Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaccctctttgtccattgaagtttgaaagtccaatctatgattaagttagggggtcttttgcatacaatttcaagtgttctcttctgcagGTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCCAAGCTTACCTGGACAGCTATGTACAGGAAGCAGCACAAGA

Basic information

species Oryza sativa
transcript LOC_Os01g59990.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g59990.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA03G34700.1 (Glycine max), 3'ss of exon 2
-------------------------------gtaaccctctttgtccattgaagtttgaaagtccaat---ctatgatta----------agttagggggtcttttgc---------------atacaatttcaagtgttctcttctgc---------agGTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCCAAGCTTACCTGGACAGCTATGTACAGGAAGCAGCACAAGA
                               ||     | | |   ||||  ||| || | || ||||   ||||||||           | ||| ||||| ||||                 ||||   |   || ||| |  | ||          ||||||| |||||||||||||| ||||| ||||| || ||||||||||||||||||||  | ||||| |||||||| ||||||||||| ||||| ||||| |
gtgacataaaatatgtctcattgaattttgggtggatgtatctcatcatttcagtctggatgttcaatttgctatgatttgatcatttttaattatggggttttttctttgttactagttatgatactgatatgagggtttttgtttgttgaatctatagGTTTTCCTGTTTGCCAACTCAAAATGTAAGCGGTATTTCCACAACCGCCTGAAGCCCTCAAAGCTCACCTGGACTGCTATGTACAGAAAGCAACACAAAA

upper sequence: LOC_Os01g59990.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA19G37370.2 (Glycine max), 3'ss of exon 2
--------------------------------------------------------------------gtaaccctctttgtccattgaagtttgaaagtccaatctatgattaagttagggggtcttttgcatacaatttcaagtgttctcttctgcagGTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCCAAGCTTACCTGGACAGCTATGTACAGGAAGCAGCACAAGA
                                                                    || | | | |||      ||| | ||    ||    |   |  ||| | ||  |   ||  |      | |||    ||||   | || |||||||| |||||||| ||||| ||||| ||| | || |||||||| |||||||||||| | ||||| |||||||| || |||||||| ||||| ||||| |
gtaacataaaatatgttttgggttgatgtgtcgcattatttcagtctggttgttctgtttgcaatgatgtgatcattttttagttatgagggttttttgtttg-ttgctagttatgatattgatactgatatgaggatttttgtttgttgaat-ctacagGTTTTCCTGTTTGCAAACTCAAAATGTAAGAGGTATTTCCACAATCGCCTGAAGCCTTCAAAGCTCACCTGGACTGCAATGTACAGAAAGCAACACAAAA

upper sequence: LOC_Os01g59990.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA10G07680.1 (Glycine max), 3'ss of exon 2
---------------------------------------gtaaccctctttgtccattgaagtttgaaa------gtccaatctatgattaagttagggggtcttttgc--------atacaatttcaagtgttctcttc--------tgcagGTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCCAAGCTTACCTGGACAGCTATGTACAGGAAGCAGCACAAGA
                                        |     | |||    || || |||           | | ||   || || || || |   || |||| |        ||||   |  | | | | | ||         | |||||||| |||||||| ||||||||||| ||| | || ||||||||| |  |||||||  | ||||| |||||||| || |||||||| ||||| |||||||
gtgacataatatgtttctcattgaattttgggttgatgtattgtgttattttgatatggatgttctgtgtactttgacaaaatcatcatcaattttgatcgttttttactagttattatactgatataggggatttgtttgttgaatatacagGTTTTCCTGTTTGCTAACTCGAAATGTAAGAGGTATTTCCACAACAGGTTGAAGCCATCAAAGCTCACCTGGACTGCAATGTACAGAAAGCAACACAAGA

upper sequence: LOC_Os01g59990.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv13s0074g00140.t01 (Vitis vinifera), 3'ss of exon 2
------------------------------------------------------------------------------gtaaccctctttgtccattgaagtttgaaagtccaatctatgattaagtta----------gggggtcttttg-----catacaatttc--aagtgttctcttctgcagGTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCCAAGCTTACCTGGACAGCTATGTACAGGAAGCAGCACAAGA
                                                                               |||    |||  |  ||| |      |  ||      | | |||  | |           |   |||  ||       ||| ||| ||  || || ||  || |  |||| ||||| |||||||| || ||||||||| | ||||| |||||||| || |||||| | |||||||||||||| |||||||| || ||||| || ||||
gtaaaaatgtggatttaattacatattttcaagtctcatatgaatatttaatttgcttgattgcctatcaaaaaatatttaatttccttgatttatttagagagcagtgttggggttgttattgtgctttttatattctgaatgtccattaatatttatataatctcgtaattgatcaattgt-tagGTATTTCTATTTGCCAATTCAAAATGCAAGAGATACTTTCACAACCGACTTAAGCCTTCAAAGCTTACCTGGACGGCTATGTATAGAAAGCAACATAAGA

upper sequence: LOC_Os01g59990.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv16s0100g00650.t01 (Vitis vinifera), 3'ss of exon 1
-------------------------------------------gtaaccctctttgtccattgaagtttgaaagtccaatctatgattaagttagggggtctt---ttgc----atacaatttcaagtgttctcttctg--cagGTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCCAAGCTTACCTGGACAGCTATGTACAGGAAGCAGCACAAGA
                                           ||| |  ||   |   ||   |  || |||  |    || | |||   |||      |||   || |    |   |||  ||  ||||   ||     ||||||||||| |||||||| || ||||||||| | |||||||||||||| || |||||  | |||||||| |||||||| |||||||| |||||||||||||
gtaaaatgtgatgatattttcaatttggttctgtcaggggcatgtatcattcagagcatatcctacattcaaacgcttccctgt-attggcttaattttacttcaattactgtaactgaatagcatctgtttcatttatatcagGTTTTTCTCTTTGCCAATTCTAAATGCAAGAGGTACTTCCACAACCGGCTTAAGCCATCGAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGA

upper sequence: LOC_Os01g59990.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv08s0007g04210.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------------------------------------------------gtaaccctctttgtccattgaagtttgaaagtccaatctatgattaagttagggggtcttttgcatacaatttcaagtgttctct---tctgcagGTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCCAAGCTTACCTGGACAGCTATGTACAGGAAGCAGCACAAGA
                                                                      ||| | ||||| | |||||    |||   |  |  ||   | || |  |   |    | ||  ||  |  || || |  ||||    | |  |||| ||||| |||||||| || ||||||||| | |||||||||||||| ||||||||  | ||||||||||||||||| |||||||||||||| || || |
gtaattttatagctcattaaaatttatgttctgtatcagattattagccaactaaatttctactgaatgttaatcttctttcttcattgt--cttggttgggc--tcaggggttgacctcttgtacttgtttaattgacattaaattactctcaatatatttagGTGTTTCTATTTGCCAATTCAAAATGCAAGAGGTACTTCCACAACCGGCTGAAGCCATCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAACATAAAA

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|30228671|gb|CB966561.1|CB966561
EST:     AGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAG                         GTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
genomic: AGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAGgtaaccctct ... tcttctgcagGTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
EST: gi|38476375|gb|CF960508.1|CF960508
EST:     AGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAG                         GTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
genomic: AGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAGgtaaccctct ... tcttctgcagGTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
EST: gi|88576762|gb|CI673287.1|CI673287
EST:     AGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAG                         GTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
genomic: AGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAGgtaaccctct ... tcttctgcagGTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
EST: gi|88328544|gb|CI676754.1|CI676754
EST:     AGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAG                         GTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
genomic: AGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAGgtaaccctct ... tcttctgcagGTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
EST: gi|218481886|gb|FG948632.1|FG948632
EST:     AGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAG                         GTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
genomic: AGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAGgtaaccctct ... tcttctgcagGTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
EST: gi|33806682|gb|CF329222.1|CF329222
EST:     AGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTTCCAG                         G-TTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
genomic: AGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAGgtaaccctct ... tcttctgcagGTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
EST: gi|14981286|gb|BI305964.1|BI305964
EST:     AGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAG                         GTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
genomic: AGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAGgtaaccctct ... tcttctgcagGTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
EST: gi|88404907|gb|CI685341.1|CI685341
EST:     AGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAG                         GTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
genomic: AGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAGgtaaccctct ... tcttctgcagGTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
EST: gi|87018104|gb|CI275918.1|CI275918
EST:     AGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAG                         GTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
genomic: AGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAGgtaaccctct ... tcttctgcagGTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
EST: gi|163922730|gb|EG712201.1|EG712201
EST:     AGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAG                         GTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
genomic: AGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAGgtaaccctct ... tcttctgcagGTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
EST: gi|33690835|gb|CF319074.1|CF319074
EST:     AGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAG                         GTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
genomic: AGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAGgtaaccctct ... tcttctgcagGTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
EST: gi|86594449|gb|CI253348.1|CI253348
EST:     AGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAG                         GTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
genomic: AGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAGgtaaccctct ... tcttctgcagGTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
EST: gi|58602306|gb|CK012834.1|CK012834
EST:     AGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAG                         GTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
genomic: AGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAGgtaaccctct ... tcttctgcagGTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
EST: gi|86854019|gb|CI252010.1|CI252010
EST:     ACCCAGGCAAGGGTATCA-GTCTCATTCGTGCTGATTCCCAG                         GTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
genomic: ACCCAGGCAAGGGTATCAGGT-TCATTCGTGCTGATTCCCAGgtaaccctct ... tcttctgcagGTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
EST: gi|58681869|gb|CK070556.1|CK070556
EST:     GAAGATATACCCAGGCAAGGGTATCAGGTTCAGTTCGTGCTGATTCCCAG                         GTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
genomic: GAAGATATACCCAGGCAAGGGTATCAGGTTCA-TTCGTGCTGATTCCCAGgtaaccctct ... tcttctgcagGTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
EST: gi|58593374|gb|CF991682.1|CF991682
EST:     AGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCGCAG                         GTTTTTCTG-TTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
genomic: AGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAGgtaaccctct ... tcttctgcagGTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
EST: gi|58591772|gb|CF990080.1|CF990080
EST:     AGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAG                         GTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
genomic: AGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAGgtaaccctct ... tcttctgcagGTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
EST: gi|163927525|gb|EG709957.1|EG709957
EST:     AGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAG                         GTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
genomic: AGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAGgtaaccctct ... tcttctgcagGTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
EST: gi|38480261|gb|CF964350.1|CF964350
EST:     AGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAG                         GTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG
genomic: AGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAGgtaaccctct ... tcttctgcagGTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTG

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: 74 (upstream exon), 74 (downstream exon)
Score: 248

GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAGgtaaccctct ... tcttctgcagGTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCCAAGCTTACCTGGACAGCTATGTACAGGAAGCAGCACAAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatgattaagttagggggtcttttgcatacaatttcaagtgttctcttctgcagGTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCCAAGCTTACCTGGACAGCTATGTACAGGAAGCAGCACAAGA
                                        tgttctcttct  CT-rich tract
     attaagtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaccctctttgtccattgaagtttgaaagtccaatctatgattaagttagggggtcttttgcatacaatttcaagtgttctcttctgcagGTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCCAAGCTTACCTGGACAGCTATGTACAGGAAGCAGCACAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT