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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagcgattagatgattgtactgcttattgatgttatttttccttttttttttattttgaataactaatggctggaatgccttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA

Basic information

species Oryza sativa
transcript LOC_Os12g01390.1
intron # 26
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 26
lower sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 25
gtaaagcgattagatgattgtactgct-tattgatgttatttttccttttttttttattttgaataactaatggctggaatgccttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA
|||||   |  | |  || |     |  |  ||   ||  | |  ||     ||||| ||| |||| |   ||     |||   |||| ||||||||||||||||||||||| ||||||||||||||||| |||||||||||||||||||||||||| |||||||| || ||||| || |||||||||||||
gtaaaataaaaataaaatagccagacagtcgtgcaattcctgtcgctaccgcttttaattt-aatagcatgtgtt---aatttattgagcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATCGCCGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAGTCGATTGCTCTATCGAAGAAAGACA

upper sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 26
lower sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 3
--gtaaagcgattagatgattgtactgcttattgatgttattttt-----------ccttttttttttattttgaat--aactaatggctggaatgccttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA
    ||| |    |||||   | | ||| ||||| |||| || |            | | || ||  | |||| |||  || ||   |     ||  ||||| ||||| |||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| ||||||||||| ||||| || || |||||||| |
gtacaaaacagccagatg--cgcagtgcctattgttgttgttgtaatggtgtgatgcttattgttactgttttcaatttaattacctgtgttcatttcttgagcagCTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA

upper sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 26
lower sequence: GRMZM2G395549_T01 (Zea mays), 3'ss of exon 11
gtaaagcgattagatgattgtactgct-tattgatgttatttttccttttttttttattttgaataactaatggctggaatgccttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA
|||||   |  | |  || |     |  |  ||   ||  | |  ||     ||||| ||| ||||||   ||     |||   |||| |||||| |||||||||||||||| ||||||||||||||||| |||||||||||||||||||||| ||| |||||||| || ||||| || |||||||||||||
gtaaaataaaaataaaatagccagacagtcgtgcaattcctatcgctaccgcttttaattt-aataacatgtgtt---aatttattgagcagCTTCAGAAGCATGAATTGCTGGAGATGAGGAGGATCGCCGCCTACATTTACAAGAAGGCTGACAGGTGGAAGCAGTCGATTGCTCTATCGAAGAAAGACA

upper sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 26
lower sequence: GRMZM2G062042_T02 (Zea mays), 3'ss of exon 11
gtaaagcgattagatgattgtactgct-tattgatgttatttttccttttttttttattttgaataactaatggctggaatgccttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA
|||||   |  | |  || |     |  |  ||   ||  | |  ||     ||||| ||| ||||||   ||     |||   |||| ||||||||||||||||||||||| ||||||||||||||||| |||||||||||||||||||||||||| |||||||| || ||||| || |||||||||||||
gtaaaataaaaataaaatagccagacagtcgtgcaattcctatcgctaccgcttttaattt-aataacatgtgtt---aatttattgagcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATCGCCGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAGTCCATTGCTCTATCGAAGAAAGACA

upper sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 26
lower sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 3
--gtaaagcgattagatgat--tgtactgcttattgatgttatttttccttt--------------ttttttta-----ttttgaataactaatggctgga-atgccttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA
    |||      |||| ||  || | ||| ||||| || |  | ||  | |              | || |||     |||| | | | |||    ||   ||  || || ||||||||||||||||||||||| |||||||||||||| ||||||||||||||||||||||||||||| ||||||||||| ||||| || || |||||||| |
gtacaaaatagccagataatcttgcagtgcctattgctgctgctgttgttgtaatcgtgcgatgcatattgttactgctttttaatttaataacctgtgtccatttctggagcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA

upper sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 26
lower sequence: GRMZM2G091121_T01 (Zea mays), 3'ss of exon 6
gtaaagcgattagatgattgtactgct-tattgatgttatttttccttttttttttattttgaataactaatggctggaatgccttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA
|||||   |  | |  || |     |  |  ||   ||  | |  ||     ||||| ||| ||||||   ||     |||   |||| ||||||||||||||||||||||| ||||||||||||||||| |||||||||||||||||||||||||| |||||||| || ||||| || |||||||||||||
gtaaaataaaaataaaatagccagacagtcgtgcaattcctatcgctaccgcttttaattt-aataacatgtgtt---aatttattgagcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATCGCCGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAGTCGATTGCTCTATCGAAGAAAGACA

upper sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 26
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 26
--------------------------gtaaagcgattagatgattgtactgcttattgatgttatttttccttt----tttttttattttgaataactaatggctggaatgc-cttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA
                           |    | |||||   |   |   | | |   |||||||      |||    | |||  ||| | | | | |     |   ||| | | ||| ||| |||||||||||||| | |||||||||||| |  | |||||||||||||||||||| || || |||||||||||||| |||||  |||| ||||||||||
gtgaatcttacttatcttttgtcttattttgacaattag-caaaaatcgagatcag-aatgttatgggaaatttaaaatatttgaattattattgattggcttcaacaatacacatgagcagATTGAGAAGCATGAACTTCTTGAGATGAGGCGTGTTGCTGCCTACATTTACAAGAAAGCAGGAAGATGGAAGCAATCCATTGCTTTGTCAAAGAAAGACA

upper sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 26
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 25
gtaaagcgattagatgattgtactgcttattgatgttatttttccttttttttttattttgaataactaatgg-ctggaatgccttgat---cagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA
            | |   || | |  || || |||||   | |  |||   ||  ||| |    ||| | |||  |   ||   |||     ||| |||| ||||||||  | |||||||||||  |  ||||||| || |||||||||||||| || |||||||| || || |||||| |||| |||||||| |
------------gttagctgcatttattcttcatgttgactatt-tttcagttcaattataggaaaccagtggattattattatttggaatgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTCGCTGCTTATATTTACAAGAAGGCAGGTAGATGGAAACAGTCCATTGCCTTGTCAAAGAAAGATA

upper sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 26
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 24
-----gtaa--agcgattagatgattgtactgcttattgatgttattttt-ccttttttttttattttgaataactaatggctggaatgcct-tgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA
     ||||  ||   | |    ||   ||   || || |    |   |  ||||    ||| |   | | | | |         ||||  | ||  ||| |||||||||||||  | |||||||||||| |  | ||||| |||||||| ||||| ||||| ||||||||||| || |||||  |||| || |||||||
tttttgtaattagaagtgaagacataaaacattttgttaaaccaagcatagccttaaagtttgacaattagtgattggctttaacaatgtgtatgtgcagATTGAGAAGCATGAGCTTCTTGAGATGAGGCGTGTTGCTGCTTACATTTATAAGAAAGCTGGAAGATGGAAGCAGTCCATTGCTTTGTCAAAAAAAGACA

upper sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 26
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 26
-gtaaagcgattaga--tgattgtactgcttattgatgttatttttccttttttttttattttga--ataactaatggctggaatgccttg-at---cagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA
  |   |  |||| |  |||    |    | |||    | |      | |    ||  | |||||  ||   |  |||||  ||     || ||   ||| |||||||||||||  | |||||||||||| |  ||||||| || ||||||||||| ||||| ||||||||||| || |||||  |||| || |||||||
atttttgtaattaaaagtgaagtcagaaatcattttgttaaaccaagcatagccttaaagtttgacgattggttttggctttaacaatgtgtatttgcagATTGAGAAGCATGAGCTTCTTGAGATGAGGCGTGTCGCTGCTTATATTTACAAGAAAGCTGGAAGATGGAAGCAGTCCATTGCTTTGTCAAAAAAAGACA

upper sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 26
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 26
--------------------------gtaaagcgattagatgattgtactgcttattgatgttatttttccttt----tttttttattttgaataactaatggctggaatgccttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA
                           |    | |||||   | | |          || |||||      |||    | |||  ||| | | | | |     |   ||| | | || ||| |||||||||||||| | |||||||||||| |  | |||||||||||||||||||| || || |||||||||||||| |||||  |||| ||||||||||
gtgaatctcggttatcttttgtcttattttgacaattagcaaaatctgagatcag--gaagttatggaaaatttaaaatgtttgaattattattgattggcttcaacaatacat-gagcagATTGAGAAGCATGAACTTCTTGAGATGAGGCGTGTAGCTGCCTACATTTACAAGAAAGCAGGAAGATGGAAGCAATCCATTGCTTTGTCAAAGAAAGACA

upper sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 26
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 25
gtaaagcgattagatgattgtactgcttattgatgttatttttccttttttttttattttgaataactaatggctgg-----aatgccttgat--cagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA
            | ||  || | |  || || |||||   | |  ||||   || ||| |    |||  || | |       | |  || ||   ||| |||| ||||||||  | |||||||||||  |  | ||||| || |||||||||||||| || ||||||||||| || |||||| |||| ||||| || |
------------gttggctgcattcattcttcatgttgactat--ttttcagttaattataggaaaccgatagattattattattatctggaatgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAGGCAGGTAGATGGAAGCAGTCCATTGCCTTGTCAAAGAAGGATA

upper sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 26
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 26
gtaaagcgattagatgattgtactgcttattgatgttatttttccttttttttttattttgaataactaa---tggctggaatgc-cttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA
||  ||    ||  |  ||    |||  |||| | || ||| |  || | |       |||| |   |||   | | ||| |||   |||| ||| ||||||| || ||  | |||||||||||  |  | ||||| || ||||||||||| || ||||||||||||||||| |||||  |||||||||||||||
gtggagta--taatttctttaggtgca-attgtttttctttgtggttctatgcactggttgatttcataagccttgttggtatgtgtttgagcagATTGAGAAACACGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAAGCAGGCAGATGGAAGCAATCAATTGCATTGTCGAAGAAAGACA

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: 72 (upstream exon), 75 (downstream exon)
Score: 104

ATCTTTGAATGAGCTTTATGTTGAAGAGGAGGATTATGAGAGACTCCGTGAATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAGAAGgtaaagcgat ... ccttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttttccttttttttttattttgaataactaatggctggaatgccttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA
                            aactaat  putative branch site (score: 104)
     ttccttttttttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagcgattagatgattgtactgcttattgatgttatttttccttttttttttattttgaataactaatggctggaatgccttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA