Sequence
atgc intronic sequence ATGC exonic sequencegtatgcttttgtgttattttgagatataaggttaatatgcattattgaaataactatggttcaagagcttcacaaatatgttctgttttcctcccaaactttacttggagagaaacctacttgattctctttatcttacagGGAATTGAGATGCTATCACTTGGATCATTCAAAACTGGTGCTATTCTCTTG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g02530.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g02530.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA14G21190.1 (Glycine max), 3'ss of exon 1
gtatgcttttgtgttattttgagatataaggttaatatgcattattgaaataactatggttcaagagcttcacaaatatgttctgttttcctcccaaactttacttggagagaa-acctacttgattctctttat----cttacagGGAATTGAGATGCTATCACTTGGATCATTCAAAACTGGTGCTATTCTCTTG
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--------------------------------------------agaaagcaactaagatt--atcattcaatgaatgttttgttattcatattcaaattatgaaaagtgaaattaccccaatgactcaatatgtaatattcacagGGAATTGAAATGCTCTCTCTTGGGTCTTTCAAGACTGGTGCTATTCTCTTG
upper sequence: LOC_Os02g02530.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA06G08620.2 (Glycine max), 3'ss of exon 6
gtatgcttttgtgttattttgagatataaggttaatatgcattattgaaataactatggttcaagagcttcacaaatatgttctgttttcctcccaaactttacttggagagaaacctacttgattctctttatcttacagGGAATTGAGATGCTATCACTTGGATCATTCAAAACTGGTGCTATTCTCTTG
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----------------------------attctatcatatatgctatgaatgtttgtgt------aatactgtgaatcatttttgattactagacagtatttaac---accgatgactacatatttatca----cttacagGGAATTGAAATGCTTTCTCTTGGGTCTTTCAAGACTGGTGCTATTCTCTTG
upper sequence: LOC_Os02g02530.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA04G08510.1 (Glycine max), 3'ss of exon 6
gtatgcttttgtgttattttgagatataaggttaatatgcattattgaaataactatggttcaagagcttcacaaatatgttctgttttcctcccaaactttacttgg-agagaaacctacttgattctctttatcttacagGGAATTGAGATGCTATCACTTGGATCATTCAAAACTGGTGCTATTCTCTTG
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-------------------------------attctat-cgtttctgctgtga--atgtttgtgcaatactgtgaatcagttttgattact----aaacagtatttgacaccgatggctacatatttatca----cttacagGGAATTGAAATGCTTTCTCTTGGGTCTTTCAAGACTGGTGCTATTCTCTTG
upper sequence: LOC_Os02g02530.3 (Oryza sativa), 3'ss of exon 5
lower sequence: AT2G03120.1 (Arabidopsis thaliana), 3'ss of exon 5
-gta-tgcttttgtgttattttgagatata-aggttaatatgcattattgaaataac-tatggttcaagagcttcacaaatatgttctgttttcctcccaaactttacttggagagaaacctacttgattctctttatcttacagGGAATTGAGATGCTATCACTTGGATCATTCAAAACTGGTGCTATTCTCTTG
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gttacttcccttgcactttatgggaatacataaactctgaagcttcactgttataacataatatttaagtttaaagtgaactggagtcactgttgttgagtgtctcttttttta------ctaattaatgccgttgccaatacagGGAATTGAGATGCTCTCTCTCGGATCATTCAAGACTGGTGCCATCCTTTTGMapped 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|29629871|gb|CB634880.1|CB634880EST: AGAAGCATTGGCTAGCAAACAATGTTTTGGGGATTTCTTTCTGCATTCAG GGAATTGAGATGCTATCACTTGGATCATTCAAAAC
genomic: AGAAGCATTGGCTAGCAAACAATGTTTTGGGGATTTCTTTCTGCATTCAGgtatgctttt ... tatcttacagGGAATTGAGATGCTATCACTTGGATCATTCAAAAC
EST:
gi|58684751|gb|CK073438.1|CK073438EST: AGAAGCATTGGCTAGCAAACAATGTTTTGGGGATTTCTTTCTGCATTCAG GGAATTGAGATGCTATCACTTGGATCATTCAAAACTGGTGCTATTCTCTTG
genomic: AGAAGCATTGGCTAGCAAACAATGTTTTGGGGATTTCTTTCTGCATTCAGgtatgctttt ... tatcttacagGGAATTGAGATGCTATCACTTGGATCATTCAAAACTGGTGCTATTCTCTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcctcccaaactttacttggagagaaacctacttgattctctttatcttacagGGAATTGAGATGCTATCACTTGGATCATTCAAAACTGGTGCTATTCTCTTG
acttgat putative branch site (score: 5)
ttctctttatcttac CT-rich tract
tttatctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcttttgtgttattttgagatataaggttaatatgcattattgaaataactatggttcaagagcttcacaaatatgttctgttttcctcccaaactttacttggagagaaacctacttgattctctttatcttacagGGAATTGAGATGCTATCACTTGGATCATTCAAAACTGGTGCTATTCTCTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG