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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattatatcttgcttccatcgaaatcactccctttttgttgtttacctcctacttaactgactattctctcagGTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTACACCGAGTTTAAATTTCCGCAAATCAAAGCTCACCCATGGCACAAG

Basic information

species Oryza sativa
transcript LOC_Os05g04340.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g04340.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G155836_T01 (Zea mays), 3'ss of exon 9
gtaaatta-tatcttgcttccatcgaaatcactccctttttgttgtttacctcctacttaactgactattctctcagGTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTACACCGAGTTTAAATTTCCGCAAATCAAAGCTCACCCATGGCACAAG
||||| || ||||||  | ||    |||   || | | |   |  ||||||||| | ||||     |  |||||||||||||||| || || ||||| || || |||||||||||||| |||||||| |||||||||||||| |||||||||||||||||||||||||| |||
gtaaactactatctttgtcccgattaaactcctgcatatcgttgctttacctccaatttaatctcatcctctctcagGTTCTGGGCACACCCACACGTGAAGAAATTAAGTGCATGAATCCAAATTATACCGAGTTTAAATTCCCGCAAATCAAAGCTCACCCATGGCATAAG

upper sequence: LOC_Os05g04340.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA10G01280.1 (Glycine max), 3'ss of exon 9
---------------------gtaaattatatcttgct-tccatcgaaatcactccctttttgttgtttacctcctacttaactgactattctc--tcagGTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTACACCGAGTTTAAATTTCCGCAAATCAAAGCTCACCCATGGCACAAG
                      ||  || | | | | | | |||   | |  |    || |  ||   ||| ||  |           |||| |  ||||||| | |||||||| ||| | || || || ||||||||||| || ||||| |||||||  |||||||| ||||| |||||||||||||||||||||
tgtgattgcattttctcttaactagcttgtttgtagatattcataatagttcccttgttatcttttcatacttctgaagaggtctgtgattcacattcagGTTTTAGGTACCCCAACAAGGGAAGAAATCAAGTGCATGAATCCTAATTATACCGAGTCCAAATTTCCACAAATTAAAGCTCACCCATGGCACAAG

upper sequence: LOC_Os05g04340.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA02G01220.1 (Glycine max), 3'ss of exon 9
-------------------gtaaattatatcttgcttccatcgaaatcactccctttttgttgtt---tacctcctacttaactgactattctct--cagGTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTACACCGAGTTTAAATTTCCGCAAATCAAAGCTCACCCATGGCACAAG
                    |   |||| | |  |||    |  | ||| | || | || |  ||   ||| |   |    | |    |||| |   |||||| | || ||||| ||| | || || || ||||| ||||| || |||||||||||||| |||||||| ||||| |||||||| |||||||| |||
atccataataatagtccccttgttttatttttcccttttgcctcattcagtgccgtgttatctttgagtacttgtaaagagatttgggattcacatgcagGTTTTAGGAACCCCGACAAGGGAAGAAATCAAGTGTATGAATCCTAATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAG

upper sequence: LOC_Os05g04340.2 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv07s0005g02100.t01 (Vitis vinifera), 3'ss of exon 9
--------------------gtaaattatatcttgcttcca---tcgaaatcactccctttttgttgt-ttacctcctacttaactgactattctctcagGTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTACACCGAGTTTAAATTTCCGCAAATCAAAGCTCACCCATGGCACAAG
                     |   ||  |||||| ||      |    |||  |||||| ||  ||| ||  || | |  |       | | |   |||||| |||| ||||| ||| ||||||| |||||||||||||| || |||||||| || |||||||| || ||||| ||||| |||||||||||||||
tggtgctgagtctgcagttgctcctttccatcttgtttgtgattttagtatccatcccttattaatgtgttttctacaatattttcttatttgcatgcagGTTTTGGGCACCCCAACAAGAGAGGAAATTAAGTGCATGAATCCCAATTACACAGAATTTAAATTCCCACAAATTAAAGCCCACCCATGGCACAAG

upper sequence: LOC_Os05g04340.2 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 7
----------------------------------------------------------------------------------------------------------------------gtaaattatatcttgcttccatcgaaatcactccctttttgttgtttacctcctacttaactgactattc-tctcagGTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTACACCGAGTTTAAATTTCCGCAAATCAAAGCTCACCCATGGCACAAG
                                                                                                                       |      | |  || |      ||  || ||    |     |||    ||  |   ||  ||  | ||  | | ||||  |||| || || ||||| |||||||| ||||||||||| || || ||||| ||||| || ||||| ||||| || ||||| || |||||||||
gtagcttacatatggtagatgttgaggaagtgcaggggtctacagcagatgtcggtgctggtgtttgggttttgtccgtttgaaatgttgtgttgcgttgaaaggttgtagctggtacttgctcggtgtgatgttagttatgacttcgctagaatggatatgtaggacttatgggtagttgggtgttaatgttagGTGTTGGGGACACCCACACGCGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCTCAAATTAAGGCTCATCCTTGGCACAAG

upper sequence: LOC_Os05g04340.2 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S60_100V6.1 (Physcomitrella patens), 3'ss of exon 8
--------------------------------------------gtaaattatatcttgcttccat--cgaaatcactccctttttgttgtttacctcctacttaactgac-tattctctcagGTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTACACCGAGTTTAAATTTCCGCAAATCAAAGCTCACCCATGGCACAAG
                                             |   ||     |||   |  |  ||  |    |    |  ||| |  |   |  || | |    |  | || |  |||||  |||| || || || || |||||||| ||||||||||| || || ||||| ||||| || |||||||||||||| ||||||||||||||||| 
gtagggcacaggcgatgcacggtgttgtgttgaagggtggcgtacttgcttgctggttgtgactgttgcgggagtgttatgatgctgtggagtgtatgttattgaggaaaagttttgtggcagGTGTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCATGGCACAAA

upper sequence: LOC_Os05g04340.2 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S60_85V6.1 (Physcomitrella patens), 3'ss of exon 8
---------------------------------------------------gtaaattatatcttgcttccatcgaaatcactccctttttgttgtttacctcctacttaactg-actattctctcagGTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTACACCGAGTTTAAATTTCCGCAAATCAAAGCTCACCCATGGCACAAG
                                                   |    || |  || | | |    |   |      || |    |||     |  || | |   | |||  | |  |||||  |||| || || || || |||||||| ||||||||||| || || ||||| ||||| || |||||||||||||| |||||||| |||||||| 
gtagggcacaggcggtgcacggcgttgtgttgaagggtggcgtacttgcttgctggttgtgact-gttgcgggggtgttatgatgctgtggagtgtgagtatgttattgaggagtacttgtgtggcagGTGTTGGGAACACCGACTCGTGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCGTGGCACAAA

upper sequence: LOC_Os05g04340.2 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------------------------------------gtaaattatat--cttgcttccatcgaaatcactccctttttgttgtttacctcctacttaactgactattctct----cagGTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTACACCGAGTTTAAATTTCCGCAAATCAAAGCTCACCCATGGCACAAG
                                                 ||      | |   |||   |  | | |     | | | || | |||     |     | | | |||  |||  |    |||||| |||| || || || || |||||||| ||||||||||| || || ||||| ||||| || ||||| |||||||| || ||||| |||||||| 
gtgggacacacgtggtacacgttgtttgtgtggaagggtcgccttctgggttggcggtttggtttgtagctgtggtatcttgttcgtgttggatgtgagtatggcgttgaccagacgtttccgtgtggcagGTTTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACAGAGTTCAAGTTTCCACAAATCAAGGCGCACCCGTGGCACAAA

upper sequence: LOC_Os05g04340.2 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 8
----------------------------------------------------------------------------------------------------------------gtaaattatatcttgcttccatcgaaatcactccctttttgttgtttacctcctacttaactgact----attctctcagGTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTACACCGAGTTTAAATTTCCGCAAATCAAAGCTCACCCATGGCACAAG
                                                                                                                ||   ||         || |   || | | |     |  |  |||  | ||  |   ||   |  |    ||  |  |||||  | || || |||||||| |||||||| ||||||||||| || || ||||| ||||| || ||||| ||||| || |||||||| |||||||||
gtatgttatacatggtagagtggaagcatatggagctgaagtcgtttgtactgatgtttgatgtgtatcgattaaaagtattgtattatatttaaagatgttagctgctcttgttgcttcgggtggtgttgcggtgatagcgcaagagtgatactgtagagcttatgagtaggcggatggtgatgttgacagGTGTTAGGGACACCTACACGTGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCTCAAATTAAGGCTCACCCGTGGCACAAG

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|29629993|gb|CB635002.1|CB635002
EST:     GTTGAAATCATCAAG                         GTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTAC
genomic: GTTGAAATCATCAAGgtaaattata ... attctctcagGTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTAC
EST: gi|58679859|gb|CK068546.1|CK068546
EST:     CTCTATTCCCTGGCGACAGTGGCGTTGATCAGCTTGTTGAAATCATCAAG                         GTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTAC
genomic: CTCTATTCCCTGGCGACAGTGGCGTTGATCAGCTTGTTGAAATCATCAAGgtaaattata ... attctctcagGTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTAC
EST: gi|29629559|gb|CB634568.1|CB634568
EST:     CAGCTTGTTGAAATCATCAAG                         GTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTAC
genomic: CAGCTTGTTGAAATCATCAAGgtaaattata ... attctctcagGTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTAC
EST: gi|58671594|gb|CK060280.1|CK060280
EST:     CTCTATTCCCTGGCGACAGTGGCGTTGATCAGCTTGTTGAAATCATCAAG                         GTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTAC
genomic: CTCTATTCCCTGGCGACAGTGGCGTTGATCAGCTTGTTGAAATCATCAAGgtaaattata ... attctctcagGTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTAC
EST: gi|66928190|gb|CX115038.1|CX115038
EST:     CTCTATTCCCTGGCGACAGTGGCGTTGATCAGCTTGTTGAAATCATCAAC                         GTTCTGGGTACCCCTACACGAG
genomic: CTCTATTCCCTGGCGACAGTGGCGTTGATCAGCTTGTTGAAATCATCAAGgtaaattata ... attctctcagGTTCTGGGTACCCCTACACGAG
EST: gi|29623769|gb|CB628780.1|CB628780
EST:     CTCTATTCCCTGGCGACAGTGGCGTTGATCAGCTTGTTGAAATCATCAAG                         GTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTAC
genomic: CTCTATTCCCTGGCGACAGTGGCGTTGATCAGCTTGTTGAAATCATCAAGgtaaattata ... attctctcagGTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTAC
EST: gi|58612435|gb|CK040147.1|CK040147
EST:     CTCTATTCCCTGGCGACAGTGGCGTTGATCAGCTTGTTGAAATCATCAAG                         GTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTAC
genomic: CTCTATTCCCTGGCGACAGTGGCGTTGATCAGCTTGTTGAAATCATCAAGgtaaattata ... attctctcagGTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTAC
EST: gi|88828410|gb|CI073280.1|CI073280
EST:     ATCAGCTTGTTGAAATCATCAAG                         GTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTAC
genomic: ATCAGCTTGTTGAAATCATCAAGgtaaattata ... attctctcagGTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTAC

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), 60 (downstream exon)
Score: 32

CCTCTATTCCCTGGCGACAGTGGCGTTGATCAGCTTGTTGAAATCATCAAGgtaaattata ... attctctcagGTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTACACCGAGTTTAAATTTCCGCAAATCAAAGCTCACCCATGGCACAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgaaatcactccctttttgttgtttacctcctacttaactgactattctctcagGTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTACACCGAGTTTAAATTTCCGCAAATCAAAGCTCACCCATGGCACAAG
                                     aactgac  putative branch site (score: 32)
                                           ctattctctc  CT-rich tract
              tttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattatatcttgcttccatcgaaatcactccctttttgttgtttacctcctacttaactgactattctctcagGTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTACACCGAGTTTAAATTTCCGCAAATCAAAGCTCACCCATGGCACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA