Sequence
atgc intronic sequence ATGC exonic sequencegtgaggatctcgtcttacatgctcgctataacctgcaggtctctgaatttcgcaatatgcaagtatggttcctacacagtactgtactgtttcagttactgtttcactgactgcctgactattgaacagCGTTTATCTCGGTGCTTCACATGTATGAAACCTTTGGCTGGTGGAGGAGAGCCGATTATATAAAGGTGCACTTTGCTGAGAGCTGGAATGAGTTCCATCA
Basic information
species | Oryza sativa |
transcript | LOC_Os04g57320.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g57320.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G102349_T01 (Zea mays), 3'ss of exon 3
gtgaggatctcgtcttacatgctcgctataacctgcag-gtctctgaatttcgcaatatgcaagtatggttcctacacagtactgtactgtttcagttactgtttcactga-ctgcctgactattgaacagCGTTTATCTCGGTGCTTCACATGTATGAAACCTTTGGCTGGTGGAGGAGAGCCGATTATATAAAGGTGCACTTTGCTGAGAGCTGGAATGAGTTCCATCA
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gtgagggctccgttttgt-catatgcttgcagttgcggtgtatgaaaaggtccctaaagagttttgcagcgttggtttcg-gtcgtgccgttgctgttctttcttttttactctgcttggttat-gaacagCGTTCATATCGGTGCTTCACATGTATGAAACCTTTGGCTGGTGGAGACGAGCTGATTATCTAAAAGTTCACTTTGCGCAGAGCTTGAACGAGTTTCATCA
upper sequence: LOC_Os04g57320.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G010555_T01 (Zea mays), 3'ss of exon 3
gtgaggatctcgtcttacatgctcgctataacctgcaggtctctgaatttcgcaatatgcaagtatggttcctacacagtactgtactgtttcagt-tactgtttcactgact--gcctgactattgaacagCGTTTATCTCGGTGCTTCACATGTATGAAACCTTTGGCTGGTGGAGGAGAGCCGATTATATAAAGGTGCACTTTGCTGAGAGCTGGAATGAGTTCCATCA
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-----------------------------ggattg--gattccagtgtttggatatggatatccaccatccattctcaggtctattggttcctggcatgcctctgtcttgactctgcttggttat-gaacagCATTCATATCGGTGCTTCACTTGTATGCGACCTTTGGATGGTGGAGACGAGCTGATTACATAAAGGTTCACTTTGCGCAGAGCTGGAACGAGTTCCATCA
upper sequence: LOC_Os04g57320.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA15G11950.1 (Glycine max), 3'ss of exon 3
gtgaggatctcgtcttacatgctcgctataacctgcaggtctctgaatttcgca-atatgcaagta--tggttcctacacagtactgtactgtttcagttactgtttcactg-actgcctgactattgaacagCGTTTATCTCGGTGCTTCACATGTATGAAACCTTTGGCTGGTGGAGGAGAGCCGATTATATAAAGGTGCACTTTGCTGAGAGCTGGAATGAGTTCCATCA
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-------------------------------caattgtgtacttaaattactcgtaaatgtagggagtcactgggtatttttcattgtgacttttcggtattaacttctgtgtactgtttatttat--gtcagCCTTTATGTCAGTTCTCCACATGTATGAGAGTTTTGGTTGGTGGAGGCGGGCGGACTATCTGAAAGTGCATTTTGCTGAGAGCTGGAATGAAATGCATCA
upper sequence: LOC_Os04g57320.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT4G22260.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgaggatctcgtcttacatgctcgctataacctgcaggtctctgaatttcgcaatatgcaagtatggttcctacacagtactgtactgtttcagttactgtttcactgactgcctgactattgaacagCGTTTATCTCGGTGCTTCACATGTATGAAACCTTTGGCTGGTGGAGGAGAGCCGATTATATAAAGGTGCACTTTGCTGAGAGCTGGAATGAGTTCCATCA
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----------tttttagtgtgtttatcactaattatggatct--ggatacca-aatg---aaaagttgttccgaggctagaacataatgtt--------tgtttctt---ctatatgctccttg--cagCGTTTATGTCTGTGCTACATATGTATGAGACCTTTGGTTGGTGGAGGAGAGCAGATTATTTGAAAGTACACTTTGCTGAGAGCTGGAATGAAATGCATCA
upper sequence: LOC_Os04g57320.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv00s0399g00060.t01 (Vitis vinifera), 3'ss of exon 3
gtgaggatctcgtcttacatgctcgctataacctgcaggtctctgaatttcgcaatatgcaagtatggttcctacacagtact--gtactgtttcagttactgtttcactgactgcctgactattgaacagCGTTTATCTCGGTGCTTCACATGTATGAAACCTTTGGCTGGTGGAGGAGAGCCGATTATATAAAGGTGCACTTTGCTGAGAGCTGGAATGAGTTCCATCA
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-----------------------------ggccagccaatgt-tgtgattagccaagtgcaattttttttaaaatagtgtattttatattattttaattggacttgtgac-attgttctgtttcattgcagCCTTTATGTCTGTTCTGCACATGTATGAGAGTTTTGGCTGGTGGAGAAGGGCGGATTATCTGAAGGTGCATTTTGCGGAGAGCTGGAATGAAATGCATCAMapped 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|29661402|gb|CB657677.1|CB657677EST: CTACGCTAGATTTTTCGTATTGGAGACGATTGCTAGGGTGCCGTATTTTG CGTTTATCTCGGTGCTTCACATGTATGAAACCTTTGGCTGGTGGAGGAGAG
genomic: CTACGCTAGATTTTTCGTATTGGAGACGATTGCTAGGGTGCCGTATTTTGgtgaggatct ... tattgaacagCGTTTATCTCGGTGCTTCACATGTATGAAACCTTTGGCTGGTGGAGGAGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacagtactgtactgtttcagttactgtttcactgactgcctgactattgaacagCGTTTATCTCGGTGCTTCACATGTATGAAACCTTTGGCTGGTGGAGGAGAGCCGATTATATAAAGGTGCACTTTGCTGAGAGCTGGAATGAGTTCCATCA
tattgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaggatctcgtcttacatgctcgctataacctgcaggtctctgaatttcgcaatatgcaagtatggttcctacacagtactgtactgtttcagttactgtttcactgactgcctgactattgaacagCGTTTATCTCGGTGCTTCACATGTATGAAACCTTTGGCTGGTGGAGGAGAGCCGATTATATAAAGGTGCACTTTGCTGAGAGCTGGAATGAGTTCCATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA