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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagttctgccgccctctgcttcttgatttctagactatcttactggatggtaatttacttacatacgtacacatgtacagGGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCGGCGGCGCGGAGGATCGTGGAGGCAGATCAGTTCATGAGGGCTGGCCTCT

Basic information

species Oryza sativa
transcript LOC_Os02g01150.1
intron # 3
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|58691582|gb|CK080269.1|CK080269
EST:     TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCT                         GGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
genomic: TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCTgtcagttctg ... acatgtacagGGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
EST: gi|38468625|gb|CF952756.1|CF952756
EST:     TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCT                         GGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
genomic: TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCTgtcagttctg ... acatgtacagGGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
EST: gi|88360976|gb|CI625282.1|CI625282
EST:     TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCT                         GGCGTTCTGACGGAGACGACGGCGGAGCT
genomic: TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCTgtcagttctg ... acatgtacagGGCGTTCTGACGGAGACGACGGCGGAGCT
EST: gi|88324430|gb|CI566243.1|CI566243
EST:     CGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAAACACGCCT                         GGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGC
genomic: CGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAA-CACGCCTgtcagttctg ... acatgtacagGGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGC
EST: gi|88443673|gb|CI591898.1|CI591898
EST:     TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCT                         GGCGTTCTGACGGAGACGACGGCGGAGC
genomic: TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCTgtcagttctg ... acatgtacagGGCGTTCTGACGGAGACGACGGCGGAGC
EST: gi|29674134|gb|CB670409.1|CB670409
EST:     TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCT                         GGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
genomic: TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCTgtcagttctg ... acatgtacagGGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
EST: gi|29680605|gb|CB676880.1|CB676880
EST:     TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCT                         GGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
genomic: TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCTgtcagttctg ... acatgtacagGGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
EST: gi|33683103|gb|CF311342.1|CF311342
EST:     TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCT                         GGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
genomic: TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCTgtcagttctg ... acatgtacagGGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
EST: gi|29616322|gb|CB621334.1|CB621334
EST:     TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCT                         GGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
genomic: TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCTgtcagttctg ... acatgtacagGGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
EST: gi|88426387|gb|CI576629.1|CI576629
EST:     TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCT                         GGCGTTCTGACGGAGACGACGGCGGAGCTG
genomic: TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCTgtcagttctg ... acatgtacagGGCGTTCTGACGGAGACGACGGCGGAGCTG
EST: gi|10794734|gb|AU108700.1|AU108700
EST:     TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCC-TCGGCAACACGCCT                         GGCGTTCTGACGGAGACGACGGCGGA-CTGGCCGCGTCTCTGTCGCTGGCG
genomic: TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCTgtcagttctg ... acatgtacagGGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
EST: gi|88368586|gb|CI645044.1|CI645044
EST:     TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCT                         GGCGTTCTGACGGAGA
genomic: TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCTgtcagttctg ... acatgtacagGGCGTTCTGACGGAGA
EST: gi|29682953|gb|CB679228.1|CB679228
EST:     TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCT                         GGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
genomic: TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCTgtcagttctg ... acatgtacagGGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
EST: gi|29682997|gb|CB679272.1|CB679272
EST:     TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCT                         GGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
genomic: TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCTgtcagttctg ... acatgtacagGGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
EST: gi|88314098|gb|CI600100.1|CI600100
EST:     TCGACGTGGAGGCCGCCAATAGGAACGGGATCGCCGTCGGCAACACGCCT                         GGCGTTCTGAC
genomic: TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCTgtcagttctg ... acatgtacagGGCGTTCTGAC
EST: gi|29655664|gb|CB651939.1|CB651939
EST:     TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCT                         GGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
genomic: TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCTgtcagttctg ... acatgtacagGGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
EST: gi|86900810|gb|CI304015.1|CI304015
EST:     TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCT                         GGCGTTCTGACGGAGA
genomic: TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCTgtcagttctg ... acatgtacagGGCGTTCTGACGGAGA
EST: gi|88385976|gb|CI568644.1|CI568644
EST:     TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCT                         GGCGTTCTGACGGAGACGA-GGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
genomic: TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCTgtcagttctg ... acatgtacagGGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
EST: gi|88404175|gb|CI575663.1|CI575663
EST:     TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCT                         GGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
genomic: TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCTgtcagttctg ... acatgtacagGGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
EST: gi|29621567|gb|CB626578.1|CB626578
EST:     TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCT                         GGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
genomic: TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCTgtcagttctg ... acatgtacagGGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
EST: gi|88425575|gb|CI569299.1|CI569299
EST:     CGACGTGGAGGCCGCCAAATAGGAACGGCATCGCCGTCGGCAACACGCCT                         GGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGAG
genomic: CGACGTGGAGGCCGCCAA-TAGGAACGGCATCGCCGTCGGCAACACGCCTgtcagttctg ... acatgtacagGGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
EST: gi|88431489|gb|CI579606.1|CI579606
EST:     TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCT                         GGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
genomic: TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCTgtcagttctg ... acatgtacagGGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
EST: gi|29667837|gb|CB664112.1|CB664112
EST:     TCGACGTGGAGGCCGCCACTAAGAACGGCATCGCCGTCGGCAACACGCCT                         GGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
genomic: TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCTgtcagttctg ... acatgtacagGGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
EST: gi|58606736|gb|CK034769.1|CK034769
EST:     TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCT                         GGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
genomic: TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCTgtcagttctg ... acatgtacagGGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
EST: gi|29660668|gb|CB656943.1|CB656943
EST:     TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCT                         GGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
genomic: TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCTgtcagttctg ... acatgtacagGGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
EST: gi|88449373|gb|CI582245.1|CI582245
EST:     TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCT                         GGCGTTCTGACGG
genomic: TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCTgtcagttctg ... acatgtacagGGCGTTCTGACGG
EST: gi|29678225|gb|CB674500.1|CB674500
EST:     TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCT                         GGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
genomic: TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCTgtcagttctg ... acatgtacagGGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
EST: gi|88388887|gb|CI592775.1|CI592775
EST:     TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCT                         GGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
genomic: TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCTgtcagttctg ... acatgtacagGGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
EST: gi|29613448|gb|CB618461.1|CB618461
EST:     TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCT                         GGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
genomic: TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCTgtcagttctg ... acatgtacagGGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
EST: gi|29676108|gb|CB672383.1|CB672383
EST:     TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCT                         GGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
genomic: TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCTgtcagttctg ... acatgtacagGGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
EST: gi|33670534|gb|CF298773.1|CF298773
EST:     TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCT                         GGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG
genomic: TCGACGTGGAGGCCGCCAATAGGAACGGCATCGCCGTCGGCAACACGCCTgtcagttctg ... acatgtacagGGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttctagactatcttactggatggtaatttacttacatacgtacacatgtacagGGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCGGCGGCGCGGAGGATCGTGGAGGCAGATCAGTTCATGAGGGCTGGCCTCT
                              tacttac  putative branch site (score: 1)
                         taatttacttacata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagttctgccgccctctgcttcttgatttctagactatcttactggatggtaatttacttacatacgtacacatgtacagGGCGTTCTGACGGAGACGACGGCGGAGCTGGCCGCGTCTCTGTCGCTGGCGGCGGCGCGGAGGATCGTGGAGGCAGATCAGTTCATGAGGGCTGGCCTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA