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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_Os01g07310.2
intron # 4
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|86899011|gb|CI296202.1|CI296202
EST:     GATCTGTCCTGTCTTTGCTCGCAATCATTACAACCTGCATTGCTCAAATC                         ATGACAAACACAATTCAGAAGAAATTCAAGGTATCTTCAACACAGCTGCTG
genomic: GATCTGTCCTGTCTTTGCTCGCAATCATTACAACCTGCATTGCTCAAATCgtatcctttt ... tagctatcagATGACAAACACAATTCAGAAGAAATTCAAGGTATCTTCAACACAGCTGCTG
EST: gi|428121|gb|D24269.1|D24269
EST:     GATCTGTCCTGTCTTTGCTCGCAATCATTACAACCTGCATTGCTCAAATC                         ATGACAAACACAATTCAGAAGAANTTCAAGGTATCTTCAACACAGCTGCTG
genomic: GATCTGTCCTGTCTTTGCTCGCAATCATTACAACCTGCATTGCTCAAATCgtatcctttt ... tagctatcagATGACAAACACAATTCAGAAGAAATTCAAGGTATCTTCAACACAGCTGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgagtatagtattgttctatggtgtctgatttgaatccttaattagctatcagATGACAAACACAATTCAGAAGAAATTCAAGGTATCTTCAACACAGCTGCTGTACCAATCATGCCCATACCAAGCATTGACCTTGTTCATCGTCGGCCCTT
                                    atccttaat  putative branch site 
      tatagtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatacttcttgtgcacaatgctgaaatcctgaagcaccatttcatttgagtatagtattgttctatggtgtctgatttgaatccttaattagctatcagATGACAAACACAATTCAGAAGAAATTCAAGGTATCTTCAACACAGCTGCTGTACCAATCATGCCCATACCAAGCATTGACCTTGTTCATCGTCGGCCCTT

- - - - cttgtgc
- - - - - - - - - -tgctgaa
- - - - - - - - - - - - - - -ctgaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgtctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaatcc