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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcgcctgcccctcgtatgcttgtgtttcatatcccatgttctatatatgaaaagaagttctgacgatctgtttcttccagCTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAG

Basic information

species Oryza sativa
transcript LOC_Os05g45310.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g45310.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G101413_T01 (Zea mays), 3'ss of exon 4
gtaagcgcctgcccctcgtatgcttgtgtttcatatcccatgt-tctatatatgaaaagaagttc--tgacgatctgtttcttccagCTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAG
|||||    |  |  | ||||| ||  || |  |||||||  | | | |||  |||  |  || |  | | | ||| | |||| |||||||| ||||||||||||| ||||||||||| ||||| |||||||| ||||| |||||||||||
gtaagt-tgtcacttttgtatggtttagtgttctatcccacatctttttatcagaattgttgtgcactaatggtctttctctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG

upper sequence: LOC_Os05g45310.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G408989_T03 (Zea mays), 3'ss of exon 3
gtaagcgcctgcccctcgtatgcttgtgtttcatatcccatgttctatatatgaaaagaagttc--tgacgatctgtttcttccagCTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAG
|||||    |  |  | ||||| |   || |  |||||||  |  | | |  |||  |  || |  | | | ||| |||||| |||||||| ||||||||||||| ||||||||||| ||||| |||||||| ||||| |||||||||||
gtaagt-tgtcacttttgtatggtatagtgttttatcccaaatgttttctcagaactgctgtccactaatggtctatttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG

upper sequence: LOC_Os05g45310.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT1G29330.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagcgcctgcccctcgtatgct---tgtgtttcatatcccatgttctatatatgaaaagaagttctgacgatctgtttcttccagCTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAG
||||        |         ||   ||  ||| | | |   |||| |   |        | ||| |    |  |   | ||||||||||  |  ||||| | |||||||||||||| ||||||||||||||||||||||| | | ||||
gtaatgtttcaacaaagaagcactaaatgcatttta-accatttgtttttcctcaatgctaatgttttacgtaaatccattttccagCTTGTGTGTCTGGTCTTGTCCAAACAGCTCTCTATGCGGATTTCTTCTACTACTACTACATAAG

upper sequence: LOC_Os05g45310.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv10s0003g01700.t01 (Vitis vinifera), 3'ss of exon 4
gtaagc---gcctgcccctcgtatgcttg----tgtttcatatcccatgttctatatatgaaaagaagttctgacgatctgtttcttccagCTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAG
|||||    | |      |   | |        | |||  |  ||  || |  || |||    |     |||     ||| | | |  |||| || ||| ||||| ||||||||||||| |||||||| ||||||||||||||||| ||  | ||
gtaagttgtgtcaataattaaaaagagcaacatttttttgtggccattgatgcatgtattctgaccgcatctttttttctttgtttatcagCCTGCATTTCTGGTCTGGTCCAAACAGCACTTTATGCAGATTTCTTCTACTACTACTTTATTAG

upper sequence: LOC_Os05g45310.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ15071 (Selaginella moellendorffii), 3'ss of exon 4
gtaagcgcctgcccctcgtatgcttgtgtttcatatcccatgttctatatatgaaaa---gaagttctgacgatctgtttcttccagCTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAG
                 ||  | || | ||  |  ||    ||| | |   ||||     ||  ||||   |      ||||  ||||||||||  | ||    || ||||||||||||||||| |||||||||||||||||| |    ||
-----------------gtgagtttcttttaaaattctagcgttttgtg-gtgaaggtctgattttcttgtggcacaattct--cagCTTGGATCTCCGGGGCAGTACAAACAGCTCTTTATGCTGATTTCTTCTACTACTATATTCACAG

upper sequence: LOC_Os05g45310.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ37620 (Selaginella moellendorffii), 3'ss of exon 4
gtaagcgcctgcccctcgtatgcttgtgtttcatatccca-tgttctatatatgaaaa---gaagttctgacgatctgtttcttccagCTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAG
                 |  |  |  | ||| |  | | |  ||| | |   ||||     ||  ||||   |      ||||  ||||||||||  | ||    || ||||||||||||||||| |||||||||||||||||| |    ||
---------------gtgagttttcttttttaaagttctagcgttttgtg-gtgaaggtctgattttcttgtggcacaattct--cagCTTGGATCTCCGGGGCAGTACAAACAGCTCTTTATGCTGATTTCTTCTACTACTATATTCACAG

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|88958435|gb|CI095952.1|CI095952
EST:     AAACTGGATTTACCGTTACTTCACTGAGGGTCACCACAGCAGATGGATCC                         CTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACT
genomic: AAACTGGATTTACCGTTACTTCACTGAGGGTCACCACAGCAGATGGATCCgtaagcgcct ... tttcttccagCTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACT
EST: gi|87018599|gb|CI252353.1|CI252353
EST:     AAACTGGATTTACCGTTACTTCACTGAGGGTCACCACAGCAGATGGATCC                         CTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACT
genomic: AAACTGGATTTACCGTTACTTCACTGAGGGTCACCACAGCAGATGGATCCgtaagcgcct ... tttcttccagCTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACT
EST: gi|33685592|gb|CF313831.1|CF313831
EST:     GGGTCACCACAGCAGATGGATCC                         CTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACT
genomic: GGGTCACCACAGCAGATGGATCCgtaagcgcct ... tttcttccagCTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACT
EST: gi|89162171|gb|CI103707.1|CI103707
EST:     AAACTGGATTTACCGTTACTTCACTGAGGGTCACCACAGCAGATGGATCC                         CTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACT
genomic: AAACTGGATTTACCGTTACTTCACTGAGGGTCACCACAGCAGATGGATCCgtaagcgcct ... tttcttccagCTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACT
EST: gi|88850836|gb|CI096226.1|CI096226
EST:     GAGGGTCACCACAGCAGATGGATCC                         CTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTAGT
genomic: GAGGGTCACCACAGCAGATGGATCCgtaagcgcct ... tttcttccagCTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACT
EST: gi|88242714|gb|CI242563.1|CI242563
EST:     AAACTGGATTTACCGTTACTTCACTGAGGGTCACCACAGCAGATGGATCC                         CTTGGATTGCTGGTTTGGTCCAAACGGCTCTTTATGCGGATTTCTTCTACT
genomic: AAACTGGATTTACCGTTACTTCACTGAGGGTCACCACAGCAGATGGATCCgtaagcgcct ... tttcttccagCTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACT
EST: gi|88241835|gb|CI241684.1|CI241684
EST:     AAACTGGATTTACCGTTACTTCACTGAGGGTCACCACAGCAGATGGATCC                         CTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACT
genomic: AAACTGGATTTACCGTTACTTCACTGAGGGTCACCACAGCAGATGGATCCgtaagcgcct ... tttcttccagCTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACT
EST: gi|86257989|gb|CI064342.1|CI064342
EST:     AAACTGGATTTACCGTTACTTCACTGAGGGTCACCACAGCAGATGGATCC                         CTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACT
genomic: AAACTGGATTTACCGTTACTTCACTGAGGGTCACCACAGCAGATGGATCCgtaagcgcct ... tttcttccagCTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACT
EST: gi|86434098|gb|CI094441.1|CI094441
EST:     AAACTGGATTGACCGTTACTTCACTGAGGGTCACCACAGCAGATGGATCC                         CTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACT
genomic: AAACTGGATTTACCGTTACTTCACTGAGGGTCACCACAGCAGATGGATCCgtaagcgcct ... tttcttccagCTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACT
EST: gi|87034306|gb|CI188930.1|CI188930
EST:     ACCACAGCAGATGGATCC                         CTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACT
genomic: ACCACAGCAGATGGATCCgtaagcgcct ... tttcttccagCTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACT

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: 71 (upstream exon), 75 (downstream exon)
Score: 13

GGCCTACCGTGCATTTTACATCCTAAACTGGATTTACCGTTACTTCACTGAGGGTCACCACAGCAGATGGATCCgtaagcgcct ... tttcttccagCTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatatcccatgttctatatatgaaaagaagttctgacgatctgtttcttccagCTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAG
                                ttctgac  putative branch site (score: 13)
                                         tctgtttcttcc  putative PPT
             ttctatatatgaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcgcctgcccctcgtatgcttgtgtttcatatcccatgttctatatatgaaaagaagttctgacgatctgtttcttccagCTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC