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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatcttttgttacagttgaatttagaattctgaaacatgcacagaacgtaattcttgctaatataaaactgaaaaactgttagcattatacttgcttgttaacaatttgtggaaactttgaaatgcagGTGGCGGCAAGCTTTGCTGCTGAAGGAACAATAATGGGTGAGCTGAAGCAATGGAATGAGTTGTACGGTGAAGGAGGCTCCAGAAAGAAACAACAGTTGA

Basic information

species Oryza sativa
transcript LOC_Os01g12660.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g12660.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G159307_T01 (Zea mays), 3'ss of exon 14
gtgaatcttt-tgttac--agttgaatttagaattctgaaacatgcacagaacgtaattcttgctaatataaaactgaaaaactgttagcattatacttgcttgttaacaatttgtggaaactttgaaatgcagGTGGCGGCAAGCTTTGCTGCTGAAGGAACAATAATGGGTGAGCTGAAGCAATGGAATGAGTTGTACGGTGAAGGAGGCTCCAGAAAGAAACAACAGTTGA
||| |||  |   ||||  ||   |||||  ||       |  || |   |   |||  |||   ||  | |||   | |||||  | |||      | |  |||||  |     || ||||| | |||| |||||||| ||||| || ||| | |||||       ||| | ||||||| ||||||||| |||||||| |||||||||||||||||||||||  |||| || |
gtggatccatgccttaccaagcgcaatttgaaac-----gatgtggatgcagattaacacttttcaacttgaaa--aataaactaatggca----gttcgaatgttataataccctgtaaactctcaaattcagGTGGCTGCAAGTTTCGCTTCCGAAGGTGTCTGCATGAGCGAGCTGAGGCAATGGAACGAGTTGTATGGTGAAGGAGGCTCCAGAAAGAAGGAACAATTAA

upper sequence: LOC_Os01g12660.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G058491_T01 (Zea mays), 3'ss of exon 14
gtgaatcttttgttacagttgaatttag--aattctgaaaca---tgcacagaacgtaattcttgctaatataaaactgaaaaactgttagcattatacttgcttgttaacaatttgtggaaactttgaaatgcagGTGGCGGCAAGCTTTGCTGCTGAAGGAACAATAATGGGTGAGCTGAAGCAATGGAATGAGTTGTACGGTGAAGGAGGCTCCAGAAAGAAACAACAGTTGA
|||||||  |      |||   |   ||   | | |||||||   || | | |   |||  |||   ||  |   |     |||||  |  || |  |     ||||||| | | |||  ||||| | |||| |||||||| ||||| || |||||||||||  | |||||| | ||||||| ||||||||| ||||||||||||||||| |||||||||||||| || |||||||
gtgaatccatccgcttagtcttaccaagtggaatttgaaacaatgtggaaacagattaacacttctcaacttggga--agtaaactaatgacagttcaa--agttgttaatactctgt--aaactctcaaattcagGTGGCTGCAAGTTTCGCTGCTGAAGGCGCCATAATGAGCGAGCTGAGGCAATGGAACGAGTTGTACGGTGAAGGCGGCTCCAGAAAGAAGCAGCAGTTGA

upper sequence: LOC_Os01g12660.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA10G37380.1 (Glycine max), 3'ss of exon 13
gtgaatcttttgttacagttgaatttagaattctgaaacatgcacagaacgtaattcttgctaatataaaactgaaaaactgttagcattatacttgcttgttaacaatttgtggaa--actttgaaatgcagGTGGCGGCAAGCTTTGCTGCTGAAGGAACAATAATGGGTGAGCTGAAGCAATGGAATGAGTTGTACGGTGAAGGAGGCTCCAGAAAGAAACAACAGTTGA
                          || | |   |||  | |  |  ||  |    |    |    || ||    | | |   |   | |||  |      ||  ||||  |  |   | ||  ||||||||||||| ||||| |||||||| |||||| |||||||| ||||||||||| | |||||||| ||||  || |||||||| || || ||||| || ||| | |
--------------------------aggaat---aaatttacttattacccagggttcaagatggcaacac----atattccaaagttaatatctatggcatagaaattgataaatgtatttgtaaatgcagGTGGCTGCAAGTTTTGCTGCAGAAGGATCAATAATGAGTGAGCTGAAGGAGTGGAATGAATTGTTTGGAGAAGGAGGTTCAAGGAAGAAGCAGCAGCTTA

upper sequence: LOC_Os01g12660.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA16G29040.1 (Glycine max), 3'ss of exon 14
gtgaatcttttgttacagttgaatttagaattctgaaacatgcacagaacgtaattcttgctaatataaaactgaaaaactgttagcattatacttgcttgttaacaatttgtggaaactt--tgaaatgcagGTGGCGGCAAGCTTTGCTGCTGAAGGAACAATAATGGGTGAGCTGAAGCAATGGAATGAGTTGTACGGTGAAGGAGGCTCCAGAAAGAAACAACAGTTGA
                     |   ||  | | | | ||| |   |  | | ||    ||   || |  ||  ||| | || ||  |||  ||| ||         || ||   || |  |  | ||||||||||||| ||||| |||||  | |||||| |  |||||  |||| ||||||| |||||||| ||||| ||||||||||| || || |||||||||||| | |
---------------------atactaacaatgtcacacaagtggaagaaggaaagtgtgt--atttccaatagaatatcttttcccat-gtacatg---------aacttacagatatctgattaaatgcagGTGGCTGCAAGTTTTGCATCAGAAGGATCTGTAATGAATGAGTTGAAGCACTGGAATGATTTGTATGGTGAAGGAGGTTCAAGGAAGAAACAACAGCTCA

upper sequence: LOC_Os01g12660.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA09G23250.1 (Glycine max), 3'ss of exon 14
gtgaatcttttgttacagttgaatttagaattctgaaacatgcacagaacgtaattcttgctaatataaaactgaaaaactgttagcattatacttgcttgttaacaatttgtggaaactttgaaatgcagGTGGCGGCAAGCTTTGCTGCTGAAGGAACAATAATGGGTGAGCTGAAGCAATGGAATGAGTTGTACGGTGAAGGAGGCTCCAGAAAGAAACAACAGTTGA
                         ||  | | | | ||| |      | | ||   ||| || | |  ||  ||| | || ||  |||  ||| ||    ||| | || | ||       | ||||||||||||| ||||| |||||  | |||||| |  |||||  |||| ||||||| |||||||| ||||| || |||||||| || || |||||||||||  | |
----------------------tactaacaatgtcacacaagtgggacaaggaaagtttgtta-tttccaatagaatatcttttcccat-gtacatgaac-ttaccgatatctga------ttaaatgcagGTGGCTGCAAGTTTTGCGTCAGAAGGATCCGTAATGAATGAGTTGAAGCAGTGGAATGATTTGTATGGAGAAGGAGGTTCAAGGAAGAAACAACAACTCA

upper sequence: LOC_Os01g12660.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA20G30360.1 (Glycine max), 3'ss of exon 14
gtgaatcttttgttacagttgaatttagaattctgaaacatgcacagaacgtaattcttgctaatataaaactgaaaaactgttagcattatacttgcttgttaacaatttgtggaaactttgaaatgcagGTGGCGGCAAGCTTTGCTGCTGAAGGAACAATAATGGGTGAGCTGAAGCAATGGAATGAGTTGTACGGTGAAGGAGGCTCCAGAAAGAAACAACAGTTGA
                   |      | | ||    |  || ||  |  |   ||    |  || | | |    ||||   ||||   |    | |     || | || |       | ||  ||||||||||||| ||||| |||||||| |||||| |||||||| ||||||||||| | |||||||| ||||  || |||||||                        
-------------------taggaaaaaatttacttattatccagggttcaagat----ggcaacacatattccaaaa---gttaatttatggcatagaaattgataaat-----gtatttgtaaatgcagGTGGCTGCAAGTTTTGCTGCAGAAGGATCAATAATGAGTGAGCTGAAGGAGTGGAATGAATTGTTTGGAGAAGGAG------------------------

upper sequence: LOC_Os01g12660.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA16G29250.1 (Glycine max), 3'ss of exon 4
gtgaatcttttgttacagttgaatttagaattctgaaacatgcacagaacgtaattcttgctaatataaaactgaaaaactgttagcattatacttgcttgttaacaatttgtggaaactttgaaatgcagGTGGCGGCAAGCTTTGCTGCTGAAGGAACAATAATGGGTGAGCTGAAGCAATGGAATGAGTTGTACGGTGAAGGAGGCTCCAGAAAGAAACAACAGTTGA
                     |   ||  | | | | ||| |   |  | | ||    ||   || |  ||  ||| | || ||  |||| ||| ||    |||   || | ||       | ||||||||| ||| ||||| |||||  | |||||| |  |||||  |||| ||||||| |||||||| ||||| ||||||||||| || || |||||||||||| | |
---------------------atactaacaatgtcacacaagtggaagaaggaaagtgtgt--atttccaatagaatagcttttcccatt-tacatgaac-ttacagatatatga------ttaaatgcagGAGGCTGCAAGTTTTGCATCAGAAGGATCTGTAATGAATGAGTTGAAGCACTGGAATGATTTGTATGGTGAAGGAGGTTCGAGGAAGAAACAACAGCTCA

upper sequence: LOC_Os01g12660.1 (Oryza sativa), 3'ss of exon 14
lower sequence: AT5G52882.1 (Arabidopsis thaliana), 3'ss of exon 12
gtgaatcttttgttacagttgaatttagaattctgaaacatgcacagaacgtaattcttg-ctaatataaaactgaaaaactgttagcattatacttgcttgttaacaatttgtggaaactttgaaatgcagGTGGCGGCAAGCTTTGCTGCTGAAGGAACAATAATGGGTGAGCTGAAGCAATGGAATGAGTTGTACGGTGAAGGAGGCTCCAGAAAGAAACAACAGTTGA
             |  |  | || |   |  | |   |||   | | |||  || ||||  || || |      |||||      |  | || |    ||    ||| | || ||    | |   | ||||||| || || || |||||  | |||||| ||  ||||  |||||| |||||||||||||| ||||| || ||||||||||| || || ||  ||||| | |
------------gtctaactaaaatcttatctgtttgacaaaaaaaaaactaaaatcttatctcattttgtcaagaaaagacaagaaaactaaaaaccct----aactagttatgttgtcgtgttattgcagGTAGCTGCGAGTTTTGCATCAGAAGGAGCAGGAATGAATGAGCTAAAGCAATGGAATGATTTGTATGGAGAAGGAGGCTCAAGGAAAAAGGAACAGCTCA

upper sequence: LOC_Os01g12660.1 (Oryza sativa), 3'ss of exon 14
lower sequence: AT1G64110.3 (Arabidopsis thaliana), 3'ss of exon 15
gtgaatcttttgttacagttgaatttagaattctgaaacatgcacagaacgtaattcttgctaatataaaactgaaaaactgttagcattatacttgcttgttaacaatttgtggaaactttgaaatgcagGTGGCGGCAAGCTTTGCTGCTGAAGGAACAATAATGGGTGAGCTGAAGCAATGGAATGAGTTGTACGGTGAAGGAGGCTCCAGAAAGAAACAACAGTTGA
                   ||||   | |  | ||    ||  | |  |    ||   |||  | |      || |    | |    ||     |||| | || | |  || |  |   ||  ||| |||||||||||| || ||||| ||||| ||| |   |||||| ||| ||||||| |||||||| ||||| || |||||||| || || |||||| ||||  | |
------------------gtgaaaacaca-ctgtggtttatatatattattacatgtatgcctacactgtggtgga----tatggaaatagcgtttgcgttttgaaacgttttaaa---ttgaaaacgcagGTGGCGGCGAGTTTTGCGGCTGAGGGAGCGGGAATGGGAGAGTTGAAGCAGTGGAATGAATTGTATGGAGAAGGAGGATCGAGGAAGAAAGAACAACTCA

upper sequence: LOC_Os01g12660.1 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv02s0025g00650.t01 (Vitis vinifera), 3'ss of exon 15
gtgaatcttttgttacagttgaatttagaattctgaaacatgcacagaacgtaattcttgctaatataaaactgaaaaactgttagcattatacttgcttgttaacaatttgtggaaactttgaaatgcagGTGGCGGCAAGCTTTGCTGCTGAAGGAACAATAATGGGTGAGCTGAAGCAATGGAATGAGTTGTACGGTGAAGGAGGCTCCAGAAAGAAACAACAGTTGA
                         || ||  |     |   |       ||  |   |      || ||  || |  ||| |     | ||| |||    ||   || | ||      |||||  ||||||| ||||||||||||||||| || ||| | |||||| ||||||||||||| ||||| || | ||| || |||||||| || || ||||| || || ||  
------------------------gtaaaaacccatctccctccttccttgtggtggctatggtgatgaaggtgtattactct----gtaatatttgtggattctgaactggta-----tttga--tgcagGTTGCGGCAAGCTTTGCTGCAGAGGGATCGATAATGAGTGAGCTGAAGCAGTGGAACGACTCGTATGGGGAAGGAGGTTCGAGGAAGAAGCAGCAATTAT

upper sequence: LOC_Os01g12660.1 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv16s0050g01850.t01 (Vitis vinifera), 3'ss of exon 16
gtgaatcttttgttacagttgaatttagaattctgaaacatgcacagaacgtaattcttgctaatataaaactga-aaaactgttagcattatacttgcttgttaacaatttgtggaaactttga----aatgcagGTGGCGGCAAGCTTTGCTGCTGAAGGAACAATAATGGGTGAGCTGAAGCAATGGAATGAGTTGTACGGTGAAGGAGGCTCCAGAAAGAAACAACAGTTGA
                                     || |        | |  |||||  | | ||  ||   | ||||||  | || ||  ||  || ||   |    |  |   | |||| |      ||||||| ||  | || |||||| |||| ||| || |||||  |||||||||||| |||||||||||||| || ||||| || || || |||||  ||||  |||
-------------------------------gtaactacttctgagtctcatttttcttcttgaaatgcaatgcacaaaacttctggc-tttcacaggcgtggacatgcatc-taatatctttaacctggttgcagGTTGCTTCTAGTTTTGCTTCTGAGGGAGCAGTAATGAATGAGCTGAAGCAGTGGAATGAGTTGTATGGAGAAGGCGGTTCAAGGAAGAAGAAACAACTGA

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|88989249|gb|CI043748.1|CI043748
EST:     TCATACTAAGGCCACTAAACATGAAAGATTTGAAAGAAGCAAAAAACCAG                         GTGGCGGCAAGCTTTGCTGCTGAAGGAACAATAATGGGTGAGCTGAAGCAA
genomic: TCATACTAAGGCCACTAAACATGAAAGATTTGAAAGAAGCAAAAAACCAGgtgaatcttt ... tgaaatgcagGTGGCGGCAAGCTTTGCTGCTGAAGGAACAATAATGGGTGAGCTGAAGCAA
EST: gi|88242213|gb|CI242062.1|CI242062
EST:     TCATACTAAGGCCACTAAACATGAAAGATTTGAAAGAAGCAAAAAACCAG                         GTGGCGGCAAGCTTTGCTGCTGAAGGAACAATAATGGGTGAGCTGAAGCAA
genomic: TCATACTAAGGCCACTAAACATGAAAGATTTGAAAGAAGCAAAAAACCAGgtgaatcttt ... tgaaatgcagGTGGCGGCAAGCTTTGCTGCTGAAGGAACAATAATGGGTGAGCTGAAGCAA
EST: gi|66917644|gb|CX104492.1|CX104492
EST:     TCATACTAAGGCCACTAAACATGAAAGATTTGAAAGAAGCAAAAAACCAG                         GTGGCGGCAAGCTTTGCTGCTGAAGGAACAATAATGGGTGAGCTGAAGCAA
genomic: TCATACTAAGGCCACTAAACATGAAAGATTTGAAAGAAGCAAAAAACCAGgtgaatcttt ... tgaaatgcagGTGGCGGCAAGCTTTGCTGCTGAAGGAACAATAATGGGTGAGCTGAAGCAA
EST: gi|88265156|gb|CI368930.1|CI368930
EST:     TCATACTAAGGCCACTAAACATGAAAGATTTGAAAGAAGCAAAAAACCAG                         GTGGCGGCAATCTTTGCTGCTGAAGGAACAATAATGGGTGAGCTGAAGCAA
genomic: TCATACTAAGGCCACTAAACATGAAAGATTTGAAAGAAGCAAAAAACCAGgtgaatcttt ... tgaaatgcagGTGGCGGCAAGCTTTGCTGCTGAAGGAACAATAATGGGTGAGCTGAAGCAA
EST: gi|88504916|gb|CI432422.1|CI432422
EST:     TCATACTAAGGCCACTAAACATGAAAGATTTGAAAGAAGCAAAAAACCAG                         GTGGCGGCAAGCTTTGCTGCTGAAGGAACAATAATGGGTGAGCTGAAGCAA
genomic: TCATACTAAGGCCACTAAACATGAAAGATTTGAAAGAAGCAAAAAACCAGgtgaatcttt ... tgaaatgcagGTGGCGGCAAGCTTTGCTGCTGAAGGAACAATAATGGGTGAGCTGAAGCAA

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: 65 (upstream exon), 73 (downstream exon)
Score: 6

AGGAGGCAATGCTTCAGATGCTTCGAAGATGAAAGAGAAGGACGAGACGATCATACTAAGGCCACTAAACATGAAAGATTTGAAAGAAGCAAAAAACCAGgtgaatcttt ... tgaaatgcagGTGGCGGCAAGCTTTGCTGCTGAAGGAACAATAATGGGTGAGCTGAAGCAATGGAATGAGTTGTACGGTGAAGGAGGCTCCAGAAAGAAACAACAGTTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaactgttagcattatacttgcttgttaacaatttgtggaaactttgaaatgcagGTGGCGGCAAGCTTTGCTGCTGAAGGAACAATAATGGGTGAGCTGAAGCAATGGAATGAGTTGTACGGTGAAGGAGGCTCCAGAAAGAAACAACAGTTGA
                       tgttaac  putative branch site (score: 6)
                         ttaacaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaatcttttgttacagttgaatttagaattctgaaacatgcacagaacgtaattcttgctaatataaaactgaaaaactgttagcattatacttgcttgttaacaatttgtggaaactttgaaatgcagGTGGCGGCAAGCTTTGCTGCTGAAGGAACAATAATGGGTGAGCTGAAGCAATGGAATGAGTTGTACGGTGAAGGAGGCTCCAGAAAGAAACAACAGTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA