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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCACTTTATGATTCCATGGTTTGAGAGGCCAATCATTTATGATGTCCGTGCTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATGgtacgtttgcatctttttaattctatattttcatcgttggaatgtgtgtatacttctcatctaatgatagatatacttgatttgatttgcatgctctatt...

Basic information

species Oryza sativa
transcript LOC_Os07g15880.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g15880.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA09G30410.1 (Glycine max), 5'ss of exon 4
TCACTTTATGATTCCATGGTTTGAGAGGCCAATCATTTATGATGTCCGTGCTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATGgtacgtt-tgcatctttttaattctatattttcatcgttggaatgtgtgtatacttctcatctaatgatagatatacttgatttgatttgcatgctctatt---
|||||| || ||||| ||||||||||||||  | || |||||||||||||| || ||| |||| || |||||||| ||||| ||  | ||||| |||||||||  |  | ||  ||  ||    |    | |  ||   |  |  ||  | |  |    ||| |||       |  ||  |   || ||     ||  ||    
TCACTTCATAATTCCGTGGTTTGAGAGGCCGGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGGAGTCGTGATCTACAGATGgtaaataatacaagttgctaggatttgcgtgtagtcacagagaaatggttttggt----atcaaattcgtagaaccctaaaaaagaattctgaccttaatcata

upper sequence: LOC_Os07g15880.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA12G33520.1 (Glycine max), 5'ss of exon 3
TCACTTTATGATTCCATGGTTTGAGAGGCCAATCATTTATGATGTCCGTGCTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATGgtacgtttgcatctttttaattctatattttcatcgttggaatgtgtgtatacttctcatctaatga---tagatatacttgatttgatttgcatgctctatt
 |||||||||||||| ||||||||||||||  | || |||||||||||||| || ||| |||| || |||||||| ||||| ||  | ||||| |||||||||  |   ||| ||  |||  ||    | |  ||   |  |  ||  | |  |    |  |  |     |  | | |    || |||  | |||  | ||| 
ACACTTTATGATTCCGTGGTTTGAGAGGCCTGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGTAGTCGTGATCTACAGATGgtaaat--acattttgctaagacttacatgtagtcacagagaaatggttttgttatcaaattcgtacaactgaaaaaaaaaaatctgaccttcatattgtat-

upper sequence: LOC_Os07g15880.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT2G20530.2 (Arabidopsis thaliana), 5'ss of exon 4
TCACTTTATGATTCCATGGTTTGAGAGGCCAATCATTTATGATGTCCGTGCTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATGgtacgtt--tgcatctttttaattctatattttcatcgttggaatgtgtgtatact-tctcatctaatgatagatatacttgatttgatttgcatgctctatt---------
|||| |||||||||||||||| || ||||||||||| ||||| || |||||    ||  |||| || ||||| || ||||| ||| | |||||||||||||||      | ||| |  | | ||||| ||  | || | |  |||  |    |    | |  ||   |||   | ||  |    ||   |||  || | | |          
TCACCTTATGATTCCATGGTTCGAAAGGCCAATCATCTATGACGTTCGTGCAAAGCCTTATCTAGTTGAGAGCACATCTGGGAGCCGTGATCTCCAGATGgtattccgcttcatttcatcacttcta-atactaatgggtataatcaggtcgtgtggttttgtcgtgtgaactacatgataagcttatgttgtgtggtatttaaacattcag

upper sequence: LOC_Os07g15880.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv15s0048g02350.t01 (Vitis vinifera), 5'ss of exon 4
TCACTTTATGATTCCATGGTTTGAGAGGCCAATCATTTATGATGTCCGTGCTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATGgtacgtttgcatctttttaattctatattttcatcgttggaatgtgtgtatacttctcatctaatgatagatatacttgatttgatttgcatgctctatt------
|||| | ||||| ||||||||||| |||||| | || |||||||||||||| || ||  |||| |||||||||||||| || ||| | || ||||||||||||   |||    ||| || |||| | || |      ||   ||||  |||  | || |||   || |      |     |  ||  |   |||    ||      
TCACCTGATGATCCCATGGTTTGAAAGGCCAGTTATCTATGATGTCCGTGCACGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATGgtaatattg---ttttctagttct-tgttatagaaaatgt--tgtggttatgttgctgatcatgtgttcaggtgatgaagtgagacatagctgcaactttcagact

upper sequence: LOC_Os07g15880.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv19s0085g00730.t01 (Vitis vinifera), 5'ss of exon 4
TCACTTTATGATTCCATGGTTTGAGAGGCCAATCATTTATGATGTCCGTGCTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATGgtacgtttgcatctttttaattctatattttcatcgttggaatgtgtgtatacttc-tcatctaat-gatagatatacttgatttgatttgcatgctctatt--
|||| | ||||| ||||||||||| |||||| |||| |||||||||||| | || ||  ||||||||||||||||||| || |||   || ||||||||||||  ||||    ||| || |||| | || |      ||   ||  | | |  ||  |||| |  | |   |||  | |       | |||||   |  |    
TCACCTGATGATCCCATGGTTTGATAGGCCAGTCATCTATGATGTCCGTACGCGCCCTCATCTTGTGGAGAGTACTTCAGGGAGCCATGACCTCCAGATGgtaattttg---ttttctagttct-tgttgtagaaaatgttgtgattatgttgttgatcatgtgtttgggtgatgaagtgagacatagttgcaaatttcagact

upper sequence: LOC_Os07g15880.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ20024 (Selaginella moellendorffii), 5'ss of exon 2
TCACTTTATGATTCCATGGTTTGAGAGGCCAATCATTTATGATGTCCGTGCTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATGgtacgtttgcatctttttaattctatattttcatcgttggaatgtgtgtatacttctcatctaatgatagatatacttgatttgatttgcatgctctatt
 || || ||| | || |||||||| |||||| | || || |||||||||||| | |||||  | || |||||||||||||| |||| |||||||||||||||| | |    || |||||      | | |||  ||      | | |   |  |  ||||    |||  | |  |  ||||||    | | ||||||   
GCATTTGATGGTGCCGTGGTTTGACAGGCCAGTGATCTACGATGTCCGTGCTAGACCCAACTTGGTCGAGAGTACTTCTGGCAGCAAGGATCTCCAGATGgtaagatcagttcgttttag-----tgtgttctacgagaacttttctagttcttgttcattccgtga-ggctggaactgattttgcgttcttgctctcag

upper sequence: LOC_Os07g15880.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ07463 (Selaginella moellendorffii), 5'ss of exon 2
TCACTTTATGATTCCATGGTTTGAGAGGCCAATCATTTATGATGTCCGTGCTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATGgtacgtttgcatctttttaattctatattttcatcgttggaatgtgtgtatacttctcatctaatgatagatatacttgatttgatttgcatgctctatt
 || || ||| | || |||||||| |||||| | || || |||||||||||| | |||||  | || ||||||||||| || |||| |||||||||||||||| | |    || |||||      | | |||  ||      | | |   |  |  ||||    |||  | |  |  ||||||  | | | ||||||   
GCATTTGATGGTGCCGTGGTTTGACAGGCCAGTGATCTACGATGTCCGTGCTAGACCCAACTTGGTCGAGAGTACTTCCGGCAGCAAGGATCTCCAGATGgtaagatcagttcgttttag-----tgtgttctacgagaacttttctagttcttgttcattccgtga-ggctggaactgattttgtgttcttgctctcag

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|32948492|gb|BP185064.1|BP185064
EST:     CTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATG                         GTGAAAATTGGTCTCCGTGTCCTTACAAGGCCCATGCCAGAGAAGCTACCA
genomic: CTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATGgtacgtttgc ... ttttgggcagGTGAAAATTGGTCTCCGTGTCCTTACAAGGCCCATGCCAGAGAAGCTACCA
EST: gi|58693615|gb|CK082302.1|CK082302
EST:     CTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATG                         GTGAAAATTGGTCTCCGTGTCCTTACAAGGCCCATGCCAGAGAAGCTACCA
genomic: CTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATGgtacgtttgc ... ttttgggcagGTGAAAATTGGTCTCCGTGTCCTTACAAGGCCCATGCCAGAGAAGCTACCA
EST: gi|218496989|gb|FG950832.1|FG950832
EST:     CTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATG                         GTGAAAATTGGTCTCCGTGTCCTTACAAGGCCCATGCCAGAGAAGCTACCA
genomic: CTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATGgtacgtttgc ... ttttgggcagGTGAAAATTGGTCTCCGTGTCCTTACAAGGCCCATGCCAGAGAAGCTACCA
EST: gi|27578030|gb|CB000725.1|CB000725
EST:     CTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATG                         GTGAAAATTGGTCTCCGTGTCCTTACAAGGCCCATGCCAGAGAAGCTACCA
genomic: CTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATGgtacgtttgc ... ttttgggcagGTGAAAATTGGTCTCCGTGTCCTTACAAGGCCCATGCCAGAGAAGCTACCA
EST: gi|33803697|gb|CF327723.1|CF327723
EST:     CTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATG                         GTGAAAATTGGTCTCCGTGTCCTTACAAGGCCCATGCCAGAGAAGCTACCA
genomic: CTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATGgtacgtttgc ... ttttgggcagGTGAAAATTGGTCTCCGTGTCCTTACAAGGCCCATGCCAGAGAAGCTACCA
EST: gi|8335502|gb|BE040419.1|BE040419
EST:     CTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATG                         GTGAAAATTGGTCTCCGTGTCCTTACAAGGCCCATGCCAGAGAAGCTACCA
genomic: CTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATGgtacgtttgc ... ttttgggcagGTGAAAATTGGTCTCCGTGTCCTTACAAGGCCCATGCCAGAGAAGCTACCA
EST: gi|117233393|gb|CT848123.1|CT848123
EST:     CTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATG                         GTGAAAATTGGTCTCCGTGTCCTTACAAGGCCCATGCCAGAGAAGCTACCA
genomic: CTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATGgtacgtttgc ... ttttgggcagGTGAAAATTGGTCTCCGTGTCCTTACAAGGCCCATGCCAGAGAAGCTACCA
EST: gi|218488311|gb|FG953544.1|FG953544
EST:     CTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATG                         GTGAAAATTGGTCTCCGTGTCCTTACAAGGCCCATGCCAGAGAAGCTACCA
genomic: CTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATGgtacgtttgc ... ttttgggcagGTGAAAATTGGTCTCCGTGTCCTTACAAGGCCCATGCCAGAGAAGCTACCA
EST: gi|8335500|gb|BE040418.1|BE040418
EST:     CTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATG                         GTGAAAATTGGTCTCCGTGTCCTTACAAGGCCCATGCCAGAGAAGCTACCA
genomic: CTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATGgtacgtttgc ... ttttgggcagGTGAAAATTGGTCTCCGTGTCCTTACAAGGCCCATGCCAGAGAAGCTACCA
EST: gi|27576598|gb|CA999292.1|CA999292
EST:     CTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATG                         GTGAAAATTGGTCTCCGTGTCCTTACAAGGCCCATGCCAGAGAAGCTACCA
genomic: CTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATGgtacgtttgc ... ttttgggcagGTGAAAATTGGTCTCCGTGTCCTTACAAGGCCCATGCCAGAGAAGCTACCA
EST: gi|218492453|gb|FG950899.1|FG950899
EST:     TGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATG                         GTGAAAATTGGTCTCCGTGTCCTTACAAGGCCCATGCCAGAGAAGCTACCA
genomic: TGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATGgtacgtttgc ... ttttgggcagGTGAAAATTGGTCTCCGTGTCCTTACAAGGCCCATGCCAGAGAAGCTACCA
EST: gi|58686687|gb|CK075374.1|CK075374
EST:     CTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATG                         GTGAAAATTGGTCTCCGTGTCCTTACAAGGCCCATGCCAGAGAAGCTACCA
genomic: CTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATGgtacgtttgc ... ttttgggcagGTGAAAATTGGTCTCCGTGTCCTTACAAGGCCCATGCCAGAGAAGCTACCA
EST: gi|11118160|gb|AU163348.1|AU163348
EST:     CTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATG                         GTGAAAATTGGTCTCCGTGTCCTTACAAGGCCCATGCCAGAGAAGCTACCA
genomic: CTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATGgtacgtttgc ... ttttgggcagGTGAAAATTGGTCTCCGTGTCCTTACAAGGCCCATGCCAGAGAAGCTACCA
EST: gi|218481986|gb|FG957221.1|FG957221
EST:     CTTCTGGAAGCA-GGATCTCCAGATG                         GTGAAAATTGGTCTCCGTGTCCTTACAAGGCCCATGCCAGAGAAGCTACCA
genomic: CTTCTGGAAGCAGGGATCTCCAGATGgtacgtttgc ... ttttgggcagGTGAAAATTGGTCTCCGTGTCCTTACAAGGCCCATGCCAGAGAAGCTACCA

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: 73 (upstream exon), 74 (downstream exon)
Score: 77

TCACTTTATGATTCCATGGTTTGAGAGGCCAATCATTTATGATGTCCGTGCTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATGgtacgtttgc ... ttttgggcagGTGAAAATTGGTCTCCGTGTCCTTACAAGGCCCATGCCAGAGAAGCTACCAACTATCTACAGGACTCTGGGGGAGAACTTCAATGAGAGAGTTTTGCCTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCACTTTATGATTCCATGGTTTGAGAGGCCAATCATTTATGATGTCCGTGCTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATGgtacgtttgcatctttttaattctatattttcatcgttggaatgtgtgtatacttctcatctaatgatagatatacttgatttgatttgcatgctctatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG