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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatacttcttgtgcacaatgctgaaatcctgaagcaccatttcatttgagtatagtattgttctatggtgtctgatttgaatccttaattagctatcagATGACAAACACAATTCAGAAGAAATTCAAGGTATCTTCAACACAGCTGCTGTACCAATCATGCCCATACCAAGCATTGACCTTGTTCATCGTCGGCCCTT

Basic information

species Oryza sativa
transcript LOC_Os01g07310.1
intron # 5
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g07310.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G116053_T01 (Zea mays), 3'ss of exon 5
---------------------------------------------------------------atatacttcttgtgcac--aatgctgaaatc----ctgaagcaccatttcatttgagtatagtattgttctatggtgtctgatttgaatccttaattagctatcagATGACAAACACAATTCAGAAGAAATTCAAGGTATCTTCAACACAGCTGCTGTACCAATCATGCCCATACCAAGCATTGACCTTGTTCATCGTCGGCCCTT
                                                                 |   ||    | |||  ||   || | |     || ||||| | | | ||||||||||  || |||||| ||| || | | |||| |||||||  ||| ||||||||||||| ||||| |||||||| ||||||||||||||||||||||| |||||||| |||||||||||||| |||||||| |||||| | ||||| || |
gtatccttttgattgtacattacccactattttttttatgtggcatatctgtcacagtatccagaaccatttgcatacaccaaactttgcatttgccactaaagcatcctgtaatttgagtat--tagtgttctgtggcgtataacttgagtccttaacaagccatcagATGACAAATACAATACAGAAGAAGTTCAAGGTATCTTCAACACAGCTCCTGTACCAGTCATGCCCATACCAGGCATTGACGTTGTTCCTTGTCGGTCCAT

upper sequence: LOC_Os01g07310.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G081848_T05 (Zea mays), 3'ss of exon 5
atatacttcttgtgcacaatgctgaaatc-ctgaagcaccatttcatttgagtatagtattgttctatggtgtctg--atttgaatccttaattagctatcagATGACAAACACAATTCAGAAGAAATTCAAGGTATCTTCAACACAGCTGCTGTACCAATCATGCCCATACCAAGCATTGACCTTGTTCATCGTCGGCCCTT
  ||            |   ||||    | || ||||| | ||| ||||||||||   | |||||| ||| || |   | |||| |||||||  ||| ||||||||||||| ||||| |||||||| |||||||||||||| |||||||| ||||||||||| |||||||||||||||||||| |||||| |||||||||| |
-cattaaaaaaaaaagcggggctgctgccactaaagcagcctttaatttgagtat--cagtgttctgtggcgtatataacttgagtccttaacaagccatcagATGACAAATACAATACAGAAGAAGTTCAAGGTATCTTCGACACAGCTCCTGTACCAATCGTGCCCATACCAAGCATTGACTTTGTTCCTCGTCGGCCCAT
















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|33679023|gb|CF307262.1|CF307262
EST:     GATCTGTCCTGTCTTTGCTCGCAATCATTACAACCTGCATTGCTCAAATC                         ATGACAAACACAATTCAGAAGAAATTCAAGGTATCTTCAACACAGCTGCTG
genomic: GATCTGTCCTGTCTTTGCTCGCAATCATTACAACCTGCATTGCTCAAATCgtatcctttt ... tagctatcagATGACAAACACAATTCAGAAGAAATTCAAGGTATCTTCAACACAGCTGCTG
EST: gi|33679263|gb|CF307502.1|CF307502
EST:     GATCTGTCCTGTCTTTGCTCGCAATCATTACAACCTGCATTGCTCAAATC                         ATGACAAACACAATTCAGAAGAAATTCAAGGTATCTTCAACACAGCTGCTG
genomic: GATCTGTCCTGTCTTTGCTCGCAATCATTACAACCTGCATTGCTCAAATCgtatcctttt ... tagctatcagATGACAAACACAATTCAGAAGAAATTCAAGGTATCTTCAACACAGCTGCTG
EST: gi|218500395|gb|FG958811.1|FG958811
EST:     GATCTGTCCTGTCTTTGCTCGCAATCATTACAACCTGCATTGCTCAAATC                         ATGACAAACACAATTCAGAAGAAATTCAAGGTATCTTCAACACAGCTGCTG
genomic: GATCTGTCCTGTCTTTGCTCGCAATCATTACAACCTGCATTGCTCAAATCgtatcctttt ... tagctatcagATGACAAACACAATTCAGAAGAAATTCAAGGTATCTTCAACACAGCTGCTG
EST: gi|58693672|gb|CK082359.1|CK082359
EST:     GATCTGTCCTGTCTTTGCTCGCAATCATTACAACCTGCATTGCTCAAATC                         ATGACAAACACAATTCAGAAGAAATTCAAGGTATCTTCAACACAGCTGCTG
genomic: GATCTGTCCTGTCTTTGCTCGCAATCATTACAACCTGCATTGCTCAAATCgtatcctttt ... tagctatcagATGACAAACACAATTCAGAAGAAATTCAAGGTATCTTCAACACAGCTGCTG
EST: gi|29666174|gb|CB662449.1|CB662449
EST:     GATCTGTCCTGTCTTTGCTCGCAATCATTACAACCTGCATTGCTCAAATC                         ATGACAAACACAATTCAGAAGAAATTCAAGGTATCTTCAACACAGCTGCTG
genomic: GATCTGTCCTGTCTTTGCTCGCAATCATTACAACCTGCATTGCTCAAATCgtatcctttt ... tagctatcagATGACAAACACAATTCAGAAGAAATTCAAGGTATCTTCAACACAGCTGCTG
EST: gi|218479998|gb|FG959805.1|FG959805
EST:     GATCTGTCCTGTCTTTGCTCGCAATCATTACAACCTGCATTGCTCAAATC                         ATGACAAACACAATTCAGAAGAAATTCAAGGTATCTTCAACACAGCTGCTG
genomic: GATCTGTCCTGTCTTTGCTCGCAATCATTACAACCTGCATTGCTCAAATCgtatcctttt ... tagctatcagATGACAAACACAATTCAGAAGAAATTCAAGGTATCTTCAACACAGCTGCTG
EST: gi|58665638|gb|CK054324.1|CK054324
EST:     GATCTGTCCTGTCTTTGCTCGCAATCATTACAACCTGCATTGCTCAAATC                         ATGACAAACACAATTCAGAAGAAATTCAAGGTATCTTCAACACAGCTGCTG
genomic: GATCTGTCCTGTCTTTGCTCGCAATCATTACAACCTGCATTGCTCAAATCgtatcctttt ... tagctatcagATGACAAACACAATTCAGAAGAAATTCAAGGTATCTTCAACACAGCTGCTG
EST: gi|29663298|gb|CB659573.1|CB659573
EST:     GATCTGTCCTGTCTTTGCTCGCAATCATTACAACCTGCATTGCTCAAATC                         ATGACAAACACAATTCAGAAGAAATTCAAGGTATCTTCAACACAGCTGCTG
genomic: GATCTGTCCTGTCTTTGCTCGCAATCATTACAACCTGCATTGCTCAAATCgtatcctttt ... tagctatcagATGACAAACACAATTCAGAAGAAATTCAAGGTATCTTCAACACAGCTGCTG
EST: gi|29645955|gb|CB650962.1|CB650962
EST:     GATCTGTCCTGTCTTTGCTCGCAATCATTACAACCTGCATTGCTCAAATC                         ATGACAAACACAATTCAGAAGAAATTCAAGGTATCTTCAACACAGCTGCT
genomic: GATCTGTCCTGTCTTTGCTCGCAATCATTACAACCTGCATTGCTCAAATCgtatcctttt ... tagctatcagATGACAAACACAATTCAGAAGAAATTCAAGGTATCTTCAACACAGCTGCT
EST: gi|428121|gb|D24269.1|D24269
EST:     GATCTGTCCTGTCTTTGCTCGCAATCATTACAACCTGCATTGCTCAAATC                         ATGACAAACACAATTCAGAAGAANTTCAAGGTATCTTCAACACAGCTGCTG
genomic: GATCTGTCCTGTCTTTGCTCGCAATCATTACAACCTGCATTGCTCAAATCgtatcctttt ... tagctatcagATGACAAACACAATTCAGAAGAAATTCAAGGTATCTTCAACACAGCTGCTG
EST: gi|33796589|gb|CF324162.1|CF324162
EST:     GATCTGTCCTGTCTTTGCTCGCAATCATTACAACCTGCATTGCTCAAATC                         ATGACAAACACAATTCAGAAGAAATTCAAGGTATCTTCAACACAGCTGCTG
genomic: GATCTGTCCTGTCTTTGCTCGCAATCATTACAACCTGCATTGCTCAAATCgtatcctttt ... tagctatcagATGACAAACACAATTCAGAAGAAATTCAAGGTATCTTCAACACAGCTGCTG
EST: gi|29681211|gb|CB677486.1|CB677486
EST:     GATCTGTCCTGTCTTTGCTCGCAATCATTACAACCTGCATTGCTCAAATC                         ATGACAAACACAATTCAGAAGAAATTCAAGGTATCTTCAACACAGCTGCTG
genomic: GATCTGTCCTGTCTTTGCTCGCAATCATTACAACCTGCATTGCTCAAATCgtatcctttt ... tagctatcagATGACAAACACAATTCAGAAGAAATTCAAGGTATCTTCAACACAGCTGCTG
EST: gi|86899011|gb|CI296202.1|CI296202
EST:     GATCTGTCCTGTCTTTGCTCGCAATCATTACAACCTGCATTGCTCAAATC                         ATGACAAACACAATTCAGAAGAAATTCAAGGTATCTTCAACACAGCTGCTG
genomic: GATCTGTCCTGTCTTTGCTCGCAATCATTACAACCTGCATTGCTCAAATCgtatcctttt ... tagctatcagATGACAAACACAATTCAGAAGAAATTCAAGGTATCTTCAACACAGCTGCTG

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: 68 (upstream exon), 67 (downstream exon)
Score: 50

TTTTGGTGTTGGAGTTGCAACTGTGACTGACCTGCAGCTTAATGCTGTGGGATCTGTCCTGTCTTTGCTCGCAATCATTACAACCTGCATTGCTCAAATCgtatcctttt ... tagctatcagATGACAAACACAATTCAGAAGAAATTCAAGGTATCTTCAACACAGCTGCTGTACCAATCATGCCCATACCAAGCATTGACCTTGTTCATCGTCGGCCCTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgagtatagtattgttctatggtgtctgatttgaatccttaattagctatcagATGACAAACACAATTCAGAAGAAATTCAAGGTATCTTCAACACAGCTGCTGTACCAATCATGCCCATACCAAGCATTGACCTTGTTCATCGTCGGCCCTT
                                    atccttaat  putative branch site 
      tatagtatt  TA-rich tract