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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgaaggttctactcttttaggtctctctgcttatgaagttgccaatgatcatgtcctcaatatgtaaaataagctaaaataagttacttttcctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAG

Basic information

species Oryza sativa
transcript LOC_Os07g14150.4
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g14150.4 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G008216_T03 (Zea mays), 3'ss of exon 1
gttgaaggttctactcttttaggtctctctgcttatgaa--gttgccaatg-atcatgtcctcaatatgtaaaataagctaaaataagttacttttc--ctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAG
  |||||    |  ||  |||    |   ||  ||  ||        || | |||   | ||    ||  |  || | || ||   |    |||| |  ||| |||||||||||||||||||||||||||||| ||||||||||||||||||||| | || ||||
--tgaag---ttggtcgcttaaaattggttgtataataacgaacattaacgtatcggtttcttctgataaatcatgaccttaatgtatgcgctttcctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTTATCAGGAAG

upper sequence: LOC_Os07g14150.4 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G082924_T01 (Zea mays), 3'ss of exon 1
gttgaaggttctactcttttaggtctctctgctt-atgaagttgccaatgatcatgtcctcaatatgtaaaataagctaaaataagt-tacttttc--ctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAG
    ||  |  |      |||| | | | |  |  ||        ||  | |  |      ||    | |  | |     ||    | | |||||   ||| ||||||||||||||||||||||||||||||||||||||||||||||| || ||| || ||||
----aatttaatcgctgattagctgtatataatcgatattagcagcacggtttcttctgataaaccatgacctcaatctcaacgtatgtgcttttgtactgcagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGTTGCTCATCAGGAAG

upper sequence: LOC_Os07g14150.4 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA13G17790.1 (Glycine max), 3'ss of exon 1
gttgaaggttctactcttttaggtctctct-gcttatgaagttgccaatgatcatgtcctcaatatgtaaaataagctaaaa-taagttacttttcctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAG
  ||||      |     |  ||| | | | |   |  | |||  || | ||    |  |   ||| | |  |   ||     |   ||| | ||  |  ||| |||||  | |||||||||||  ||||||| ||| |||| |||||||||||||| ||||
-ctgaacaacagagcaaatatggtgtatttagaacacaatgtt-tcatttatttcattgtgtttattttatgttttctttgtcttttttaatattatttcagTCGTGGAAACTAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCACCAGGAAG

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|88326542|gb|CI644645.1|CI644645
EST:     GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGT                         TTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
genomic: GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGTgtacgtctct ... tttcctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
EST: gi|33684397|gb|CF312636.1|CF312636
EST:     GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGT                         TTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
genomic: GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGTgtacgtctct ... tttcctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
EST: gi|88376916|gb|CI639241.1|CI639241
EST:     GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGT                         TTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
genomic: GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGTgtacgtctct ... tttcctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
EST: gi|33684446|gb|CF312685.1|CF312685
EST:     GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGT                         TTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
genomic: GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGTgtacgtctct ... tttcctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
EST: gi|33670472|gb|CF298711.1|CF298711
EST:     GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGT                         TTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCTTTTTCTGGTC
genomic: GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGTgtacgtctct ... tttcctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
EST: gi|88348203|gb|CI637664.1|CI637664
EST:     GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGT                         TTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
genomic: GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGTgtacgtctct ... tttcctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
EST: gi|33681048|gb|CF309287.1|CF309287
EST:     GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGT                         TTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
genomic: GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGTgtacgtctct ... tttcctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
EST: gi|33681325|gb|CF309564.1|CF309564
EST:     GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGT                         TTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
genomic: GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGTgtacgtctct ... tttcctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
EST: gi|33680862|gb|CF309101.1|CF309101
EST:     GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGT                         TTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
genomic: GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGTgtacgtctct ... tttcctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
EST: gi|55413799|gb|CV726175.1|CV726175
EST:     GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGT                         TTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
genomic: GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGTgtacgtctct ... tttcctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
EST: gi|88576116|gb|CI670261.1|CI670261
EST:     GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGT                         TTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
genomic: GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGTgtacgtctct ... tttcctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
EST: gi|88324909|gb|CI644920.1|CI644920
EST:     GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGT                         TTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
genomic: GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGTgtacgtctct ... tttcctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
EST: gi|33682363|gb|CF310602.1|CF310602
EST:     GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGGGGCCCAGT                         TTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
genomic: GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGTgtacgtctct ... tttcctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
EST: gi|88328922|gb|CI647002.1|CI647002
EST:     GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGT                         TTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
genomic: GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGTgtacgtctct ... tttcctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
EST: gi|33670643|gb|CF298882.1|CF298882
EST:     GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGT                         TTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCANTTGCTGGTC
genomic: GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGTgtacgtctct ... tttcctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
EST: gi|33820665|gb|CF336142.1|CF336142
EST:     GTTTGCTGGATTTGCTCCTCTCCCTCTCTACGCCATGGATGAGGCCCAGC                         TTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
genomic: GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGTgtacgtctct ... tttcctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
EST: gi|33679899|gb|CF308138.1|CF308138
EST:     GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGT                         TTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
genomic: GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGTgtacgtctct ... tttcctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
EST: gi|88575933|gb|CI670078.1|CI670078
EST:     GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGT                         TTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
genomic: GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGTgtacgtctct ... tttcctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
EST: gi|33683865|gb|CF312104.1|CF312104
EST:     GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGT                         TTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
genomic: GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGTgtacgtctct ... tttcctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
EST: gi|88351621|gb|CI628841.1|CI628841
EST:     GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAG-                         TTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
genomic: GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGTgtacgtctct ... tttcctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
EST: gi|88327608|gb|CI646801.1|CI646801
EST:     GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGT                         TTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
genomic: GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGTgtacgtctct ... tttcctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
EST: gi|33654855|gb|CF277469.1|CF277469
EST:     GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGT                         TTGTGGAGTCAAAGGGTGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
genomic: GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGTgtacgtctct ... tttcctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
EST: gi|58592974|gb|CF991282.1|CF991282
EST:     TTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGTGAGGCCCACGT                         TTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGT
genomic: TTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAG-GAGGCCCA-GTgtacgtctct ... tttcctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGT
EST: gi|88334769|gb|CI647151.1|CI647151
EST:     GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGT                         TTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
genomic: GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGTgtacgtctct ... tttcctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
EST: gi|33680734|gb|CF308973.1|CF308973
EST:     GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGT                         TTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
genomic: GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGTgtacgtctct ... tttcctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
EST: gi|88337228|gb|CI628314.1|CI628314
EST:     GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGNCATGGAGGAGGCCCAG-                         TTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
genomic: GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGTgtacgtctct ... tttcctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgatcatgtcctcaatatgtaaaataagctaaaataagttacttttcctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAG
                            agctaaa  putative branch site (score: 3)
                                        ttacttttcct  putative PPT
               aatatgtaaaataagc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgaaggttctactcttttaggtctctctgcttatgaagttgccaatgatcatgtcctcaatatgtaaaataagctaaaataagttacttttcctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA