCAAA ATTGGTGATCTTGGACTATCAAAGGTGAAGCAGCACACTTTGGTGTCTGGC
genomic: GGTCAACATGAGGGATCCACAACGACCAATCTGCAAAgtttgatccc ... ttctgctcagATTGGTGATCTTGGACTATCAAAGGTGAAGCAGCACACTTTGGTGTCTGGC
EST:
gi|66924155|gb|CX111003.1|CX111003EST: GTGAGAACCTACTGGTCAACATGAGGGATCCACAACGACCAATCTGCAAA ATTGGTGATCTTGGACTAT
genomic: GTGAGAACCTACTGGTCAACATGAGGGATCCACAACGACCAATCTGCAAAgtttgatccc ... ttctgctcagATTGGTGATCTTGGACTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttgcttcaaatggttgttacctgactgtcatcccacctccattttctgctcagATTGGTGATCTTGGACTATCAAAGGTGAAGCAGCACACTTTGGTGTCTGGCGGTGTTAGAGGAACCTTACCATGGATGGCACCAGAGCTTCTGAGTGGGA
acctgac putative branch site (score: 3)
tcccacctccattttc putative PPT
ttcaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgatccctgccctctcatcttcatttcctcagctcttgcttcaaatggttgttacctgactgtcatcccacctccattttctgctcagATTGGTGATCTTGGACTATCAAAGGTGAAGCAGCACACTTTGGTGTCTGGCGGTGTTAGAGGAACCTTACCATGGATGGCACCAGAGCTTCTGAGTGGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT