Sequence
atgc intronic sequence ATGC exonic sequence...ctctggccatgttatacattgtttgtcttacaggtcacctgagtacctctgcatgggtatactattgatcactgctttgctctttgctatttgctatcagGGGGCATCTGATTCACTGAACCTACCCGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGAAACGCTGCTGAACATGCTAGTGCAATAATGTTTG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g55940.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g55940.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G040017_T02 (Zea mays), 3'ss of exon 7
-----ctctg--gccatgttatacattgtttgtcttacagg--tcacctgagtacctctgcatgggtatactattgatcactgctttgctctttgctatttgctatcagGGGGCATCTGATTCACTGAACCTACCCGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGAAACGCTGCTGAACATGCTAGTGCAATAATGTTTG
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tattaccatgatgtacaattgtacattggtagtattacagagatcatctga-tacctctgcaatgatgta--actggtcactgttttgatctat------tgctgttagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGCAATGCAGCTGAACATGCAAGTGCAATAATGTTTG
upper sequence: LOC_Os04g55940.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G143356_T01 (Zea mays), 3'ss of exon 8
---------ctctggccatgttatacattgtttgtcttacaggtcacctgagtacctctgcatgggtatactattgatcactgctttgctctttgctatttgctatcagGGGGCATCTGATTCACTGAACCTACCCGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGAAACGCTGCTGAACATGCTAGTGCAATAATGTTTG
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tagttattattattaccatgatgtacatcagtagtattacaggtcatctga-tacctctgcgatgatgta--actggtcactgttttgatctat------tgttgtcagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGCAATGCAGCTGAACATGCAAGCGCAATAATGTTTG
upper sequence: LOC_Os04g55940.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv09s0018g01840.t01 (Vitis vinifera), 3'ss of exon 7
----ctctggccatgttatacattgtttgtcttacaggtcacctgagtacctctgcatgggtatactattgatcactgctttgctctttgctatttgctatcagGGGGCATCTGATTCACTGAACCTACCCGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGAAACGCTGCTGAACATGCTAGTGCAATAATGTTTG
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tttattatgctttccttcaacattaatttatgttctggaggtagaaaggctattggtt--gtgaacagttgacaaatcaatttttttctg--gtttcttttcagGGAGCATCTGAGTCATTAAACATGCCAGTGGCTTTTATTAGTGTCATTCTGCTTCCAATTGTAGGAAATGCTGCTGAGCATGCCAGTGCAATTATGTTTGMapped 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|286840|gb|D15647.1|D15647EST: TGACATTATGGGGGTCTATTCTTTCTGAATACCTGGTTAATGCCATTGAG GGGGCATCTGATTCACTGAACCTACCCGTGGCTTTTATCAGTGTNATNTTG
genomic: TGACATTATGGGTGTCTATTCTTTCTGAATACCTGGTTAATGCCATTGAGgtattccttc ... ttgctatcagGGGGCATCTGATTCACTGAACCTACCCGTGGCTTTTATCAGTGTTATTTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctctgcatgggtatactattgatcactgctttgctctttgctatttgctatcagGGGGCATCTGATTCACTGAACCTACCCGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGAAACGCTGCTGAACATGCTAGTGCAATAATGTTTG
tattgat putative branch site (score: 3)
tatactatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctctggccatgttatacattgtttgtcttacaggtcacctgagtacctctgcatgggtatactattgatcactgctttgctctttgctatttgctatcagGGGGCATCTGATTCACTGAACCTACCCGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGAAACGCTGCTGAACATGCTAGTGCAATAATGTTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT