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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctcaaacaagtcttctgcatttcctcgtttataccagcttccgattcttctcttatctcttctccaacaattctactccctgaattggtccaaaattctaaatttcttcctggtgaattgttgcagGGCTCCAAAGATGCGGCAAGAGCTGCAGGCTGAGGTGGATAAACTATCTGAGGCCTGACCTCAAGAGAGGTGCATTCTCTCAGGAGGAAGAAGACCTCAT

Basic information

species Oryza sativa
transcript LOC_Os05g04820.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g04820.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G127490_T01 (Zea mays), 3'ss of exon 1
-----------------------------------------gtgagctcaaacaagtcttctgcatttcct-cgttt-----ataccagcttccgattcttctcttatctcttctccaacaattctact--ccctgaattggtccaaaattctaaatttcttcctggtgaattgttgcagGGCTCCAAAGATGCGGCAAGAGCTGCAGGCTGAGGTGGATAAACTATCTGAGGCCTGACCTCAAGAGAGGTGCATTCTCTCAGGAGGAAGAAGACCTCAT
                                          | | |||  |    ||  || | |   || | |||      | |||| | || | |    |||       |||||      || | |  | ||   |  || |||    ||||||| |     |   ||||||||||||||||||||| ||||| ||||| || ||||||||||||||||||||||||||||| |||||||||||||| |||||||| || || ||||||||||||||
gtatgtacaacaattttttttcttccctttggtcctcagttatcaactctcaattctccccttcttcctctgcatttttctcgttccagttgccaactgaaatctctctctctctcctgtctctcaaatacctcttggtcagttcaattacctaaatt-cgagaagacaaattgttgcagGGCTCCAAAGGTGCGGAAAGAGTTGTAGGCTGAGGTGGATAAACTATCTGAGGCCAGACCTCAAGAGAGGGGCATTCTCCCAAGACGAAGAAGACCTCAT

upper sequence: LOC_Os05g04820.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G171781_T01 (Zea mays), 3'ss of exon 1
---------------------------------------gtgagctcaaacaagtcttctgcatttcctcgt---ttataccagcttccgattcttctcttatctcttctccaacaattctactcc-ctgaattggtccaaaattctaaatttcttcctggtgaattgttgcagGGCTCCAAAGATGCGGCAAGAGCTGCAGGCTGAGGTGGATAAACTATCTGAGGCCTGACCTCAAGAGAGGTGCATTCTCTCAGGAGGAAGAAGACCTCAT
                                        | | |||  |    ||  || |   |||   |   || | |    |||| |||     || |   |        |  |   |  || ||   |  || |||   |||||||| |     |   ||||||||||||||| ||||| ||||| ||||| || ||||||||||||||||||||||||||||| |||||||||||||| |||||| | || || ||||||||||||||
gtatgtacgatgaaatttttcttcccttggtcctcagttatcaactctcaatcctccccttctcctccctctgcatttttctcatttccaattgccagctgaaacccctcttgtctctcaaatacctctcggtcagttcaattatctaaatt-cgagaagacaaattgttgcagGGCTTCAAAGGTGCGGAAAGAGTTGTAGGCTGAGGTGGATAAACTATCTGAGGCCAGACCTCAAGAGAGGGGCATTCGCCCAAGACGAAGAAGACCTCAT

upper sequence: LOC_Os05g04820.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S277_14V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgagctcaaacaagtcttctgcatttcctcgtttataccagcttccgattcttctcttatctcttctccaacaattctactccc-tgaattggtccaaaattctaaatttcttcctggtgaat--tgttgcagGGCTCCAAAGATGCGGCAAGAGCTGCAGGCTGAGGTGGATAAACTATCTGAGGCCTGACCTCAAGAGAGGTGCATTCTCTCAGGAGGAAGAAGACCTCAT
                         |  |   |||| |         | ||||| || |     |  |  ||  | |||| ||   || |    |  |  | |     || ||      |||||  ||   |||| |||||||| ||||| |||||||||||| || ||||||| ||||| ||  |||| ||  | ||  |||| | ||| ||    |  || ||  || | ||
-------------------------taacatatttaaagtgaaaaaaggttcttttcat-----tgatgtaaggaatctaatcgtgtggagaaattgatgaat----gttcctggacaatgaatgctgcaacagGTCTCCAAAGGTGCGGGAAGAGCTGCAGGTTGCGGTGGATCAACTACCTCCGGCCGGATTTGAAACGAGGCGTATTTTCGGCAGCAGAGGAGAACTTGAT

upper sequence: LOC_Os05g04820.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S189_29V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgagctcaaacaagtcttctgcatttcctcgtttataccagcttccgattcttctcttatctcttctccaacaattctactccctgaattg-gtccaaaattctaaatttcttcctggtgaattgttgcagGGCTCCAAAGATGCGGCAAGAGCTGCAGGCTGAGGTGGATAAACTATCTGAGGCCTGACCTCAAGAGAGGTGCATTCTCTCAGGAGGAAGAAGACCTCAT
                        ||||||| ||  |   |       |   |||   || | | |   || ||||| ||      || ||| |||    |  ||    | |  |||||   |      ||||| | || ||||| || || ||||||||| | ||||||||||||||||||||||| ||| | ||| |||| |  ||||| |  |  || ||  | || ||
------------------------tttcctctttgctctaaaaaaagaaaagttcagataccccgttgacaccaatt-tagaataagagttgtgtcgctgacgctggtgtgc--cctggaaca-----acagGGTTACAGAGATGTGGAAAAAGCTGCAGGTTAAGGTGGATAAACTATCTGAGGCCAGACTTAAAGCGAGGGGTTTTCTCACCAGCAGAGGAGAATCTGAT

upper sequence: LOC_Os05g04820.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S24_48V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgagctcaaacaagtcttctgcatttcctcgtttataccagcttccgattcttctcttatctcttctccaacaattctactccctgaattggtccaaaattctaaatttcttcctggtgaattgttgcagGGCTCCAAAGATGCGGCAAGAGCTGCAGGCTGAGGTGGATAAACTATCTGAGGCCTGACCTCAAGAGAGGTGCATTCTCTCAGGAGGAAGAAGACCTCAT
                        |  | || ||| | |        ||   |    ||    ||       ||||  |  |   |    || || |    |   | ||   | ||   |||      ||||  | ||  |||| || |||||||||||| | ||||||||||| ||||||||||| ||| | ||| ||||||  |||||||  | ||| ||  | || ||
------------------------tcgcttcatttgttcggaa----gaagttaaagttgctcctcgcatggcaatagtgttggattgggtgatctagctcttacacttgtgtgctacggaacaa---cagGATTACAGCGATGTGGGAAGAGCTGCAGGTTAAGGTGGATAAATTATCTGAGGCCCGACTTAAAGCGAGGTGTCTTCTCTCCAGCGGAGGAGAATCTGAT

upper sequence: LOC_Os05g04820.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ38262 (Selaginella moellendorffii), 3'ss of exon 1
gtgagctcaaacaagtcttctgcatttcctcgtttataccagcttccgattcttctcttatctcttctccaacaattctactccctgaattggtccaaaattctaaatttcttcctggtga-attgttgcagGGCTCCAAAGATGCGGCAAGAGCTGCAGGCTGAGGTGGATAAACTATCTGAGGCCTGACCTCAAGAGAGGTGCATTCTCTCAGGAGGAAGAAGACCTCAT
                                                         | |    || | |  |||||  |    ||   |  |  || ||||||           |||||  |||||  |||| ||||||||||| || ||||||||||||||||| ||||| ||||||||  |||| ||| | || || ||    || || ||  ||||||||||  | ||
--------------------------------------------------------gtgagtatttgtacctcaatttcaagttctcg-tgagctcacaattct-----------tggtggcattgtcacagGCCTCCAAAGATGTGGGAAGAGCTGCAGGCTGAGATGGATCAACTATCTCCGGCCCGACTTGAAAAGGGGCCACTTTTCGCAACAGGAAGAAGAGTTGAT

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|58595580|gb|CK006108.1|CK006108
EST:     CATAACCAAGCATGGCCATGGCTGCTGGAGTTCTGTTCCTAAACTTGCAG                         GGCTCCAAAGATGCGGCAAGAGCTGCAGGCTGAGGTGGATAAACTATCTGA
genomic: CATAACCAAGCATGGCCATGGCTGCTGGAGTTCTGTTCCTAAACTTGCAGgtgagctcaa ... attgttgcagGGCTCCAAAGATGCGGCAAGAGCTGCAGGCTGAGGTGGATAAACTATCTGA
EST: gi|58666768|gb|CK055454.1|CK055454
EST:     CATAACCAAGCATGGCCATGGCTGCTGGAGTTCTGTTCCTAAACTTGCAG                         GGCTCCAAAGATGCGGCAAGAGCTGCAGGCTGAGGTGGATAAACTATCTGA
genomic: CATAACCAAGCATGGCCATGGCTGCTGGAGTTCTGTTCCTAAACTTGCAGgtgagctcaa ... attgttgcagGGCTCCAAAGATGCGGCAAGAGCTGCAGGCTGAGGTGGATAAACTATCTGA
EST: gi|33653484|gb|CF276098.1|CF276098
EST:     TAACCAAGCATGGCCATGGCNTGCTGGAAGTTCTGTTCCTAAACTTGCAG                         GGCTCCAAAGATGCGGCAAGAGCTGCAGGCTGAGGTGGATAAACTATCTGA
genomic: TAACCAAGCATGGCCATGGC-TGCTGGA-GTTCTGTTCCTAAACTTGCAGgtgagctcaa ... attgttgcagGGCTCCAAAGATGCGGCAAGAGCTGCAGGCTGAGGTGGATAAACTATCTGA
EST: gi|88405488|gb|CI588694.1|CI588694
EST:     CATAACCAAGCATGGCCATGGCTGCTGGAGTTCTGTTCCTAAACTTGCAG                         GGCTCCAAAGATGCGGCAAGAGCTGCAGGCTGAGGTGGATAAACTA
genomic: CATAACCAAGCATGGCCATGGCTGCTGGAGTTCTGTTCCTAAACTTGCAGgtgagctcaa ... attgttgcagGGCTCCAAAGATGCGGCAAGAGCTGCAGGCTGAGGTGGATAAACTA
EST: gi|58610479|gb|CK038191.1|CK038191
EST:     CATAACCAAGCATGGCCATGGCTGCTGGAGTTCTGTTCCTAAACTTGCAG                         GGCTCCAAAGATGCGGCAAGAGCTGCAGGCTGAGGTGGA
genomic: CATAACCAAGCATGGCCATGGCTGCTGGAGTTCTGTTCCTAAACTTGCAGgtgagctcaa ... attgttgcagGGCTCCAAAGATGCGGCAAGAGCTGCAGGCTGAGGTGGA
EST: gi|7274003|gb|AU083547.1|AU083547
EST:     CATAACCAAGCATGGCCATGGCTGCTGGAGTTCTGT-CCTAAACTTGCAG                         GGCTCCAAAGATGCGGCAAGAGCTGCAGGCTGAGGTGGATAAACTATCTGA
genomic: CATAACCAAGCATGGCCATGGCTGCTGGAGTTCTGTTCCTAAACTTGCAGgtgagctcaa ... attgttgcagGGCTCCAAAGATGCGGCAAGAGCTGCAGGCTGAGGTGGATAAACTATCTGA
EST: gi|29660292|gb|CB656567.1|CB656567
EST:     CATAACCAAGCATGGCCATGGCTGCTGGAGTTCTGTTCCTAAACTTGCAG                         GGCTCCAAAGATGCGGCAAGAGCTGCAGGCTGAGGTGGATAAACTATCTGA
genomic: CATAACCAAGCATGGCCATGGCTGCTGGAGTTCTGTTCCTAAACTTGCAGgtgagctcaa ... attgttgcagGGCTCCAAAGATGCGGCAAGAGCTGCAGGCTGAGGTGGATAAACTATCTGA
EST: gi|58605277|gb|CK033310.1|CK033310
EST:     CATAACCAAGCATGGCCATGGCTGCTGGAGTTCTGTTCCTAAACTTGCAG                         GGCTCCAAAGATGCGGCAAGAGCTGCAGGCTGAGGTGGATAAACTATCTGA
genomic: CATAACCAAGCATGGCCATGGCTGCTGGAGTTCTGTTCCTAAACTTGCAGgtgagctcaa ... attgttgcagGGCTCCAAAGATGCGGCAAGAGCTGCAGGCTGAGGTGGATAAACTATCTGA
EST: gi|87005467|gb|CI285689.1|CI285689
EST:     CATAACCAAGCATGGCCATGGCTGCTGGAGTTCTGTTCCTAAACTTGCAG                         GGCTCCAAAGATGCGGCAAGAGCTGCAGGCTGAGGTGGATAAACTATCTGA
genomic: CATAACCAAGCATGGCCATGGCTGCTGGAGTTCTGTTCCTAAACTTGCAGgtgagctcaa ... attgttgcagGGCTCCAAAGATGCGGCAAGAGCTGCAGGCTGAGGTGGATAAACTATCTGA
EST: gi|117245058|gb|CT843321.1|CT843321
EST:     CATAACCAAGCATGGCCATGGCTGCTGGAGTTCTGTTCCTAAACTTGCAG                         GGCTCCAAAGGTGCGGCAAGAGCTGCAGGCTGAGGTGGATAAACTATCTGA
genomic: CATAACCAAGCATGGCCATGGCTGCTGGAGTTCTGTTCCTAAACTTGCAGgtgagctcaa ... attgttgcagGGCTCCAAAGATGCGGCAAGAGCTGCAGGCTGAGGTGGATAAACTATCTGA
EST: gi|58665920|gb|CK054606.1|CK054606
EST:     CATAACCAAGCATGGCCATGGCTGCTGGAGTTCTGTTCCTAAACTTGCAG                         GGCTCCAAAGATGCGGCAAGAGCTGCAGGCTGAGGTGGATAAACTATCTGA
genomic: CATAACCAAGCATGGCCATGGCTGCTGGAGTTCTGTTCCTAAACTTGCAGgtgagctcaa ... attgttgcagGGCTCCAAAGATGCGGCAAGAGCTGCAGGCTGAGGTGGATAAACTATCTGA

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: 56 (upstream exon), 73 (downstream exon)
Score: 5

TTGAGGAAGGGGCTCTGGTCCCCTGAGGAGGATGAGAAGCTCATGAATCACATAACCAAGCATGGCCATGGCTGCTGGAGTTCTGTTCCTAAACTTGCAGgtgagctcaa ... attgttgcagGGCTCCAAAGATGCGGCAAGAGCTGCAGGCTGAGGTGGATAAACTATCTGAGGCCTGACCTCAAGAGAGGTGCATTCTCTCAGGAGGAAGAAGACCTCAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctactccctgaattggtccaaaattctaaatttcttcctggtgaattgttgcagGGCTCCAAAGATGCGGCAAGAGCTGCAGGCTGAGGTGGATAAACTATCTGAGGCCTGACCTCAAGAGAGGTGCATTCTCTCAGGAGGAAGAAGACCTCAT
                        ttctaaa  putative branch site (score: 5)
                    aaaattctaaatttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctcaaacaagtcttctgcatttcctcgtttataccagcttccgattcttctcttatctcttctccaacaattctactccctgaattggtccaaaattctaaatttcttcctggtgaattgttgcagGGCTCCAAAGATGCGGCAAGAGCTGCAGGCTGAGGTGGATAAACTATCTGAGGCCTGACCTCAAGAGAGGTGCATTCTCTCAGGAGGAAGAAGACCTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG