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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactagcaccattcatcgaaagccagagataaaactacagctcctttcttcctcctttgtaattgctgtagtaaaaaaacaatcctccttttgcctctttcctgaacatacttaccccttggatgcttgagtttattggaaccactgatgcaatcggcgcttctgctgcagGAGCTCGGTGGCAATGCGACACTGATCTTCTATGGAACTGAAGAGGCAAAAGAAGGCAAAAATGCATACATGGAGCGACGGCGCCCTGATTTCTCAAAGT

Basic information

species Oryza sativa
transcript LOC_Os01g47350.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g47350.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G060156_T01 (Zea mays), 3'ss of exon 8
gtactagcaccattcatcgaaagccagagataaaactacagctcctttcttcctcctttgtaattgctgtagtaaaaaaacaatcctccttttgcctctttcctgaacatacttaccccttggatgcttgagtttattggaaccactgatgcaatcggcgcttctgctgcagGAGCTCGGTGGCAATGCGACACTGATCTTCTATGGAACTGAAGAGGCAAAAGAAGGCAAAAATGCATACATGGAGCGACGGCGCCCTGATTTCTCAAAGT
                                                           ||||   |||    ||||    || ||| |  |||    ||    ||||     | |  || |   ||||   | |    |   || |  ||     ||||||||||||  ||||||| || || ||||| || || || ||||| || || || |||||||| ||||| || || || ||||||||| |||| ||||| |||||||| ||||
-----------------------------------------------------------gtaaagcctgc--caaaatgctaacccttcccttggaagttg---gaac-----tgctgctggtgagcttctatctgcatgttgcattactga---tggcgcttctgctctagGAGCTTGGCGGGAATGCCACGCTAATATTCTACGGCACGGAGGAGGCAAAGGAAGGGAAGAACGCGTACATGGAGAGACGACGCCCAGATTTCTCCAAGT
















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|29668522|gb|CB664797.1|CB664797
EST:     TGCTGAAATCTGCACTCAATGCAGCTGATGATGGCCATGCTGGCCTTCAG                         GAGCTCGGTGGCAATGCGACACTGATCTTCTATGGAACTGAAGAGGCAAAA
genomic: TGCTGAAATCTGCACTCAATGCAGCTGATGATGGCCATGCTGGCCTTCAGgtactagcac ... tctgctgcagGAGCTCGGTGGCAATGCGACACTGATCTTCTATGGAACTGAAGAGGCAAAA
EST: gi|86842072|gb|CI338435.1|CI338435
EST:     AAATCTGCACTCAATGCAGCTGATGATGGCCATGCTGGCCTTCAG                         GAGCTCGGTGGCAATGCGACACTGATCTTCTATGGAACTGAAGAGGCAAAA
genomic: AAATCTGCACTCAATGCAGCTGATGATGGCCATGCTGGCCTTCAGgtactagcac ... tctgctgcagGAGCTCGGTGGCAATGCGACACTGATCTTCTATGGAACTGAAGAGGCAAAA
EST: gi|58675867|gb|CK064554.1|CK064554
EST:     TGCTGAAATCTGCACTCAATGCAGCTGATGATGGCCATGCTGGCCTTCAG                         GAGCTCGGTGGCAATGCGACACTGATCTTCTATGGAACTGAAGAGGCAAAA
genomic: TGCTGAAATCTGCACTCAATGCAGCTGATGATGGCCATGCTGGCCTTCAGgtactagcac ... tctgctgcagGAGCTCGGTGGCAATGCGACACTGATCTTCTATGGAACTGAAGAGGCAAAA
EST: gi|86251256|gb|CI055389.1|CI055389
EST:     GATGATGGCCATGCTGGCCTTCAG                         GAGCTCGGTGGCAATGCGACACTGATCTTCTATGGAACTGAAGAGGCAAAA
genomic: GATGATGGCCATGCTGGCCTTCAGgtactagcac ... tctgctgcagGAGCTCGGTGGCAATGCGACACTGATCTTCTATGGAACTGAAGAGGCAAAA
EST: gi|29656537|gb|CB652812.1|CB652812
EST:     TGCTGAAATCTGCACTCAATGCAGCTGATGATGGCCATGCTGGCCTTCAG                         GAGCTCGGTGGCAATGCGACACTGATCTTCTATGGAACTGAAGAGGCAAAA
genomic: TGCTGAAATCTGCACTCAATGCAGCTGATGATGGCCATGCTGGCCTTCAGgtactagcac ... tctgctgcagGAGCTCGGTGGCAATGCGACACTGATCTTCTATGGAACTGAAGAGGCAAAA
EST: gi|86896008|gb|CI330025.1|CI330025
EST:     TGCTGAAATCTGCACTCAATGCAGCTGATGATGGCCATGCTGGCCTTCAG                         GAGCTCGGTGGCAATGCGACACTGATCTTCTATGGAACTGAAGAGGCAAAA
genomic: TGCTGAAATCTGCACTCAATGCAGCTGATGATGGCCATGCTGGCCTTCAGgtactagcac ... tctgctgcagGAGCTCGGTGGCAATGCGACACTGATCTTCTATGGAACTGAAGAGGCAAAA
EST: gi|38479469|gb|CF963584.1|CF963584
EST:     TGCTGAAATCTGCACTCAATGCAGCTGATGATGGCCATGCTGGCCTTCAG                         GAGCTCGGTGGCAATGCGACACTGATCTTCTATGGAACTGAAGAGGCAAAA
genomic: TGCTGAAATCTGCACTCAATGCAGCTGATGATGGCCATGCTGGCCTTCAGgtactagcac ... tctgctgcagGAGCTCGGTGGCAATGCGACACTGATCTTCTATGGAACTGAAGAGGCAAAA
EST: gi|29668603|gb|CB664878.1|CB664878
EST:     TGCTGAAATCTGCACTCAATGCAGCTGATGATGGCCATGCTGGCCTTCAG                         GAGCTCGGTGGCAATGCGACACTGATCTTCTATGGAACTGAAGAGGCAAAA
genomic: TGCTGAAATCTGCACTCAATGCAGCTGATGATGGCCATGCTGGCCTTCAGgtactagcac ... tctgctgcagGAGCTCGGTGGCAATGCGACACTGATCTTCTATGGAACTGAAGAGGCAAAA
EST: gi|29668562|gb|CB664837.1|CB664837
EST:     TGCTGAAATCTGCACTCAATGCAGCTGATGATGGCCATGCTGGCCTTCAG                         GAGCTCGGTGGCAATGCGACACTGATCTTTTATGGAACTGAAGAGGCAAAA
genomic: TGCTGAAATCTGCACTCAATGCAGCTGATGATGGCCATGCTGGCCTTCAGgtactagcac ... tctgctgcagGAGCTCGGTGGCAATGCGACACTGATCTTCTATGGAACTGAAGAGGCAAAA

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: 69 (upstream exon), 46 (downstream exon)
Score: 9

GGTGAAATGGTGCCGAAAAATCTTGAGGAACAGTCCAACAGCCATCCGGGTGCTGAAATCTGCACTCAATGCAGCTGATGATGGCCATGCTGGCCTTCAGgtactagcac ... tctgctgcagGAGCTCGGTGGCAATGCGACACTGATCTTCTATGGAACTGAAGAGGCAAAAGAAGGCAAAAATGCATACATGGAGCGACGGCGCCCTGATTTCTCAAAGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttggatgcttgagtttattggaaccactgatgcaatcggcgcttctgctgcagGAGCTCGGTGGCAATGCGACACTGATCTTCTATGGAACTGAAGAGGCAAAAGAAGGCAAAAATGCATACATGGAGCGACGGCGCCCTGATTTCTCAAAGT
                          cactgat  putative branch site (score: 9)
                                           cttctgct  putative PPT
             agtttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactagcaccattcatcgaaagccagagataaaactacagctcctttcttcctcctttgtaattgctgtagtaaaaaaacaatcctccttttgcctctttcctgaacatacttaccccttggatgcttgagtttattggaaccactgatgcaatcggcgcttctgctgcagGAGCTCGGTGGCAATGCGACACTGATCTTCTATGGAACTGAAGAGGCAAAAGAAGGCAAAAATGCATACATGGAGCGACGGCGCCCTGATTTCTCAAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA