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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatttttttacaatggaaatctggtataagcttatctgtgtgcaaataaattctaatacttatctttcaatttacagCTGAGGTTTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTA

Basic information

species Oryza sativa
transcript LOC_Os05g44560.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g44560.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G173700_T01 (Zea mays), 3'ss of exon 10
-------------gtatatttttttacaa--tggaaatctggtataagcttatct-gtgtgcaaat---aaattctaatacttatctttcaatttacagCTGAGGTTTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTA
              | || |||   | ||  ||  ||| |  ||| |  || | | ||||   |||   | ||||| ||  || ||| | | ||||||||||||||||| || ||||| ||||| ||||| ||||||||||| ||||||||||| |||||||||||||| ||||| || |||||||| || ||||||||
gtatgttgttttcttttaatttaaaagaaattgataatttaatatcacattttgtagtgttataatctgatattctgattattctctatgattttacagCTGAGGTTTTTTCTGACATACAACCACTGATCCGATCAGTTCTGGATGGATTCAACGTTTGTATTTTTGCATATGGCCAGACTGGTTCTGGCAAAACTTA

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA08G04580.1 (Glycine max), 3'ss of exon 5
--------------gtatatttttttacaatggaaatctggtataagcttatctgtgtgcaaataaat--tctaatacttatctt---tcaatt--tacagCTGAGGTTTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTA
               | | |||| | ||| |      ||| | |||| |  | |||   ||    |||  | || || | || ||   |  | |  | |||| ||||| | ||| ||||||||| |  | ||  |||||||||| |||||||  ||||| ||||| ||||||||||| |||||||||||||| ||||||||
aggttttaggattaattttttttatcacagtttctccctgat-taagttgttatgttaacattctaatgttgtactaatgatattaaattgaataatgcagCGGAGGTATACTCTGACATTCAATCCTTTATAAGATCAGTTCTAGATGGATATAATGTGTGTATATTTGCTTATGGCCAAACTGGTTCAGGGAAAACTTA

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA08G01800.1 (Glycine max), 3'ss of exon 13
-----------------------------------gtatatttttttacaatggaaatc--tggtataagcttatctgtgtgcaaataaattctaatacttatctt-----tcaat--------ttacagCTGAGGTTTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTA
                                    |   | || |||  ||    ||   |||||   | ||     |||  ||||  ||  ||||  ||| |||     |||||        ||  ||  ||  | |||  ||||| ||||||  |||||||||| ||||||||||| | |||||||||||| |||||||||||||||||||| || ||||| || ||
gtactgcgtttttttttcttttctctttcatgattattattattattattattattattattggtacttgttttctattgttgaaattgatagtaatgtttaacttatatgtcaatatttttctttgtagAGGAAATATTCAAGGACACTCAACCATTGATTCGATCTGTTCTTGATGGGTACAATGTTTGTATATTTGCTTATGGTCAAACTGGCTCGGGAAAGACATA

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA05G37800.1 (Glycine max), 3'ss of exon 13
-----------------gtatatttttttacaatggaaatc--tggtataagcttatctgtgtgcaaataaattctaatacttatctt-----tcaat--------ttacagCTGAGGTTTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTA
                  | |  | ||| |  ||    ||   | |||   | ||     |||  ||||  ||  ||||  | | |||     |||||        ||  ||  ||  | |||  ||||| ||||||  |||||||||| ||||||||||| | |||||||||||| ||||||||||||||||| || || ||||| || ||
gtactgcatttttttttcttttctatttcatgattattattattagtacttgttttctattgttgaaattgatagtaatgttcaacttatacatcaatatttttctttgtagGGGAAATATTCAAGGACACTCAACCATTGATTCGATCTGTTCTTGATGGGTACAATGTTTGTATATTTGCTTATGGTCAAACCGGCTCGGGAAAGACATA

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA13G33390.1 (Glycine max), 3'ss of exon 9
---------------------------------------------------------------------gtatatttttttacaatggaaatc--tggtata-agcttatctgtgtgcaaataa-attctaatacttat--ctttcaatt-tacagCTGAGGTTTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTA
                                                                        ||||| | || | |  || |   || |||   | || | |       | |    |  | ||  ||||  || | |||  | |||||||||| |   | ||||| ||| |  | || |||||||| |||||||| || ||||| ||||| ||||||||||| || ||||||||||| ||||||||
gtttatttctatatactcaccatttgccattaggctttgaatggaaaaacattttttcattataatactacctatttatatagactccaatttcttgttatttggattttttacactttattgttgtgttgattgttattactctaaatgatgcagCTGAGGTGTATGCTGACATACAAGCCTTTATACGATCAGTACTTGATGGGTTTAATGTATGTATATTTGCTTATGGCCAGACTGGTTCAGGGAAAACTTA

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA05G35130.1 (Glycine max), 3'ss of exon 11
--------gtatatttttttacaatggaaat--ctggtataagcttatctgtgtgcaaataaat--tctaatacttatctt---tcaatt--tacagCTGAGGTTTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTA
         |  |||||||||  |  |      |   | | || |  | |||   |     |||  | || || | || ||   |  | |  | |||| ||||| | ||| ||||||||| |  | ||  |||||||||| ||||| |  ||||| ||||| ||||||||||| |||||||||||||| ||||||||
gttttaagattaatttttttaacacagtttctcccttttttagttgttatgttaaccttctaatgttgtactaatgatattaaattgaataatgcagCGGAGGTATACTCTGACATTCAATCCTTTATAAGATCAGTTCTAGATGGGTATAATGTGTGTATATTTGCTTATGGCCAAACTGGTTCAGGGAAAACTTA

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 3'ss of exon 13
lower sequence: AT5G41310.1 (Arabidopsis thaliana), 3'ss of exon 11
-----------------gtatatttttttaca-atggaaatctggtataagcttatctgtgtgcaaataaattctaatacttatctttcaatttacagCTGAGGTTTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTA
                  ||| || ||| | | ||| ||||   |||||   ||     |||   ||| ||||  ||||  ||| | |     | |||  || |||||||  || | || |||  ||||||||||  |||||||||| | |||||| ||||| ||||||||||| || || ||||| ||||| |||||
gttcaagcctcttccacttattttatttcatatatgaaaat---gtatagttttggacttgt---aattaatt--aatatgtatatat--gcgtgcagAGGAAGTTTTCTTAGATACTCGACCTATGATTCGATCCATTCTTGATGGCTACAATGTATGTATATTTGCTTATGGCCAGACGGGTTCTGGAAAGACTTA

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 3'ss of exon 13
lower sequence: AT1G73860.1 (Arabidopsis thaliana), 3'ss of exon 12
------------------------------------------------------------------gtatatttttttacaatggaaatctggta-taagcttatctgtgtgcaaataaattctaatacttatctttcaat-ttacagCTGAGGTTTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTA
                                                                   |       || |   |  |  ||  | | |||  |||| |   |   |  || ||| | |   ||| ||  | | || ||||||| || || || |||||   ||||||| || | ||||| |||||||| | |||||||||||| ||||| ||||| || || || ||||| ||||||||
gtgtgttcatctgttaccggttctgttatatatccttatgcttttcagttctgttttgtgtgatctatgcgagaattcatggtacatctcgagaaataatattatattgatatcaccaagttc-atttgatattttggattcttgcagCTGACGTCTTTTCAGACATAAGACCGCTGGTTAGGTCAGTACTTGATGGGTACAATGTTTGTATATTTGCATATGGCCAGACAGGATCAGGGAAAACTTA

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 3'ss of exon 13
lower sequence: AT1G63640.1 (Arabidopsis thaliana), 3'ss of exon 13
--gtatatttttttacaatggaaatctggtataagcttatctgtgtg-caaataa-attctaatactta-tctttcaatttac--agCTGAGGTTTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTA
   || |  | ||| |     |  | | ||    | ||  || | |   | || | ||||  || || | ||| | |  |||   ||  ||||||||||  || | || |||  | ||||||||  |||||||||| |  ||||||||||| ||||| |||||||| |||||||| |||||||||||
gtttaaacctctttccctcttatgtattgttagcgttttcctctataatatatgatattcatatcctgaatctgttatcttatgtagAGGAGGTTTTCTTAGATACTCGACCATTAATTCGATCCATTCTTGATGGCTATAATGTTTGTATATTTGCCTATGGTCAGACTGGTTCTGGAAAAACTTA

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 3'ss of exon 13
lower sequence: AT1G18410.1 (Arabidopsis thaliana), 3'ss of exon 12
-------------------gtatatttttttacaatggaaatctggt---ataagcttatctgtgtg------caaataaattctaatacttat----------ctttcaatt--tacagCTGAGGTTTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTA
                       |||||| | ||||  |  | | ||   ||  |  | |   || |      |||| |||||   ||||||||          |||| ||||  | |||||||||| || || || ||  |||| || ||||||||||||||||| || | |||||| ||||| ||||| |||||||| || || ||||| ||||||||
gtgttcttttgtttgcctgaggaatttttcttcaatatactttttgttggattggtgtgttcttgggactaatcaaaaaaattaatatacttatgtcattgtatcttttaattcttgcagCTGAGGTATTTTCAGATATAAAACCTCTTATTCGATCAGTTCTTGACGGGTACAATGTATGTATCTTTGCATATGGTCAGACAGGATCAGGGAAAACTTA

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv17s0000g03700.t01 (Vitis vinifera), 3'ss of exon 12
---------gtatatttttttacaatggaaatctggtataagcttatctgtgtgcaa----ataaattctaatac---ttatctttcaa-----tttacagCTGAGGTTTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTA
            ||| ||||   | | | |  || | |||    | | |      |     ||||    | |  |   ||||  ||  |     |||  ||||||||| || || |||| ||||||  || | ||||| ||||||||||| |  ||||| ||||| ||||||||||||||||||||||| || || || ||
gtttttcatccttatattttataatttggatccttgaatagatctctttcaagaaatcattataatgcttgactcatattatgcttggaaaatgtttgtagCTGAGGTGTTTTCTGACACTCAACCCTTGGTACGATCTGTTCTTGATGGCTATAATGTATGTATATTTGCTTATGGTCAAACTGGTTCGGGCAAGACATA

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv02s0025g03480.t01 (Vitis vinifera), 3'ss of exon 14
-------------------------------------------gtatatttttttacaatggaaatctggtataagcttatctgtgtgcaaataaattctaa-----tacttatctttcaatttaca-----------gCTGAGGTTTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTA
                                            | ||| |  | | | |   | ||   |         | |||  | ||| || || |||     ||| | | |||  || ||||           |  ||||| || |  |||| ||||||  | |||||||| || |||||||||| |||||| ||||| ||||| |||||||||||||| || |||||||| ||
gttatcttcttataatattttatatttggccttgtttctttatttgtatatcctcagatttctattccacttagcatgcttttgttaggaaagaacttttaacttactacctttatttgtatatacattgtgttatcagAGGAGGTATTTTTAGACACTCAACCATTAATTCGATCTGTACTTGATGGATACAATGTCTGTATATTTGCCTATGGTCAAACTGGCTCTGGAAAAACCTA

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 3'ss of exon 13
lower sequence: EFJ30678 (Selaginella moellendorffii), 3'ss of exon 9
gtatatttttttacaatggaaatctggtataagcttatctgtgtgcaaataaattctaatacttatctttcaatttacagCTGAGGTTTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTA
                          |||    ||    | ||  | ||||    | |  ||   |         | |||  ||||||||   |||    || ||  |||||||||| || |||||||| ||||| || ||||||||||| ||||| || |||||||| |||||||| ||
--------------------------gtacgttctatattttgctccaatagtcacaatgacacgt------gcatgcagACGAGGTTTTTCTGGATGCGCAGCCTTTGATTCGATCGGTGCTTGATGGTTTCAACGTCTGTATTTTTGCGTATGGACAGACTGGTTCTGGAAAAACATA

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 3'ss of exon 13
lower sequence: EFJ19920 (Selaginella moellendorffii), 3'ss of exon 8
gtatatttttttacaatggaaatctggtataagcttatctgtgtgcaaataaattctaatacttatctttcaatttacagCTGAGGTTTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTA
                        | ||| ||||||  | ||       |  ||    | ||||    |    ||| |||   | || |||  ||| | ||| ||  |||| || |||||||||||||| | ||| || ||||||||||| ||||||||||| || || |||||||| ||
-----------------------gtagta-aagctt--ccgttaaagtcttgatgtataaacttgatat---gtttgcagAACAAGTATTCCTGGATACTCAGCCATTGATACGGTCAGTTCTTGATGGTTACAACGTGTGTATTTTTGCGTATGGTCAAACAGGCTCGGGAAAAACGTA

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 3'ss of exon 13
lower sequence: EFJ12333 (Selaginella moellendorffii), 3'ss of exon 8
gtatatttttttacaatggaaatctggtataagcttatctgtgtgcaaataaattctaatacttatctttcaatttacagCTGAGGTTTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTA
                        | ||| ||||||  | ||       |  ||    | ||||    |    ||| |||   | || |||  ||| | ||| ||  |||| || |||||||||||||| | ||| || ||||||||||| ||||||||||| || || |||||||| ||
-----------------------gtagta-aagctt--ccgttaaagtcttgatgtagaaacttgctat---gtttgcagAACAAGTATTCCTGGATACTCAGCCATTGATACGGTCAGTTCTTGATGGTTACAACGTGTGTATTTTTGCGTATGGTCAAACAGGCTCGGGAAAAACGTA

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|86901422|gb|CI308403.1|CI308403
EST:     ACATCGGATGTTCAAGTTTAACAAGGTTTTTAGTCCATTTTCTTCTCAAG                         CTGAGGTTTTCTCGGACATTCAACCGCTAATTCGATCAGTTCTTGATGGAT
genomic: ACATCGGATGTTCAAGTTTAACAAGGTTTTTAGTCCATTTTCTTCTCAAGgtatattttt ... caatttacagCTGAGGTTTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGAT




















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: 30 (upstream exon), 55 (downstream exon)
Score: 11

GAAAATGGTGAGCTTTTGATCTCAAATCCATTTAAACAAGGAAAGGATGGACATCGGATGTTCAAGTTTAACAAGGTTTTTAGTCCATTTTCTTCTCAAGgtatattttt ... caatttacagCTGAGGTTTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtataagcttatctgtgtgcaaataaattctaatacttatctttcaatttacagCTGAGGTTTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTA
                            ttctaat  putative branch site (score: 11)
                                    cttatctttc  CT-rich tract
                     aaataaattctaatac  TA-rich tract