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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttcttgtcttcttcaatttagacagtacttacacctgaagcgtgaatctagactgaactgcatacttctggactttgacagGTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG

Basic information

species Oryza sativa
transcript LOC_Os01g02020.1
intron # 9
splice site 3'
intron type U2

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|58609247|gb|CK037280.1|CK037280
EST:     GTCTCCAAACTTCGCAAATAGATTATTATGAGATAAACGAAGCTTTCTCC                         GTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
genomic: GTCTCCAAACTTCACAAATAGATTATTATGAGATAAACGAAGCTTTCTCCgtatgttctt ... actttgacagGTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
EST: gi|89182799|gb|CI045557.1|CI045557
EST:     CACAAATAGATTATTATGAGATAAACGAAGCTTTCTCC                         GTCATTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
genomic: CACAAATAGATTATTATGAGATAAACGAAGCTTTCTCCgtatgttctt ... actttgacagGTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
EST: gi|86431728|gb|CI085339.1|CI085339
EST:     TCACAAATAGATTATTATGAGATAAACGAAGCTTTCTCC                         GTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
genomic: TCACAAATAGATTATTATGAGATAAACGAAGCTTTCTCCgtatgttctt ... actttgacagGTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
EST: gi|88223118|gb|CI222967.1|CI222967
EST:     GTCTCCAAACTTCACAAATAGATTATTATGAGATAAACGAAGCTTTCTCC                         GTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
genomic: GTCTCCAAACTTCACAAATAGATTATTATGAGATAAACGAAGCTTTCTCCgtatgttctt ... actttgacagGTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
EST: gi|88982218|gb|CI027795.1|CI027795
EST:     AATAGATTATTATGAGATAAACGAAGCTTTCTCC                         GTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
genomic: AATAGATTATTATGAGATAAACGAAGCTTTCTCCgtatgttctt ... actttgacagGTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
EST: gi|58657491|gb|CK046171.1|CK046171
EST:     GTCTCCCAACTTCACAAATAGATTATTATGAGATAAACGAAGCTTTCTCC                         GTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
genomic: GTCTCCAAACTTCACAAATAGATTATTATGAGATAAACGAAGCTTTCTCCgtatgttctt ... actttgacagGTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
EST: gi|29675317|gb|CB671592.1|CB671592
EST:     GTCTCCAAACTTCACAAATAGATTATTATGAGATAAACGAAGCTTTCTCC                         GTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
genomic: GTCTCCAAACTTCACAAATAGATTATTATGAGATAAACGAAGCTTTCTCCgtatgttctt ... actttgacagGTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
EST: gi|218504789|gb|FG958555.1|FG958555
EST:     GTCTCCAAACTTCACAAATAGATTATTATGAGATAAACGAAGCTTTCTCC                         GTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
genomic: GTCTCCAAACTTCACAAATAGATTATTATGAGATAAACGAAGCTTTCTCCgtatgttctt ... actttgacagGTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
EST: gi|88243051|gb|CI244173.1|CI244173
EST:     GTCTCCAAACTTCACAAATAGATTATTATGAGATAAACGAAGCTTTCTCC                         GTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
genomic: GTCTCCAAACTTCACAAATAGATTATTATGAGATAAACGAAGCTTTCTCCgtatgttctt ... actttgacagGTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
EST: gi|86427944|gb|CI073041.1|CI073041
EST:     GTCTCCAAACTTCACAAATAGATTATTATGAGATAAACGAAGCTTTCTCC                         GTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
genomic: GTCTCCAAACTTCACAAATAGATTATTATGAGATAAACGAAGCTTTCTCCgtatgttctt ... actttgacagGTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
EST: gi|88214442|gb|CI214291.1|CI214291
EST:     GAAGCTTTCTCC                         GTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
genomic: GAAGCTTTCTCCgtatgttctt ... actttgacagGTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
EST: gi|86831084|gb|CI295561.1|CI295561
EST:     GTCTCCAAACTTCACAAATAGATTATTATGAGATAAACGAAGCTTTCTCC                         GTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
genomic: GTCTCCAAACTTCACAAATAGATTATTATGAGATAAACGAAGCTTTCTCCgtatgttctt ... actttgacagGTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
EST: gi|29640751|gb|CB645758.1|CB645758
EST:     GTCTCCAAACTTCACAAATAGATTATTATGAGATAAACGAAGCTTTCTCC                         GTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
genomic: GTCTCCAAACTTCACAAATAGATTATTATGAGATAAACGAAGCTTTCTCCgtatgttctt ... actttgacagGTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
EST: gi|29641200|gb|CB646207.1|CB646207
EST:     GTCTCCAAACTTCACAAATAGATTATTATGAGATAAACGAAGCTTTCTCC                         GTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
genomic: GTCTCCAAACTTCACAAATAGATTATTATGAGATAAACGAAGCTTTCTCCgtatgttctt ... actttgacagGTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
EST: gi|66915792|gb|CX102640.1|CX102640
EST:     GTCTCCAAACTTCGCAAATAGATTATTATGAGATAAACGAAGCTTTCTCC                         GTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
genomic: GTCTCCAAACTTCACAAATAGATTATTATGAGATAAACGAAGCTTTCTCCgtatgttctt ... actttgacagGTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
EST: gi|88248007|gb|CI247856.1|CI247856
EST:     GTCTCCCAACTTCACAAATAGATTATTATGAGATAAACGAAGCTTTCTCC                         GTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
genomic: GTCTCCAAACTTCACAAATAGATTATTATGAGATAAACGAAGCTTTCTCCgtatgttctt ... actttgacagGTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
EST: gi|218487009|gb|FG958888.1|FG958888
EST:     GTCTCCAAACTTCACAAATAGATTATTATGAGATAAACGAAGCTTTCTCC                         GTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
genomic: GTCTCCAAACTTCACAAATAGATTATTATGAGATAAACGAAGCTTTCTCCgtatgttctt ... actttgacagGTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
EST: gi|86851471|gb|CI314069.1|CI314069
EST:     GTCTCCCAACTTCACAAATAGATTATTATGAGATAAACGAAGCTTTCTCC                         GTCG-TGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
genomic: GTCTCCAAACTTCACAAATAGATTATTATGAGATAAACGAAGCTTTCTCCgtatgttctt ... actttgacagGTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
EST: gi|89169716|gb|CI110075.1|CI110075
EST:     GTCTCCAAACTTCACAAATAGATTATTATGAGATAAACGAAGCTTTCTCC                         GTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
genomic: GTCTCCAAACTTCACAAATAGATTATTATGAGATAAACGAAGCTTTCTCCgtatgttctt ... actttgacagGTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
EST: gi|86528447|gb|CI168653.1|CI168653
EST:     GTCTCCAAGCTTCACAAATAGATTATTATGAGATAAACGAAGCTTTCTCC                         GTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
genomic: GTCTCCAAACTTCACAAATAGATTATTATGAGATAAACGAAGCTTTCTCCgtatgttctt ... actttgacagGTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttacacctgaagcgtgaatctagactgaactgcatacttctggactttgacagGTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG
 tacttac  putative branch site (score: 1)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttcttgtcttcttcaatttagacagtacttacacctgaagcgtgaatctagactgaactgcatacttctggactttgacagGTCGTTGCTTTAGCCAACCAGAAGCTTCTTGGTATTCCTTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC