Sequence
atgc intronic sequence ATGC exonic sequence...atttgtaatgtccactgggtagatatgttgtgttatccacctatcgtgactggtaggtcaacatgatgtttgctttccttctccttttgtgaacttccagGTTTCGATGCGACAACACAAAGATTGCAATTTCTCTTATGCTGGTCTGAAGACTCAAGTTCGATTGGCTATTGAATCCAGAAACATGTATGGCTGTTTTA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g19140.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g19140.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G420055_T01 (Zea mays), 3'ss of exon 4
atttgtaatgtccactgggtagatatgttgt-gttatccacctatcgtgact--ggtaggtcaacatgatgtttgctttccttctccttttgtgaacttccagGTTTCGATGCGACAACACAAAGATTGCAATTTCTCTTATGCTGGTCTGAAGACTCAAGTTCGATTGGCTATTGAATCCAGAAACATGTATGGCTGTTTTA
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-attgt--tgtttaagatgtagttattatgttgttatccatttatttttattatgcttaggctacgtgattctattgcttatatttttcttataagctttcagGTTCCAATGCGACAGCATAAAGATTGCAATTTTTCTTATGCTGGACTGAAGACTCAAGTTCGATTGGCAATTGAATCTAAGAACTT--------------
upper sequence: LOC_Os01g19140.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT2G45270.1 (Arabidopsis thaliana), 3'ss of exon 7
---atttgtaa--tgtccactgggtagatatgttgtgttatccacctatcgtgactggtaggtcaacatgatgtttgctttccttctccttttgtgaacttccagGTTTCGATGCGACAACACAAAGATTGCAATTTCTCTTATGCTGGTCTGAAGACTCAAGTTCGATTGGCTATTGAATCCAGAAACATGTATGGCTGTTTTA
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gtaagtgacaaactagttgctggttggttagatatcttttttca--tgttctactcaat--gttcacatcatttctgtgatattgtttaccatgt---ttatcagGTTCCAATGAAATATCATAAAGATTGCAACTTTTCTTATGCTGGTTTGAAGACACAAGTGAGGCTAGCCATTGAAGCCAAAGAAAT--------------Mapped 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|58696199|gb|CK084886.1|CK084886EST: CTGCCTATTGTTGGAGTTCATCATATGGAGGCACAGGCATTAGTTTCCAG GTTTCGATGCGACAACACAAAGATTGCAATTTCTCTTATGCTGGTCTGAAG
genomic: CTGCCTATTGTTGGAGTTCATCATATGGAGGCACAGGCATTAGTTTCCAGgtatcgcctt ... gaacttccagGTTTCGATGCGACAACACAAAGATTGCAATTTCTCTTATGCTGGTCTGAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgactggtaggtcaacatgatgtttgctttccttctccttttgtgaacttccagGTTTCGATGCGACAACACAAAGATTGCAATTTCTCTTATGCTGGTCTGAAGACTCAAGTTCGATTGGCTATTGAATCCAGAAACATGTATGGCTGTTTTA
tttgctttccttctcc CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttgtaatgtccactgggtagatatgttgtgttatccacctatcgtgactggtaggtcaacatgatgtttgctttccttctccttttgtgaacttccagGTTTCGATGCGACAACACAAAGATTGCAATTTCTCTTATGCTGGTCTGAAGACTCAAGTTCGATTGGCTATTGAATCCAGAAACATGTATGGCTGTTTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT