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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcactaattattttgatctttattttgtctgttgagatctatataacaatttcagcatgaatgtctttagGTTGTTGAGGATGGCTACGAGTTCTTTGCGCAAAGGAGATTAGTGACAATCTTTTCAGCTCCAAACTATTGTGGGGAATTTGATAATGCGGGTGCTCTGT

Basic information

species Oryza sativa
transcript LOC_Os01g24750.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g24750.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G120202_T01 (Zea mays), 3'ss of exon 2
------gtaa-gcactaattattttgatctttat----------tttgtctgttgagatctatataacaatttc-agcatgaatgtcttta--------gGTTGTTGAGGATGGCTACGAGTTCTTTGCGCAAAGGAGATTAGTGACAATCTTTTCAGCTCCAAACTATTGTGGGGAATTTGATAATGCGGGTGCTCTGT
       | |  ||| | || |||  || || |           ||  | | | |||||  || |  ||||||  | | | | ||||  ||        ||| || || ||||||||||||||||||||  | || ||| ||||||| |||||||||||||||||||| ||||| |||||||||||||| |||||||| |
aatgaaatgatacacaacttttttgcatgttcaagaaaatgatgttcttttttcgagattcatgtggcaatttttaacgtaattgtccctacctccatagGTGGTAGAAGATGGCTACGAGTTCTTTGCAGAGAGAAGACTAGTGACCATCTTTTCAGCTCCAAACTACTGTGGCGAATTTGATAATGCAGGTGCTCTAT

upper sequence: LOC_Os01g24750.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA19G42050.1 (Glycine max), 3'ss of exon 2
----------------------gtaagcactaattattttgatcttt---attttgtctgttgagatctatataacaatttcagcatgaatgtctt--tagGTTGTTGAGGATGGCTACGAGTTCTTTGCGCAAAGGAGATTAGTGACAATCTTTTCAGCTCCAAACTATTGTGGGGAATTTGATAATGCGGGTGCTCTGT
                       |  |   |   | | ||  |  ||   | ||  |||| | |   |   ||   | ||||   ||   | | ||  |||||||| |||||||| || ||||| |||||  |||| |||||||| || || ||||| |||||||| ||| ||||||||||||| ||||| |||||  |||
ttccttgctttcttactttaacctttgtcttttatgtgttacttcttccaacttcctctgatcaaggcctcattttactttcc-tattttttttttaatagGTTGTGGAGGATGGATATGAGTTTTTTGCTAAAAGAAGATTAGTCACGATATTTTCTGCTCCAAATTATGGTGGGGAATTTGACAATGCTGGTGCGTTGT

upper sequence: LOC_Os01g24750.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA03G39440.1 (Glycine max), 3'ss of exon 2
-------------------gtaagcactaattattt---tgatctttattttgtctgt-tgagatctatataacaattt-cagcatgaatgtctt--tagGTTGTTGAGGATGGCTACGAGTTCTTTGCGCAAAGGAGATTAGTGACAATCTTTTCAGCTCCAAACTATTGTGGGGAATTTGATAATGCGGGTGCTCTGT
                    | | |  |  |  |||   || |  |||||    ||   |  | || |  |  || ||| |      | | ||||  |||||||| |||||||| || ||||| |||||  |||| |||||||| || || ||||| |||||||| ||  ||||||||||||| ||||| |||||  |||
atcttccctgcttttttactttaacctttgtcttttatgtgttacttattccaacttcctctggtcaaggtctcattttactttcctattttcttaatagGTTGTGGAGGATGGATATGAGTTTTTTGCTAAAAGAAGATTAGTCACGATATTTTCTGCTCCAAATTACGGTGGGGAATTTGACAATGCTGGTGCATTGT

upper sequence: LOC_Os01g24750.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G27840.2 (Arabidopsis thaliana), 3'ss of exon 2
----------------------------------------------------gtaagcactaatt-attttgatctttattttgtctgttgagatc-tatataacaatttcagcatgaatgtctt-tagGTTGTTGAGGATGGCTACGAGTTCTTTGCGCAAAGGAGATTAGTGACAATCTTTTCAGCTCCAAACTATTGTGGGGAATTTGATAATGCGGGTGCTCTGT
                                                     | |||  |  |  ||   | |    | ||| |   ||   | | |||   |||  |  |       |||  |  |||| || || || || || ||||| || ||  || |||||||||| || || || ||||||||||||||| ||||||| ||||| || || |||||  | |
gtaaaacaaacaagacctcctcgaaacctgtgaaattgttcttgatggtttgattagcgtttgtccataaagctagagactttttgaattcttaccatatcggacatgtgtaatggttttgtgatgcagGTAGTAGAAGACGGGTATGAGTTTTTCGCAAAACGGAGATTAGTCACGATATTCTCAGCTCCAAACTATGGTGGGGAGTTTGACAACGCTGGTGCGTTAT

upper sequence: LOC_Os01g24750.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv14s0060g01750.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------gtaagcactaattattttgatctttattttgtctgttga-gatctatataacaatttcagcatgaatgtctttagGTTGTTGAGGATGGCTACGAGTTCTTTGCGCAAAGGAGATTAGTGACAATCTTTTCAGCTCCAAACTATTGTGGGGAATTTGATAATGCGGGTGCTCTGT
                          || | |||  |   |   | | | ||  |          | || | |  | |||      | |      |  |||| || |||||||| || || ||||||||  || |  ||||||| ||||| |||||||| ||||||||| |||| || ||||||||||| |||||||| |
tcataccagccagcttgagtcatatctagggactggtgtctgataacatcatactaaaaacaagtggtccagactaaaatcgttctaagctgaattgcagGTGGTGGAGGATGGATATGAATTCTTTGCTAAACGACGATTAGTCACAATTTTTTCAGCACCAAACTATGGTGGAGAGTTTGATAATGCCGGTGCTCTTT

upper sequence: LOC_Os01g24750.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S39_109V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------gtaagcactaattattttgatctttattttgtctgttgagatctatataacaatt-tcagcatga-atgtctt-----tagGTTGTTGAGGATGGCTACGAGTTCTTTGCGCAAAGGAGATTAGTGACAATCTTTTCAGCTCCAAACTATTGTGGGGAATTTGATAATGCGGGTGCTCTGT
                   |       ||  | | || | ||    |  ||  | |    | || ||||   |  || |   |  |||||        ||||||| |||||||| |||||||| || ||  |  |   | | || || ||||| || || ||||| |||||||| ||||||||||||||||||||  || 
tgaccagttgtcttttcatgctgttggtagatctcttcagctgctgtaggttagattctttgtacataatgctgatctgtgcgggatgtcccatgcacagGTTGTGGAGGATGGTTACGAGTTTTTCGCTAAGCGCCAACTGGTCACTATCTTCTCTGCACCAAATTATTGTGGTGAATTTGATAATGCGGGTGCAATGA

upper sequence: LOC_Os01g24750.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S97_286V6.1 (Physcomitrella patens), 3'ss of exon 3
-----------------------gtaagcactaattattt-tgatctttattttgtctgttgagatctatataacaatttcagcatgaa--tgtctttagGTTGTTGAGGATGGCTACGAGTTCTTTGCGCAAAGGAGATTAGTGACAATCTTTTCAGCTCCAAACTATTGTGGGGAATTTGATAATGCGGGTGCTCTGT
                        |   ||    |  |     | | |  |||| | |  |  |     |||    || |  |   ||   |   |  |||| || |||||||| || || || || ||  |  |   | | || || || ||||| |||||||| |||||||| ||||||||||||||||||||  || 
gacgaatttgaacctccgatgcgattgacatgtctcttccaccaccatacttttatattctttgtatactatgctgatctgtgtgggatgttacatacagGTAGTAGAGGATGGTTATGAATTTTTCGCTAAGCGCCAACTGGTTACCATTTTTTCTGCTCCAAATTATTGTGGTGAATTTGATAATGCGGGTGCAATGA

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|86892837|gb|CI312133.1|CI312133
EST:     AAGAATGATNCTTGATCCTTANAATGCCGCGCTCATCAG                         GTTTGTTGAGGATGGCTACGAGTTCTTTGCGCAAAGGAGATTAGTGACAAT
genomic: AAGAATGAT-CTTGAT-CTTA-TATGCCGCGCTCATCAGgtaagcacta ... atgtctttagG-TTGTTGAGGATGGCTACGAGTTCTTTGCGCAAAGGAGATTAGTGACAAT
EST: gi|38470216|gb|CF954347.1|CF954347
EST:     AGAATTTTTGGAGAAGAATGATCTTGAGTCGTATATGCCGCGCTCATCAG                         GTTGTTGAGGATGGCTACGAGTTCTTTGCGCAAAGGAGATTAGTGACAATC
genomic: AGAATTTTTGGAGAAGAATGATCTTGA-TCTTATATGCCGCGCTCATCAGgtaagcacta ... atgtctttagGTTGTTGAGGATGGCTACGAGTTCTTTGCGCAAAGGAGATTAGTGACAATC
EST: gi|29640983|gb|CB645990.1|CB645990
EST:     TAGAATTTTTGGAGAAGAATGATCTTGATCTTATATGCCGCGCTCATCAG                         GTTGTTGAGGATGGCTACGAGTTCTTTGCGCAAAGGAGATTAGTGACAATC
genomic: TAGAATTTTTGGAGAAGAATGATCTTGATCTTATATGCCGCGCTCATCAGgtaagcacta ... atgtctttagGTTGTTGAGGATGGCTACGAGTTCTTTGCGCAAAGGAGATTAGTGACAATC
EST: gi|86496183|gb|CI138816.1|CI138816
EST:     TAGAATTTTTGGAGAAGAATGATCTTGATCTTATATGCCGCGCTCATCAG                         GTTGTTGAGGATGGCTACGAGTTCTTTGCGCAAAGGAGATTAGTGACAATC
genomic: TAGAATTTTTGGAGAAGAATGATCTTGATCTTATATGCCGCGCTCATCAGgtaagcacta ... atgtctttagGTTGTTGAGGATGGCTACGAGTTCTTTGCGCAAAGGAGATTAGTGACAATC
EST: gi|29614158|gb|CB619171.1|CB619171
EST:     TAGAATTTTTGGAGAAGAATGATCTTGATCTTATATGCCGCGCTCATCAG                         GTTGTTGAGGATGGCTACGAGTTCTTTGCGCAAAGGAGATTAGTGACAATC
genomic: TAGAATTTTTGGAGAAGAATGATCTTGATCTTATATGCCGCGCTCATCAGgtaagcacta ... atgtctttagGTTGTTGAGGATGGCTACGAGTTCTTTGCGCAAAGGAGATTAGTGACAATC
EST: gi|58610876|gb|CK038588.1|CK038588
EST:     TAGAATTTTTGGAGAAGAATGATCTTGATCTTATATGCCGCGCTCATCAG                         GTTGTTGAGGATGGCTACGAGTTCTTTGCGCAAAGGAGATTAGTGACAATC
genomic: TAGAATTTTTGGAGAAGAATGATCTTGATCTTATATGCCGCGCTCATCAGgtaagcacta ... atgtctttagGTTGTTGAGGATGGCTACGAGTTCTTTGCGCAAAGGAGATTAGTGACAATC
EST: gi|29669872|gb|CB666147.1|CB666147
EST:     TAGAATTTTTGGAGAAGAATGATCTTGATCTTATATGCCGCGCTCATCAG                         GTTGTTGAGGATGGCTACGAGTTCTTTGCGCAAAGGAGATTAGTGACAATC
genomic: TAGAATTTTTGGAGAAGAATGATCTTGATCTTATATGCCGCGCTCATCAGgtaagcacta ... atgtctttagGTTGTTGAGGATGGCTACGAGTTCTTTGCGCAAAGGAGATTAGTGACAATC

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: 75 (upstream exon), 74 (downstream exon)
Score: 18

GGGAGAGAGTGACAGAGGTGTTTCCTGCACTTTTGGTGCAGATAAGCTTGTAGAATTTTTGGAGAAGAATGATCTTGATCTTATATGCCGCGCTCATCAGgtaagcacta ... atgtctttagGTTGTTGAGGATGGCTACGAGTTCTTTGCGCAAAGGAGATTAGTGACAATCTTTTCAGCTCCAAACTATTGTGGGGAATTTGATAATGCGGGTGCTCTGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctttattttgtctgttgagatctatataacaatttcagcatgaatgtctttagGTTGTTGAGGATGGCTACGAGTTCTTTGCGCAAAGGAGATTAGTGACAATCTTTTCAGCTCCAAACTATTGTGGGGAATTTGATAATGCGGGTGCTCTGT
                         atataac  putative branch site (score: 18)
                                              tgtcttt  putative PPT
                     atctatataacaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcactaattattttgatctttattttgtctgttgagatctatataacaatttcagcatgaatgtctttagGTTGTTGAGGATGGCTACGAGTTCTTTGCGCAAAGGAGATTAGTGACAATCTTTTCAGCTCCAAACTATTGTGGGGAATTTGATAATGCGGGTGCTCTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC