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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatgctcaatatcttttttggataaatacttcaaaattcaggaaattttaattatgcttccttcatgcagGTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATTTCACCCTCAAGACAATAATATCATAGCAATTGGAATGGAAGATTCAACCA

Basic information

species Oryza sativa
transcript LOC_Os01g15020.2
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G416836_T01 (Zea mays), 3'ss of exon 18
gtaaatgctcaatatcttttttggataaatacttcaaaattcaggaaattttaattatgcttccttcatgcagGTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATTTCACCCTCAAGACAATAATATCATAGCAATTGGAATGGAAGATTCAACCA
||||   || | | | || ||  ||| ||   |||| | |||| |||  |||||| |||| ||||||||||||||| |||||||||||||||| ||||| ||||||||||| ||||||||||||||||||||||| ||||| ||||||||||| |||||||||||||||||||
gtaatgtctaactgttttattctgatgaaattttcagatttcaagaagatttaatcatgcatccttcatgcagGTGCTGACAACATTCATGCCGCCACCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGATAATAACATCATAGCAATAGGAATGGAAGATTCAACCA

upper sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 20
----------------gtaaatgctca-atatctttt---ttggataa-atacttc------aaaattcaggaaattttaattatgcttccttcatgcagGTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATTTCACCCTCAAGACAATAATATCATAGCAATTGGAATGGAAGATTCAACCA
                 || ||||| | |||     |    ||||| | ||| |         |||   |       ||||| |||| |||||| |||||||||||||||||||||||||||| || ||||||||||| ||||||||||||||||||||||||||||| ||||||||||| |||||||||||||||||||
atctataagcaggtcattagatgcttatataatccataagctggattatataatcttgagaggaaacaaacatggccttaatcatgcatccttcttgcagGTGATGACAACATTCATGCCACCTCCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGACAATAACATCATAGCAATAGGAATGGAAGATTCAACCA

upper sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 20
lower sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 21
gtaaatgctca-atatcttttttggataa---atacttcaaaattcaggaaattttaattatgcttccttcatg-cagGTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATTTCACCCTCAAGACAATAATATCATAGCAATTGGAATGGAAGATTCAACCA
||| |||  || | ||        || |    ||||  |   | |    |   | || ||| | ||  ||  |  ||||| ||||||||||||||||||||||| || || || |||||| |||| || ||||||||||| ||||| |||||||| ||||| ||||| |||||||| |
gtacatgtccagagatacaaccatgacattccatacagccgcaatgtttactgtatacttaggtttattttctatcagGTAATGACAACATTCATGCCACCACCACCCGCCTCTACCTTTCTAGCTTTCCACCCTCAAGATAATAACATCATAGCCATTGGGATGGAGGATTCAACAA

upper sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 20
lower sequence: GLYMA19G41840.1 (Glycine max), 3'ss of exon 20
gtaaatgctca-atatcttttttggataaatacttcaaaattcag-gaaat--------tttaattatgcttc--cttcatgcagGTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATTTCACCCTCAAGACAATAATATCATAGCAATTGGAATGGAAGATTCAACCA
||| |||  || | ||     |   |  | ||| |     | |   |  ||        |||| ||||| ||    |||   ||||| ||||||||||||||||||||||| || || || |||||| | || || ||||||||||| || || |||||||| ||||| ||||| |||||||| |
gtacatgtccagagatacaagtacaaccattacattccgttccgctgctatgttttctgtttacttatggtttattttctatcagGTAATGACAACATTCATGCCACCACCCCCTGCCTCTACCTTTCTGGCTTTCCACCCTCAAGATAACAACATCATAGCCATTGGGATGGAGGATTCAACAA

upper sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 20
lower sequence: AT3G16830.1 (Arabidopsis thaliana), 3'ss of exon 20
-------------------------------------------gtaaatgctcaatatcttt----tttggataaatacttcaaaattcaggaaattttaat-tatgcttcc--ttcatgcagGTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATTTCACCCTCAAGACAATAATATCATAGCAATTGGAATGGAAGATTCAACCA
                                            ||||| ||  ||| ||       |     || || || |  | |  |  ||  | |||  ||  ||||  ||| ||||||| |||||||| ||||||||||| || ||||| ||||| || || |||||||| |||||||| |||||||| || ||||| || ||||| || || |  |
gtaagcagcttaatccaactttttctgttctcgggagcatctcctaaatact-gatacctcaggagctaatgaaactatttgagtaatatgcgaagctaaatgcatttttccctttcgtgcagGTAATGACAACTTTCATGCCACCGCCACCAGCTTCAACTTTCTTGGCATTTCATCCTCAAGATAATAATATTATTGCAATCGGGATGGAGGACTCGAGTA

upper sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 20
lower sequence: AT5G27030.1 (Arabidopsis thaliana), 3'ss of exon 20
------------------------------------------------gtaaatgctcaatatcttttttggataaatacttcaaaattcaggaaatttta--attatgct-tccttcatgcagGTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATTTCACCCTCAAGACAATAATATCATAGCAATTGGAATGGAAGATTCAACCA
                                                | ||||| ||   |   |  |    ||||  |||     |     || ||  |  |  |  || |    | |  |||||||||||||||||||||| || || ||||||||||| ||||| || || || ||||| ||||||||  |||| || |||||||||||||| || || |
gtatatattatctatatgaacttaaaaaaagccacaagatttctaactgaaaatgttct-cacactaatctagtaaactcttttggttgttctaatttccacaaaaaaactattggccttatagGTGATGACAACATTCATGCCGCCTCCACCAGCATCAACGTTTTTGGCGTTCCATCCTCAGGACAATAACGTCATCGCCATTGGAATGGAAGACTCTACGA

upper sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 20
lower sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 20
gtaaatgctcaatatcttttttggataaatacttcaaa------attcaggaaatttta--attatgcttccttcat--gcagGTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATTTCACCCTCAAGACAATAATATCATAGCAATTGGAATGGAAGATTCAACCA
|||  | || || |||    ||    |  | | |||||      |||    |   ||||  || ||| | | |||||  | |||| ||||||||||||||| |||| || || || ||||||||  |||| || || |||||||||||||| |||||||| || |||||||| ||||| ||||
gtatgt-ctaaacatcacagttttgcatcttcatcaaatttggcatttgaaatggtttagcatgatgttgctttcatttgtagGTAATGACAACATTCATGTCACCTCCCCCTGCTTCAACCTTCCTAGCCTTCCATCCTCAAGACAATAACATCATAGCCATAGGAATGGAGGATTCTACCA

upper sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 20
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 20
-----------------------gtaaatgctcaatatcttttttggata-aatacttcaaaattcaggaaattttaattatgcttccttcatg---cagGTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATTTCACCCTCAAGACAATAATATCATAGCAATTGGAATGGAAGATTCAACCA
                        | | |  | || |  |  | ||      || ||| || ||    |   |   | ||    |    |  ||   ||||| ||||| ||||||||||| |||||||||||| | || ||| | || || || || |||||||| || ||||| || || |||||||| |||||||| |
tattaaaaaaattgaagccattttttattattaaaaaattactctgctggtgatgcttgaacatggcagttctgacagttgccttcggattgtgattcagGTCATGACGACATTCATGCCGCCACCTCCAGCAGCTACTTTTCTTGCGTTCCATCCCCAAGACAACAACATCATTGCCATAGGAATGGAGGATTCAACAA

upper sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 20
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 20
---------------------------------------------gtaa-atgctcaatatcttttttggataaatacttcaaaattcaggaaattttaattatg----cttccttc--------atgcagGTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATTTCACCCTCAAGACAATAATATCATAGCAATTGGAATGGAAGATTCAACCA
                                              ||| ||| | |  | | ||||    |   || ||   |     |  |||||| ||| ||     || ||||        |  ||||| ||||| |||||||||||||||||||||||| | || ||| | |||||||| || |||||||| |||||||| || || |||||||||||||| || |
gtaaagtccgcgaatcatgaggagtctattttattctttgttctaataatatggtgagaagcgttttgtttttggtaattttgacagttgtcaatttttattctgacgcttttcttcggattttgactcagGTCATGACGACATTCATGCCACCACCTCCAGCAGCTACTTTTCTTGCATTTCATCCACAAGACAACAATATCATTGCTATCGGAATGGAAGATTCGACAA

upper sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 20
lower sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
gtaaatgctcaatatcttttttggataaatacttcaaaattcaggaaattttaattatgcttccttcatgcagGTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATTTCACCCTCAAGACAATAATATCATAGCAATTGGAATGGAAGATTCAACCA
                      | ||  | | ||     |   |     | |||     ||| |    | |||||||||||| ||||||||||||| || |||||| |||| ||  | || ||||||||||||||||| ||||||||||| ||||||||||||||||| || |
----------------------gtatgcacatttttccttcttgaccggtgtaa--gaacttgccatgtccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA

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|58694171|gb|CK082858.1|CK082858
EST:     CATGTGGTGGGAAGGTTTCACTGTTTAACATGATGACATTTAATG                         GTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATT
genomic: CATGTGGTGGGAAGGTTTCACTGTTTAACATGATGACATTTAA-Ggtaaatgctc ... cttcatgcagGTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATT
EST: gi|29625565|gb|CB630576.1|CB630576
EST:     TGTCTGCATGTGGTGGGAAGGTTTCACTGTTTAACATGATGACATTTAAG                         GTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATTT
genomic: TGTCTGCATGTGGTGGGAAGGTTTCACTGTTTAACATGATGACATTTAAGgtaaatgctc ... cttcatgcagGTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATTT
EST: gi|58680385|gb|CK069072.1|CK069072
EST:     TGTCTGCATGTGGTGGGAAGGTTTCACTGTTTAACATGATGACATTTAAG                         GTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATTT
genomic: TGTCTGCATGTGGTGGGAAGGTTTCACTGTTTAACATGATGACATTTAAGgtaaatgctc ... cttcatgcagGTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATTT
EST: gi|88828342|gb|CI000451.1|CI000451
EST:     TTCACTGTTTAACATGATGACATTTAAG                         GTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATTT
genomic: TTCACTGTTTAACATGATGACATTTAAGgtaaatgctc ... cttcatgcagGTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATTT
EST: gi|58606459|gb|CK034492.1|CK034492
EST:     TGTCTGCATGTGGTGGGAAGGTTTCACTGTTTAACATGATGACATTTAAG                         GTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATTT
genomic: TGTCTGCATGTGGTGGGAAGGTTTCACTGTTTAACATGATGACATTTAAGgtaaatgctc ... cttcatgcagGTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATTT
EST: gi|58601227|gb|CK011755.1|CK011755
EST:     TGTCTGCATGTGGTGGGAAGGTTTCACTGTTTAACATGATGACATTTAAG                         GTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATTT
genomic: TGTCTGCATGTGGTGGGAAGGTTTCACTGTTTAACATGATGACATTTAAGgtaaatgctc ... cttcatgcagGTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATTT
EST: gi|29626131|gb|CB631142.1|CB631142
EST:     TGTCTGCATGTGGTGGGAAGGTTTCACTGTTTAACATGATGACATTTAAG                         GTGATNGACA-CATTCATGCCACCACCT
genomic: TGTCTGCATGTGGTGGGAAGGTTTCACTGTTTAACATGATGACATTTAAGgtaaatgctc ... cttcatgcagGTGAT-GACAACATTCATGCCACCACCT
EST: gi|29619450|gb|CB624462.1|CB624462
EST:     TGTCTGCATGTGGTGGGAAGGTTTCACTGTTTAACATGATGACATTTAAG                         GTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATTT
genomic: TGTCTGCATGTGGTGGGAAGGTTTCACTGTTTAACATGATGACATTTAAGgtaaatgctc ... cttcatgcagGTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATTT
EST: gi|163927986|gb|EG712962.1|EG712962
EST:     TGTCTGCATGTGGTGGGAAGGTTTCACTGTTTAACATGATGACATTTAAG                         GTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATTT
genomic: TGTCTGCATGTGGTGGGAAGGTTTCACTGTTTAACATGATGACATTTAAGgtaaatgctc ... cttcatgcagGTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATTT

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: 61 (upstream exon), 70 (downstream exon)
Score: 41

TGAGGATGCAGTTCCATGCATTGCTCTCTCCAAGAATGATTCTTATGTGATGTCTGCATGTGGTGGGAAGGTTTCACTGTTTAACATGATGACATTTAAGgtaaatgctc ... cttcatgcagGTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATTTCACCCTCAAGACAATAATATCATAGCAATTGGAATGGAAGATTCAACCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttggataaatacttcaaaattcaggaaattttaattatgcttccttcatgcagGTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATTTCACCCTCAAGACAATAATATCATAGCAATTGGAATGGAAGATTCAACCA
                              ttttaat  putative branch site (score: 41)
                                       tgcttccttc  putative PPT
      ataaatacttcaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatgctcaatatcttttttggataaatacttcaaaattcaggaaattttaattatgcttccttcatgcagGTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATTTCACCCTCAAGACAATAATATCATAGCAATTGGAATGGAAGATTCAACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA