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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtcatggctatacatagttttgtttttttttacctttaccatcttattctgacatagtttcaccttcttttgctattaccaatttattatgatgggtcatatttccagCCAATAAGATACGCCTTTGGAACAAGGGTGTTGATTCAGAAAGCTTCCATCCCCGTTTCCGTAATGACGAAATGCGTGCAAGGCTAAC

Basic information

species Oryza sativa
transcript LOC_Os07g01030.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g01030.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G100652_T03 (Zea mays), 3'ss of exon 5
gttgtcatggctatacatagttttgtttttttttacctttaccatcttattctgacatagtttcaccttcttttgctattaccaatttattatgatgggtcatatttccagCCAATAAGATACGCCTTTGGAACAAGGGTGTTGATTCAGAAAGCTTCCATCCCCGTTTCCGTAATGACGAAATGCGTGCAAGGCTAAC
|||  | |  |||   |||   |    | | | || || ||   |||| ||||    || ||  ||| | | |  ||     |||      | | ||  | || |||||||||||||| |||||||||||||||||||||||||| ||||||||||||||||| |||||||| ||    ||||||||| ||||||||||
gtttacttaacta---ataaccta---tctatgtatctgtagtttcttgttcttgt-taattgtaccatatatctct-----caa------acggtgcat-atgtttccagCCAATAAAATACGCCTTTGGAACAAGGGTGTTGACTCAGAAAGCTTCCATCCTCGTTTCCGCAACATGGAAATGCGTTCAAGGCTAAC

upper sequence: LOC_Os07g01030.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA18G42540.1 (Glycine max), 3'ss of exon 7
-----------gttgtcatggctatacatagttttgtttttttttacctttaccatcttattctg-acatagtttcaccttctt-ttgctat--taccaatttattatgatgggt----catatt----tccagCCAATAAGATACGCCTTTGGAACAAGGGTGTTGATTCAGAAAGCTTCCATCCCCGTTTCCGTAATGACGAAATGCGTGCAAGGCTAAC
            |   | |  ||| || |     | || ||  ||      | ||| | |   |   |||   |     | | |  | ||||  | | ||||| | |  | |  |    | | ||    |||||| || ||||| || ||||||||||||||||||||||| ||||  |||||||||   | |||     | ||||||||   ||| |||| 
gtgaacataaaatccgcttatctagacttttagctattcttaattggtgacagcatttgaaaatacgcatttctcggtatgcctactactatgctgcgaatttttgagtaagtttttctcctgttggtatccagCTAACAAGATTCGTCTTTGGAACAAGGGTGTTGATTCTGAAAAATTCCATCCCAAATACCGCTCCCATGAAATGCGATTAAGACTAAG

upper sequence: LOC_Os07g01030.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA07G17680.1 (Glycine max), 3'ss of exon 6
gttgtcatggctatacatagttttgttttttt-ttacctttaccatcttattctgacatagtttcaccttcttttgctat---taccaattt--------attatgatggg-------tcatatt----tccagCCAATAAGATACGCCTTTGGAACAAGGGTGTTGATTCAGAAAGCTTCCATCCCCGTTTCCGTAATGACGAAATGCGTGCAAGGCTAAC
||   ||| |     | |  | | || ||||   ||   |||     | ||     || ||  |     | |  || |||   ||| | | |        ||| |||  |        || | ||    |||||| || ||||| || ||||||||||||||||||||||| ||||  |||||||||   | |||     | ||||||||   ||| |||| 
gtgaacatagaatccccttatctagtcttttagctatgcttaattggtaatagcatcagagaatatgtgtttcctggtatgcctactactatgcagcaaaattttgaccgagtttttctcctgttggtatccagCTAACAAGATTCGTCTTTGGAACAAGGGTGTTGATTCTGAAAAATTCCATCCCAAATACCGCTCCCATGAAATGCGATTAAGACTAAG

upper sequence: LOC_Os07g01030.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA01G27840.1 (Glycine max), 3'ss of exon 7
----------------gttgtcatggctatacatagttttgtttttttttacctttaccatcttattctga-catagtttcaccttcttttgctattac--caatttattat---gatgggtcatatt-------tccagCCAATAAGATACGCCTTTGGAACAAGGGTGTTGATTCAGAAAGCTTCCATCCCCGTTTCCGTAATGACGAAATGCGTGCAAGGCTAAC
                 || | | |    | ||||| | |    |   ||     || ||||| |   | |  ||  ||| |   |   |||  | | |  |||||| || |     |   |  || |       |||||| || |||||  | ||||||||||||||||||||||| ||||| |||||||| || |||       | ||||||||   ||| || | 
gtgaactcaaacaccccttatgaagtgatttcatagctcttcgctgagttgataatagcatctgaacataagtatttttttatactacattgtcaatgcagcaattttttgtctaactcaattctactgttgatgtccagCGAACAAGATTTGTCTTTGGAACAAGGGTGTTGATTCTGAAAGTTTCCATCCGCGATTCAAGTCCCATGAAATGCGATTAAGACTGAG

upper sequence: LOC_Os07g01030.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA03G14200.1 (Glycine max), 3'ss of exon 7
gttgtcatggctatacatagttttgtttttttttacctttaccatcttattctgacatagt---ttcaccttcttttgctattaccaatttattatgatgggtcatatttccagCCAATAAGATACGCCTTTGGAACAAGGGTGTTGATTCAGAAAGCTTCCATCCCCGTTTCCGTAATGACGAAATGCGTGCAAGGCTAAC
      |    || | | |   |    |     ||  | ||  |||| |     |||| ||   | || |   ||||  | | ||  | || |  || ||      || |||||| || |||||  | ||||||||||||||||| ||||| ||||| |||||||| || |||       | ||||||||   |||||| | 
------aataataaatacaagataacataaacataaatgta--atctaacaactacattgtcaatgcagcaattttttgtctaactcaattctcctgttg------atgtccagCGAACAAGATTTGTCTTTGGAACAAGGGTGTCGATTCTGAAAGTTTCCATCCACGATTCAAGTCCCATGAAATGCGATTAAGGCTGAG

upper sequence: LOC_Os07g01030.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT5G01220.1 (Arabidopsis thaliana), 3'ss of exon 7
gttgtcatggctatacatagttttgtttttttttacctttaccatcttattctgacatagtttcaccttcttttgctattaccaatttattatgatgggtcatatttccagCCAATAAGATACGCCTTTGGAACAAGGGTGTTGATTCAGAAAGCTTCCATCCCCGTTTCCGTAATGACGAAATGCGTGCAAGGCTAAC
       ||   | | ||  |    |   |||||       |  | | ||| |   | | || ||  ||||| | || ||    || ||||                  ||| ||| |  | || |||||||| |||||||| ||||||||||||||| ||||||||||||||  | | |||||||||  ||| || | 
------gtgaagaaagatcatacattacatttttgtacaagctctatgattgttcaaaacttacattttcttcttctttttttcatatattga----------------agCTAATCAACTTCGACTTTGGAATAAGGGTGTCGATTCAGAAAGCTTCAATCCCCGTTTCCGTTCTCAAGAAATGCGTATAAGACTGAG

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|29613028|gb|CB618041.1|CB618041
EST:     ACCATCAGTTGCTATCGGCAAGGATCTTCAAGCTGCCCGTGTTACAGCAG                         CCAATAAGATACGCCTTTGGAACAAGGGTGTTGATTCAGAAAGCTTCCATC
genomic: ACCATCAGTTGCTATCGGCAAGGATCTTCAAGCTGCCCGTGTTACAGCAGgttgtcatgg ... atatttccagCCAATAAGATACGCCTTTGGAACAAGGGTGTTGATTCAGAAAGCTTCCATC
EST: gi|29613025|gb|CB618038.1|CB618038
EST:     ACCATCAGTTGCTATCGGCAAGGATCTTCAAGCTGCCCGTGTTACAGCAG                         CCAATAAGATACGCCTTTGGAACAAGGGTGTTGATTCAGAAAGCTTCCATC
genomic: ACCATCAGTTGCTATCGGCAAGGATCTTCAAGCTGCCCGTGTTACAGCAGgttgtcatgg ... atatttccagCCAATAAGATACGCCTTTGGAACAAGGGTGTTGATTCAGAAAGCTTCCATC
EST: gi|29657825|gb|CB654100.1|CB654100
EST:     ACCATCAGTTGCTATCGGCAAGGATCTTCAAGCTGCCCGTGTTACAGCAG                         CCAATAAGATACGCCTTTGGAACAAGGGTGTTGATTCAGAAAGCTTCCATC
genomic: ACCATCAGTTGCTATCGGCAAGGATCTTCAAGCTGCCCGTGTTACAGCAGgttgtcatgg ... atatttccagCCAATAAGATACGCCTTTGGAACAAGGGTGTTGATTCAGAAAGCTTCCATC
EST: gi|29621512|gb|CB626523.1|CB626523
EST:     ACCATCAGTTGCTATCGGCAAGGATCTTCAAGCTGCCCGTGTTACAGCAG                         CCAATAAGATACGCCTTTGGAACAAGGGTGCTGATTCAGAAAGCTTCCATC
genomic: ACCATCAGTTGCTATCGGCAAGGATCTTCAAGCTGCCCGTGTTACAGCAGgttgtcatgg ... atatttccagCCAATAAGATACGCCTTTGGAACAAGGGTGTTGATTCAGAAAGCTTCCATC
EST: gi|29669005|gb|CB665280.1|CB665280
EST:     ACCATCAGTTGCTATCGGCAAGGATCTTCAAGCTGCCCGTGTTACAGCAG                         CCAATAAGATACGCCTTTGGAACAAGGGTGTTGATTCAGAAAGCTTCCATC
genomic: ACCATCAGTTGCTATCGGCAAGGATCTTCAAGCTGCCCGTGTTACAGCAGgttgtcatgg ... atatttccagCCAATAAGATACGCCTTTGGAACAAGGGTGTTGATTCAGAAAGCTTCCATC
EST: gi|86848294|gb|CI292130.1|CI292130
EST:     CCATCAAGTTGCTATCGGCAAGGATCTTCAAGCTGCCCGTGTTACAGCAG                         CCAATAAGATACGCCTTTGGAACAAGGGTGTTGATTCAGAAAGCTTCCATC
genomic: CCATC-AGTTGCTATCGGCAAGGATCTTCAAGCTGCCCGTGTTACAGCAGgttgtcatgg ... atatttccagCCAATAAGATACGCCTTTGGAACAAGGGTGTTGATTCAGAAAGCTTCCATC

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: 43 (upstream exon), 49 (downstream exon)
Score: 4

AATTCTTGCACCGAGCTGCGGATCTCACACTGGTACCATCAGTTGCTATCGGCAAGGATCTTCAAGCTGCCCGTGTTACAGCAGgttgtcatgg ... atatttccagCCAATAAGATACGCCTTTGGAACAAGGGTGTTGATTCAGAAAGCTTCCATCCCCGTTTCCGTAATGACGAAATGCGTGCAAGGCTAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagtttcaccttcttttgctattaccaatttattatgatgggtcatatttccagCCAATAAGATACGCCTTTGGAACAAGGGTGTTGATTCAGAAAGCTTCCATCCCCGTTTCCGTAATGACGAAATGCGTGCAAGGCTAAC
                                              tatttcc  CT-rich tract
                    tattaccaatttatta  TA-rich tract