Skip to another splice site:
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 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagttggacctttcctatggctacagtttggagtcttatgtacacttggattggaaaaattcgttgaaaatattacgagttgcttcacaatattacccaacttacaagattgcaaacatttcctttttcttctttttttttgaaatagcaatttaatcatgcagGTTTCGTTCCATTGATGTGAACAATGGTGGCATGTGCGTCTTCACTGTAAACAAGCGAGGAGAGGCTATGCTTCAAGCCCTTAACATGACAGCACACATG

Basic information

species Oryza sativa
transcript LOC_Os01g13570.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g13570.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G114550_T01 (Zea mays), 3'ss of exon 4
gcaagttg---gacctttcctatggctacagtttggagtcttatgtacacttggattggaaaaattcgttgaaaatatt--acgag-ttgcttcacaatattacccaacttacaagattgcaaacatttcctttttcttctttttttttgaaa----tagcaatttaat--catgcagGTTTCGTTCCATTGATGTGAACAATGGTGGCATGTGCGTCTTCACT-------GTAAACAAGCGAGGAGAGGCTATGCTTCAAGCCCTTAACATGACAGCACACATG
|||||| |   || |||| || ||||| || ||  |     ||  |  | |||          |     || |||| ||  | ||  ||| ||  || | |||    ||  | |    | |||| |  |  ||||| ||   |||  |  ||      ||| | | |||   ||||||||||||| |||||||||| ||||| ||||||||||| ||||||| |       || ||||||| |||||| ||||||||||||||||| |||||||||||       
gcaagtcgtctgaacttttctgtggctccaattctgg---ctaactttatttgtcccacgttcaacgtctggaaatttttaatgaaattgtttgtcagtgttatgtcaccaagatttatacaaaaaacttgtttttttttcctttcctcaaatactccagctagtgaataatatgcagGTTTCGTGCCATTGATGTAAACAACGGTGGCATGTGTGTCTTCAGTCTTCACGGTGAACAAGCAAGGAGAAGCTATGCTTCAAGCCCTCAACATGACAGC-------
















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|29688716|gb|CB684991.1|CB684991
EST:     TCTATTTTGCGCGCACTCATCTGCACCGCGCTAGGTCTTCCTCCTGAGAG                         GTTTCGTTCCATTGATGTGAACAATGGTGGCATGTGCGTCTTCACTGTAAA
genomic: TCTATTTTGCGCGCACTCATCTGCACCGCGCTAGGTCTTCCTCCTGAGAGgcaagttgga ... aatcatgcagGTTTCGTTCCATTGATGTGAACAATGGTGGCATGTGCGTCTTCACTGTAAA
EST: gi|88830391|gb|CI010591.1|CI010591
EST:     TCTATTTTGCGCGCACTCATCTGCACCGCGCTAGGTCTTCCTCCTGAGAG                         GTTTCGTTCCATTGATGTGAACAATGGTGGCATGTGCGTCTTCACTGTAAA
genomic: TCTATTTTGCGCGCACTCATCTGCACCGCGCTAGGTCTTCCTCCTGAGAGgcaagttgga ... aatcatgcagGTTTCGTTCCATTGATGTGAACAATGGTGGCATGTGCGTCTTCACTGTAAA
EST: gi|86841586|gb|CI336525.1|CI336525
EST:     TCTATTTTGCGCGCACTCATCTGCACCGCGCTAGGTCTTCCTCCTGAGAG                         GTTTCGTTCCATTGATGTGAACAATGGTGGCATGTGCGTCTTCACTGTAAA
genomic: TCTATTTTGCGCGCACTCATCTGCACCGCGCTAGGTCTTCCTCCTGAGAGgcaagttgga ... aatcatgcagGTTTCGTTCCATTGATGTGAACAATGGTGGCATGTGCGTCTTCACTGTAAA
EST: gi|88981933|gb|CI027510.1|CI027510
EST:     TCTATTTTGCGCGCACTCATCTGCACCGCGCTAGGTCTTCCTCCTGAGAG                         GTTTCGTTCCATTGATGTGAACAATGGTGGCATGTGCGTCTTCACTGTAAA
genomic: TCTATTTTGCGCGCACTCATCTGCACCGCGCTAGGTCTTCCTCCTGAGAGgcaagttgga ... aatcatgcagGTTTCGTTCCATTGATGTGAACAATGGTGGCATGTGCGTCTTCACTGTAAA
EST: gi|86896257|gb|CI330152.1|CI330152
EST:     TCTATTTTGCGCGCACTCATCTGCACCGCGCTAGGTCTTCCTCCTGAGAG                         GTTTCGTTCCATTGATGTGAACAATGGTGGCATGTGCGTCTTCACTGTAAA
genomic: TCTATTTTGCGCGCACTCATCTGCACCGCGCTAGGTCTTCCTCCTGAGAGgcaagttgga ... aatcatgcagGTTTCGTTCCATTGATGTGAACAATGGTGGCATGTGCGTCTTCACTGTAAA
EST: gi|88214195|gb|CI214044.1|CI214044
EST:     TCTATTTTGCGCGCACTCATCTGCACCGCGCTAGGTCTTCCTCCTGAGAG                         GTTTCGTTCCATTGATGTGAACAATGGTGGCATGTGCGTCTTCACTGTAAA
genomic: TCTATTTTGCGCGCACTCATCTGCACCGCGCTAGGTCTTCCTCCTGAGAGgcaagttgga ... aatcatgcagGTTTCGTTCCATTGATGTGAACAATGGTGGCATGTGCGTCTTCACTGTAAA
EST: gi|88284411|gb|CI405857.1|CI405857
EST:     TCTATTTTGCGCGCACTCATCTGCACCGCGCTAGGTCTTCCTCCTGAGAG                         GTTTCGTTCCATTGATGTGAACAATGGTGGCATGTGCGTCTTCACTGTAAA
genomic: TCTATTTTGCGCGCACTCATCTGCACCGCGCTAGGTCTTCCTCCTGAGAGgcaagttgga ... aatcatgcagGTTTCGTTCCATTGATGTGAACAATGGTGGCATGTGCGTCTTCACTGTAAA
EST: gi|29663287|gb|CB659562.1|CB659562
EST:     TCTATTTTGCGCGCACTCATCTGCACCGCGCTAGGTCTTCCTCCTGAGAG                         GTTTCGTTCCATTGATGTGAACAATGGTGGCATGTGCGTCTTCACT
genomic: TCTATTTTGCGCGCACTCATCTGCACCGCGCTAGGTCTTCCTCCTGAGAGgcaagttgga ... aatcatgcagGTTTCGTTCCATTGATGTGAACAATGGTGGCATGTGCGTCTTCACT
EST: gi|88550003|gb|CI479943.1|CI479943
EST:     TCTATTTTGCGCGCACTCATCTGCACCGCGCTAGGTCTTCCTCCTGAGAG                         GTTTCGTTCCATTGATGTGAACAATGGTGGCATGTGCGTCTTCACTGTAAA
genomic: TCTATTTTGCGCGCACTCATCTGCACCGCGCTAGGTCTTCCTCCTGAGAGgcaagttgga ... aatcatgcagGTTTCGTTCCATTGATGTGAACAATGGTGGCATGTGCGTCTTCACTGTAAA
EST: gi|88284410|gb|CI405856.1|CI405856
EST:     TCTATTTTGCGCGCACTCATCTGCACCGCGCTAGGTCTTCCTCCTGAGAG                         GTTTCGTTCCATTGATGTGAACAATGGTGGCATGTGCGTCTTCACTGTAAA
genomic: TCTATTTTGCGCGCACTCATCTGCACCGCGCTAGGTCTTCCTCCTGAGAGgcaagttgga ... aatcatgcagGTTTCGTTCCATTGATGTGAACAATGGTGGCATGTGCGTCTTCACTGTAAA
EST: gi|88528739|gb|CI456998.1|CI456998
EST:     TCTATTTTGCGCGCACTCATCTGCACCGCGCTAGGTCTTCCTCCTGAGAG                         GTTTCGTTCCATTGATGTGAACAATGGTGGCATGTGCGTCTTCACTGTAAA
genomic: TCTATTTTGCGCGCACTCATCTGCACCGCGCTAGGTCTTCCTCCTGAGAGgcaagttgga ... aatcatgcagGTTTCGTTCCATTGATGTGAACAATGGTGGCATGTGCGTCTTCACTGTAAA
EST: gi|29663288|gb|CB659563.1|CB659563
EST:     TCTATTTTGCGCGCACTCATCTGCACCGCGCTAGGTCTTCCTCCTGAGAG                         GTTTCGTTCCATTGATGTGAACAATGGTGGCATGTGCGTCTTCACTGTAAA
genomic: TCTATTTTGCGCGCACTCATCTGCACCGCGCTAGGTCTTCCTCCTGAGAGgcaagttgga ... aatcatgcagGTTTCGTTCCATTGATGTGAACAATGGTGGCATGTGCGTCTTCACTGTAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcaaacatttcctttttcttctttttttttgaaatagcaatttaatcatgcagGTTTCGTTCCATTGATGTGAACAATGGTGGCATGTGCGTCTTCACTGTAAACAAGCGAGGAGAGGCTATGCTTCAAGCCCTTAACATGACAGCACACATG
                                         atttaat  putative branch site (score: 4)
              tttttcttcttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagttggacctttcctatggctacagtttggagtcttatgtacacttggattggaaaaattcgttgaaaatattacgagttgcttcacaatattacccaacttacaagattgcaaacatttcctttttcttctttttttttgaaatagcaatttaatcatgcagGTTTCGTTCCATTGATGTGAACAATGGTGGCATGTGCGTCTTCACTGTAAACAAGCGAGGAGAGGCTATGCTTCAAGCCCTTAACATGACAGCACACATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG