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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccacattctgcagaattttacgaacttcacttttgcttgcactcctgactcctctgtttactttaaaaataactatacactatccatttattcaaaacagGTTGATGATAAACTTTATATATACCTGGAGTATGTTTCTGGTGGATCCATCCATAAACTACTCCAGGAGTATGGGCAATTTGGTGAACCTGCTATCCGCA

Basic information

species Oryza sativa
transcript LOC_Os02g44642.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G093316_T01 (Zea mays), 3'ss of exon 5
-----ccacattctgcag-aattttacgaacttcacttttgcttgcactcctgactcctctgtttactttaaaaataactatacactatccatttattcaaaacagGTTGATGATAAACTTTATATATACCTGGAGTATGTTTCTGGTGGATCCATCCATAAACTACTCCAGGAGTATGGGCAATTTGGTGAACCTGCTATCCGCA
        ||||||           | | | | ||   ||  ||   ||| ||  || | || ||| |  ||| | | ||  | | |||      ||| |||||||||||||||||| ||||| ||||||||||||||||||||||||||||| || ||||| || ||||| |||||||| || ||||||||||  || || ||||
tagaattgcattcttttttggacggaaggagtacatagttatttttcctcatgcatcttgtgattattcgaaatacatctccatattat------attgaaaacagGTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGGTGGATCTATACATAAGCTTCTCCAAGAGTATGGTCAGTTTGGTGAACAGGCCATTCGCA

upper sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AC209208.3_FGT001 (Zea mays), 3'ss of exon 4
-----ccacattctgcag-aattttacgaacttcacttttgcttgcactcctgactcctctgtttactttaaaaataactatacactatccatttattcaaaacagGTTGATGATAAACTTTATATATACCTGGAGTATGTTTCTGGTGGATCCATCCATAAACTACTCCAGGAGTATGGGCAATTTGGTGAACCTGCTATCCGCA
      ||||||||        |  | | | | ||   || |||   | | ||  || | || ||  | ||||   | ||  | |        |||| ||||| ||||||||||||| ||||| ||||||||||||||||||||||||||||| || ||||| || ||||| |||||||| || ||||||||||  || ||  |||
tagaatcacattcttttctggatggagggagtacatagttacttttccccatgcatcttgtgattcttctaaatgcatctccatata------ttatacaaaatagGTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGGTGGATCTATACATAAGCTTCTCCAAGAGTATGGACAGTTTGGTGAACAAGCCATTTGCA

upper sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA09G24970.1 (Glycine max), 3'ss of exon 5
ccacattctgcagaattttacgaacttcacttttgcttgcactcctgactcctctgtttactttaaaaataactataca--ctatccatttattca--aaacagGTTGATGATAAACTTTATATATACCTGGAGTATGTTTCTGGTGGATCCATCCATAAACTACTCCAGGAGTATGGGCAATTTGGTGAACCTGCTATCCGCA
  ||||| |      || |    |||   | |    ||  |  | ||  | |  | |||   || |   ||  |||| |  ||    | | || |   |||||||| |  || || ||||| ||||| |||||||||||| |||| || |||||  ||||||| || || || ||||| |||||||||||||  ||||| || |
-tacattttttc---ttgtcatcactcatcataatattagaaacttgtttacagtatttttcttcagtctacttatagaaactgctgaatcatcccttaaacagGTAGGCGACAAGCTTTACATATATCTGGAGTATGTTGCTGGAGGCTCCATATATAAACTTCTTCAAGAATATGGACAATTTGGTGAACTAGCTATTCGTA

upper sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA10G37730.1 (Glycine max), 3'ss of exon 6
------ccacattctgcagaattttacgaacttcacttttgcttg-cactcctgactcctctgtttactttaaaaataactatacactatccatttattcaaaacagGTTGATGATAAACTTTATATATACCTGGAGTATGTTTCTGGTGGATCCATCCATAAACTACTCCAGGAGTATGGGCAATTTGGTGAACCTGCTATCCGCA
            | |     ||   |   |  |     || || | || |  |   |  | || || | ||| | |    | |  |    || ||       ||||||||||||| || ||||| |||||||| || ||||| ||||| || ||||| |||||||| || || || |||||||||||||||||||  | ||| || |
tgtttctggtggtttatctgataacatagaagtgggaatttctcgacagtatttgtttttgtggtt-ccttatagaggcttctgaatcgcccctt------gaacagGTTGATGACAAGCTTTACATATACCTTGAATATGTATCTGGAGGCTCCATACATAAACTTCTTCAAGAATATGGGCAATTTGGTGAACTAGTTATTCGTA

upper sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA16G30030.2 (Glycine max), 3'ss of exon 5
----ccacattct-gcagaattttacga-acttcacttttgcttgcact-cctgactcctctgtttactt-taaaaataactatacactatccatttattcaaaacagGTTGATGATAAACTTTATATATACCTGGAGTATGTTTCTGGTGGATCCATCCATAAACTACTCCAGGAGTATGGGCAATTTGGTGAACCTGCTATCCGCA
      ||||| |  |      | |  | | |  |   ||| || || |   || ||  || || ||||  || |||   | | |    |||| ||      |||||||| |  || || ||||| ||||| |||||||||||| |||| || |||||  ||||||| || || || ||||| |||||||||||||  ||||| || |
tggtttacatttttacttgtcatcattatattagatacttgtttacagtatttgtcttttcagtctactcatagaaactgccaaat--catccctt------aaacagGTAGGCGACAAGCTTTACATATATCTGGAGTATGTTGCTGGAGGCTCCATATATAAACTTCTTCAAGAATATGGACAATTTGGTGAACTAGCTATTCGTA

upper sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA01G42960.1 (Glycine max), 3'ss of exon 4
ccacattctgcagaattttacgaacttcacttttgcttgcactcctgactcctctgtttactttaaaaataactatacactatccat------ttattcaaaacagGTTGATGATAAACTTTATATATACCTGGAGTATGTTTCTGGTGGATCCATCCATAAACTACTCCAGGAGTATGGGCAATTTGGTGAACCTGCTATCCGCA
      | |    ||||| || | || |     | ||     |           |||| |   | || ||   | ||    ||  ||      ||||   |||||||| ||||| ||||||||||||||| |||||||||| |||||||| || ||| ||||  | || ||  ||||||| ||  || |||||  || ||| || |
------ttttagaaatttgacaatctactaaaatactaaatatttaagagaagatgttgatacttaagattgttttaagtgatttatggctctttataataaacagGTAGATGACAAACTTTATATATACTTGGAGTATGTCTCTGGTGGGTCAATCTATAAGTTGCTTCAACAGTATGGCCAGCTTAGTGAAATTGTTATTCGTA

upper sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA11G02520.1 (Glycine max), 3'ss of exon 7
----ccacattctgcagaattttacga-acttcacttttgcttgcac-tcctgactcctctgtttactttaaaaataactatacactatccatttattcaaaacagGTTGATGATAAACTTTATATATACCTGGAGTATGTTTCTGGTGGATCCATCCATAAACTACTCCAGGAGTATGGGCAATTTGGTGAACCTGCTATCCGCA
      | ||||  ||   |  ||  | |||  |  |||    | |  |  |||  | || | ||  |||     ||   || ||   | | |||||   |||||||| ||||||||||||||||||||| |||||||||| |||||||| || ||| ||||  | || ||  ||||||| ||  || |||||  || ||| || |
ttttagaaattcgacaatctactaaaatactaaatatttaagagaagatgttgatacttcagattgtttt-----tagtgattcatggttc-tttataataaacagGTAGATGATAAACTTTATATATACTTGGAGTATGTCTCTGGTGGGTCAATCTATAAGTTGCTTCAACAGTATGGCCAGCTTAGTGAAATTGTTATTCGTA

upper sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA20G30100.1 (Glycine max), 3'ss of exon 5
------ccacattctgcagaattttac-gaacttcacttttgcttgcactcctgactcctctgtttactttaaaaataactatacactatccatttattcaaaacagGTTGATGATAAACTTTATATATACCTGGAGTATGTTTCTGGTGGATCCATCCATAAACTACTCCAGGAGTATGGGCAATTTGGTGAACCTGCTATCCGCA
            | |     ||   |  ||| |     |||     |  |  |   |  | || || | ||| | |    | || |  | || ||       ||||||| ||| | || ||||| |||||||| |||||||| ||||| || ||||| |||||||| || |  || |||||||||||||||||||  | ||| || |
tgtttctggtggtttatctgataacatagaagtgggaatttctcaacggtatttgttattgtggtt-ccttatagaggcttctaaatcacccctt------gaacagGTCGATAACAAGCTTTACATATACCTTGAGTATGTATCTGGAGGCTCCATACATAAACTTCTTCGAGAATATGGGCAATTTGGTGAACTAGTTATTCGTA

upper sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 4
ccacattctgcaga-attttacgaacttcacttttgcttg-cactcctgact-cctctgtttactttaa------aaataactatacactatccatttatt---caaaacagGTTGATGATAAACTTTATATATACCTGGAGTATGTTTCTGGTGGATCCATCCATAAACTACTCCAGGAGTATGGGCAATTTGGTGAACCTGCTATCCGCA
  |  || | |||| ||||   | || |  || ||   ||  |||    |||   || | | |    |       | || |||| |  || | | ||       |||  ||||| ||||| || || |||||||| ||||||||||| || ||||| || ||| ||||||| || || |||||||| |||||||||||   ||| || || |
gtaagttttacagatatttcttggacatttctgttctctgatactatcaactgtttcagctcaaccaagtcatgcacatgactagattctttactttcccctcccaattcagGTCGATGACAAGCTGTATATATATCTGGAGTATGTCTCCGGTGGTTCGATCTATAAACTTCTTCAAGAGTATGGACAATTTGGTGAGAATGCCATTCGTA

upper sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 4
----ccacatt-ctgcagaattttacgaacttcacttttgcttgcactcctgactcctctgtttactttaaaaataactatacactatccatttattcaaaacagGTTGATGATAAACTTTATATATACCTGGAGTATGTTTCTGGTGGATCCATCCATAAACTACTCCAGGAGTATGGGCAATTTGGTGAACCTGCTATCCGCA
    | | |||  ||||  || |     | |    ||  | | |||||  ||  |    | |||  |    | |||||    ||  ||   |  ||    ||||||||| ||| ||||||||||||||| |||||||||| |||||||| |||||| ||||||| || || || ||||| ||| |||||||||  || || || |
tttgcaatattgttgcatcatgtgcaatattatgtttcagttggcacttttggttatcgtcttttgtactgatataacctccca--attattccat---gaacagGTTGGTGACAAACTTTATATATACTTGGAGTATGTATCTGGTGGCTCCATCTATAAACTTCTTCAAGAATATGGCCAACTTGGTGAACTAGCAATTCGTA

upper sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S44_113V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------ccacattctgcagaattttacg-aacttcacttttgcttgcactcctgactcctctgtttactttaaaaataactatacactatccatttat------------tcaaaacagGTTGATGATAAACTTTATATATACCTGGAGTATGTTTCTGGTGGATCCATCCATAAACTACTCCAGGAGTATGGGCAATTTGGTGAACCTGCTATCCGCA
                   ||   |  |  |||| ||   || ||  |      |  |||||  | |  |||  || ||||       ||    |   |||    |              |     ||| | || ||||   | ||||||||  |||||||||||||||| ||||| ||||||||||| ||||| ||||||||    ||    || || |   | ||||
gtgcgacgcaaaccttatgcaccttttaatatttaacatgacgtctgtcacatgttaactcc--attattcttgttgctttggggtcgacatgtcgggatctgactgcgtcgttgggatcttctggcagTTGGAAGATAGGTTGTATATATATTTGGAGTATGTTTCTGGAGGATCAATCCATAAACTGCTCCAAGAGTATGGCGCTTTCAAAGAGCCAGTGGTGCGCA

upper sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S10_200V6.2 (Physcomitrella patens), 3'ss of exon 6
----------------ccacattctgcagaattt--tacgaacttcacttttgcttgcactcctgactcctct--gtttactttaaaaataactatacactatc-catttattcaaa----acagGTTGATGATAAACTTTATATATACCTGGAGTATGTTTCTGGTGGATCCATCCATAAACTACTCCAGGAGTATGGGCAATTTGGTGAACCTGCTATCCGCA
                 |||    |  |   ||    | ||| |         |||     | | | || ||   || |       | ||  | |      ||| |||   | | ||     ||| | || || |   | ||||||||  | ||||||||||| ||||| || ||||||||||||||||| ||||| ||    ||    || ||||   | ||||
gtacgatacaaacctttcacggcttttaattttcaccatgaagtgtgacacatcttaatgccatcattcttcctggtgtgtgggtgacatgtccaggtctaatcacatggttgcgaactttgcagTTGGAGGACAGGTTGTATATATATTTAGAGTATGTTTCAGGTGGGTCAATCCATAAACTACTCCAAGAGTACGGTGCTTTCAAAGAGCCTGTCGTACGCA

upper sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S8_299V6.1 (Physcomitrella patens), 3'ss of exon 6
---ccac--attctgcagaattttacgaacttcacttttgcttg--cactcctgactcctctgttt----actttaaaaat--aactatacac---------tatccatttattcaaaacagGTTGATGATAAACTTTATATATACCTGGAGTATGTTTCTGGTGGATCCATCCATAAACTACTCCAGGAGTATGGGCAATTTGGTGAACCTGCTATCCGCA
   ||||  | |||     |  ||  ||     | | |  || |   | |  ||       |||||     || |  ||||  ||   | |||         | |   ||   |      || | || || |   | ||||||||  | |||| ||| || |||||||| ||||||||||||||||| ||||||||    |||   ||||| | | | ||||
gtaccacgaaatctttgatagcttttgattcatagtgtgactggagtagtattgtgatgagtgttttgcggctgtggaaattgaatcgtccacatttgacgatgttgcttgggtttgtgtagTTGGAGGACAGGTTGTATATATATTTAGAGTTTGTCTCAGGTGGATCAATCCATAAACTACTCCAAGAGTATGGCGCTTTTAAAGAACCGGTTGTACGCA

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), 34 (downstream exon)
Score: 4

GAAATATTACTTCTGAATCGTCTGCAACATCCAAATATTGTACGATACTATGGATCTGAAATGgtataaattt ... ttcaaaacagGTTGATGATAAACTTTATATATACCTGGAGTATGTTTCTGGTGGATCCATCCATAAACTACTCCAGGAGTATGGGCAATTTGGTGAACCTGCTATCCGCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgactcctctgtttactttaaaaataactatacactatccatttattcaaaacagGTTGATGATAAACTTTATATATACCTGGAGTATGTTTCTGGTGGATCCATCCATAAACTACTCCAGGAGTATGGGCAATTTGGTGAACCTGCTATCCGCA
                     aaataac  putative branch site (score: 4)
                                         tttattc  putative PPT
           tttactttaaaaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccacattctgcagaattttacgaacttcacttttgcttgcactcctgactcctctgtttactttaaaaataactatacactatccatttattcaaaacagGTTGATGATAAACTTTATATATACCTGGAGTATGTTTCTGGTGGATCCATCCATAAACTACTCCAGGAGTATGGGCAATTTGGTGAACCTGCTATCCGCA

- - -ttctgca
- - - - - - - - - - - - - - - - -tgcttgc
- - - - - - - - - - - - - - - - - - - - -ctcctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaata