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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattgaccccatgcaagtattacttttgcttaattcttctggtttatatagtttgttccgcctacttgtagtgaagatactaagcatgaaataaatgcagGCATTGAAATCCCCAAGTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTG

Basic information

species Oryza sativa
transcript LOC_Os08g37320.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g37320.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G157018_T01 (Zea mays), 3'ss of exon 2
aattgaccccatgcaagtattacttttgcttaattc-ttctggtttatatagtt-tgttccgcctacttgtagtg-aagatactaagcatgaaataaatgcagGCATTGAAATCCCCAAGTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTG
  || ||   |||  | | ||  |  ||  ||   | || |  | |||||| || |||||    |        |   || || ||| | |||||||||||||||||| || ||||| |||||||| ||||| || ||||| |||||||||||||||||||||||  ||
-cttcacatgatg--attgttggtcctgtgtatgccatttttttctatataattctgttctctttgtccactttctgaggtagtaaacttgaaataaatgcagGCATCGAGATCCCGAAGTACGTCGACACAGTTACTCCCCAGTACAAGCCAAAGTTTGATGCTGTG

upper sequence: LOC_Os08g37320.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA20G31790.1 (Glycine max), 3'ss of exon 2
aattgaccccatgcaagtattacttttgcttaattcttctggtttatatagtttgttccgcctacttgtagtgaagatactaa---gcatgaaataaat----gcagGCATTGAAATCCCCAAGTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTG
           ||  ||| |   | |||   ||    | ||   | | |    ||||  |||||||  ||||  |     |||   |  ||  ||  ||    ||||||||||| ||||||||||  ||||| || || |||||||| || ||||| || |||||||| || 
-----tatgtgtgtcagtgt--gtgttgtacaaccaatatgtactgtttttactgttttgcctactattagttcaacatttaatgtgtgtgtgatgcatttttgcagGCATTGAGATCCCCAAGTTTGTTGATACAGTAACTCCTCAATATAAGCCTAAATTTGATGCCCTT

upper sequence: LOC_Os08g37320.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT3G52300.2 (Arabidopsis thaliana), 3'ss of exon 2
aattgaccccatgcaagtattacttttgcttaattcttctggtttatatagtttgttccgcctacttgtagtgaag-atactaagcatgaaataaat----gcagGCATTGAAATCCCCAAGTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTG----
       |  || |  ||  ||  | |  || ||| ||    ||       | | |         || |    ||  | |||     |   ||   |    ||||||||||| || || |||||||||||||  || |||||| | ||||||||||||||||||||  ||    
-----ttcttatacttgttatatatctatttgattgttggaattgtggagatatatcaaagaagattatgagaaactaaactgcatcttttatggcttgctgcagGCATTGAGATTCCAAAGTACGTTGACAAAGTTACTCCTGAATACAAGCCAAAGTTTGATGCTTTGGTGA

upper sequence: LOC_Os08g37320.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT3G52300.1 (Arabidopsis thaliana), 3'ss of exon 2
aattgaccccatgcaagtattacttttgcttaattcttctggtttatatagtttgttccgcctacttgtagtgaag-atactaagcatgaaataaat----gcagGCATTGAAATCCCCAAGTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTG
       |  || |  ||  ||  | |  || ||| ||    ||       | | |         || |    ||  | |||     |   ||   |    ||||||||||| || || |||||||||||||  || |||||| | ||||||||||||||||||||  ||
-----ttcttatacttgttatatatctatttgattgttggaattgtggagatatatcaaagaagattatgagaaactaaactgcatcttttatggcttgctgcagGCATTGAGATTCCAAAGTACGTTGACAAAGTTACTCCTGAATACAAGCCAAAGTTTGATGCTTTG

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|33682142|gb|CF310381.1|CF310381
EST:     AAAAGGAATTGGGTCTAAAGTTGTAGATATGTACAAGGAAGCTTATGAAA                         GCATTGAAATCCCCAAGTACGTTGACACCGTGACTCCTCAGTACAAGCCAA
genomic: AAAAGGAATTGGGTCTAAAGTTGTAGATATGTACAAGGAAGCTTATGAAAgtaagcattt ... ataaatgcagGCATTGAAATCCCCAAGTACGTTGACACCGTGACTCCTCAGTACAAGCCAA
EST: gi|32948236|gb|BP184808.1|BP184808
EST:     AAAAGGAATTGGGTCTAAAGTTGTAGATATGTACAAGGAAGCTTATGAAA                         GCATTGAAATCCCCAAGTACGTTGACACCGTGACTCCTCAGTACAAGCCAA
genomic: AAAAGGAATTGGGTCTAAAGTTGTAGATATGTACAAGGAAGCTTATGAAAgtaagcattt ... ataaatgcagGCATTGAAATCCCCAAGTACGTTGACACCGTGACTCCTCAGTACAAGCCAA
EST: gi|163925925|gb|EG714977.1|EG714977
EST:     AAAAGGAATTGGGTCTAAAGTTGTAGATATGTACAAGGAAGCTTATGAAA                         GCATTGAAATCCCCAAGTACGTTGACACCGTGACTCCTCAGTACAAGCCAA
genomic: AAAAGGAATTGGGTCTAAAGTTGTAGATATGTACAAGGAAGCTTATGAAAgtaagcattt ... ataaatgcagGCATTGAAATCCCCAAGTACGTTGACACCGTGACTCCTCAGTACAAGCCAA
EST: gi|33803307|gb|CF327527.1|CF327527
EST:     AAAAGGAATTGGGTCTAAAGTTGTAGATATGTACAAGGAAGCTTATGAAA                         GCATTGAAATCCCCAAGTACGTTGACACCGTGACTCCTCAGTACAAGCCAA
genomic: AAAAGGAATTGGGTCTAAAGTTGTAGATATGTACAAGGAAGCTTATGAAAgtaagcattt ... ataaatgcagGCATTGAAATCCCCAAGTACGTTGACACCGTGACTCCTCAGTACAAGCCAA
EST: gi|58669670|gb|CK058356.1|CK058356
EST:     AAAAGGAATTGGGTCTAAAGTTGTAGATATGTACAAGGAAGCTTATGAAA                         GCATTGAAATCCCCAAGTACGTTGACACCGTGACTCCTCAGTACAAGCCAA
genomic: AAAAGGAATTGGGTCTAAAGTTGTAGATATGTACAAGGAAGCTTATGAAAgtaagcattt ... ataaatgcagGCATTGAAATCCCCAAGTACGTTGACACCGTGACTCCTCAGTACAAGCCAA
EST: gi|163926597|gb|EG713613.1|EG713613
EST:     ATTGGGTCTAAAGTTGTAGATATGTACAAGGAAGCTTATGAAA                         GCATTGAAATCCCCAAGTACCGTTGACACCGTGACTCCTCAGTACAAGCCA
genomic: ATTGGGTCTAAAGTTGTAGATATGTACAAGGAAGCTTATGAAAgtaagcattt ... ataaatgcagGCATTGAAATCCCCAAGTA-CGTTGACACCGTGACTCCTCAGTACAAGCCA
EST: gi|33802541|gb|CF327143.1|CF327143
EST:     AAAAGGAATTGGGTCTAAAGTTGTAGATATGTACAAGGAAGCTTATGAAA                         GCATTGAAATCCCCAAGTACGTTGACACCGTGACTCCTCAGTACAAGCCAA
genomic: AAAAGGAATTGGGTCTAAAGTTGTAGATATGTACAAGGAAGCTTATGAAAgtaagcattt ... ataaatgcagGCATTGAAATCCCCAAGTACGTTGACACCGTGACTCCTCAGTACAAGCCAA
EST: gi|58603329|gb|CK013857.1|CK013857
EST:     AAAAGGAATTGGGTCTAAAGTTGTAGATATGTACAAGGAAGCTTATGAAA                         GCATTGAAATCCCCAAG
genomic: AAAAGGAATTGGGTCTAAAGTTGTAGATATGTACAAGGAAGCTTATGAAAgtaagcattt ... ataaatgcagGCATTGAAATCCCCAAG
EST: gi|163920020|gb|EG709826.1|EG709826
EST:     AAAAGGAATTGGGTCTAAAGTTGTAGATATGTACAAGGAAGCTTATGAAA                         GCATTGAAATCCCCAAGTACGTTGACACCGTGACTCCTCAGTACAAGCCAA
genomic: AAAAGGAATTGGGTCTAAAGTTGTAGATATGTACAAGGAAGCTTATGAAAgtaagcattt ... ataaatgcagGCATTGAAATCCCCAAGTACGTTGACACCGTGACTCCTCAGTACAAGCCAA
EST: gi|33683470|gb|CF311709.1|CF311709
EST:     CTAAAGTTGTAGATATGTACAAGGAAGCTTATGAAA                         GCATTGAAATCCCCCAAGTACGTTGACACCGTGACTCCTCAGTACAAGCCA
genomic: CTAAAGTTGTAGATATGTACAAGGAAGCTTATGAAAgtaagcattt ... ataaatgcagGCATTGAAAT-CCCCAAGTACGTTGACACCGTGACTCCTCAGTACAAGCCA
EST: gi|33662295|gb|CF293262.1|CF293262
EST:     AAAAGGAATTGGGTCTAAAGTTGTAGATATGTACAAGGAAGCTTATGAAA                         GCATTGAAATCCCCAAGTACGTTGACACCGTGACTCCTCAGTACAAGCCAA
genomic: AAAAGGAATTGGGTCTAAAGTTGTAGATATGTACAAGGAAGCTTATGAAAgtaagcattt ... ataaatgcagGCATTGAAATCCCCAAGTACGTTGACACCGTGACTCCTCAGTACAAGCCAA
EST: gi|163918517|gb|EG711627.1|EG711627
EST:     TAAAGTTGTAGATATGTACAAGGAAGCTTATGAAA                         GCATTGAAATCCCCAAGTACGTTGACACCGTGACTCCTCAGTACAAGCCAA
genomic: TAAAGTTGTAGATATGTACAAGGAAGCTTATGAAAgtaagcattt ... ataaatgcagGCATTGAAATCCCCAAGTACGTTGACACCGTGACTCCTCAGTACAAGCCAA
EST: gi|32947994|gb|BP184566.1|BP184566
EST:     AAAAGGAATTGGGTCTAAAGTTGTAGATATGTACAAGGAAGCTTATGAAA                         GCATTGAAATCCCCAAGTACGTTGACACCGTGACTCCTCAGTACAAGCCAA
genomic: AAAAGGAATTGGGTCTAAAGTTGTAGATATGTACAAGGAAGCTTATGAAAgtaagcattt ... ataaatgcagGCATTGAAATCCCCAAGTACGTTGACACCGTGACTCCTCAGTACAAGCCAA
EST: gi|163920610|gb|EG711789.1|EG711789
EST:     AAAAGGAATTGGGTCTAAAGTTGTAGATATGTACAAGGAAGCTTATGAAA                         GCATTGAAATCCCCAAGTACGTTGACACCGTGACTCCTCAGTACAAGCCAT
genomic: AAAAGGAATTGGGTCTAAAGTTGTAGATATGTACAAGGAAGCTTATGAAAgtaagcattt ... ataaatgcagGCATTGAAATCCCCAAGTACGTTGACACCGTGACTCCTCAGTACAAGCCAA
EST: gi|27577854|gb|CB000549.1|CB000549
EST:     AAAAGGAATTGGGTCTAAAGTTGTAGATATGTACAAGGAAGCTTATGAAA                         GCATTGAAATCCCCAAGTACGTTGACACCGTGACTCCTCAGTACAAGCCAA
genomic: AAAAGGAATTGGGTCTAAAGTTGTAGATATGTACAAGGAAGCTTATGAAAgtaagcattt ... ataaatgcagGCATTGAAATCCCCAAGTACGTTGACACCGTGACTCCTCAGTACAAGCCAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 74 (upstream exon), 65 (downstream exon)
Score: 202

GAGCCCCAACCGATTGACTGGGAGTACTACAGAAAAGGAATTGGGTCTAAAGTTGTAGATATGTACAAGGAAGCTTATGAAAgtaagcattt ... ataaatgcagGCATTGAAATCCCCAAGTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatagtttgttccgcctacttgtagtgaagatactaagcatgaaataaatgcagGCATTGAAATCCCCAAGTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTG
                                        atgaaataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattgaccccatgcaagtattacttttgcttaattcttctggtttatatagtttgttccgcctacttgtagtgaagatactaagcatgaaataaatgcagGCATTGAAATCCCCAAGTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - ccatgca
- - - - - - - - - - - - - tgcttaa
- - - - - - - - - - - - - - - - - -cttctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctacttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgaa