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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgcctccgctcccccctccgccgcctgctccattcgccgctacgggccccgccgccgccgcctagggttttgacggggtttcgttttgctcggggggcggccttccgcatcgcagCACGCGGCGGACTACGAGGCGATCATATCGGCCGTGAAGGGGCAGAGCGTGAAGGCGAAGCAGCTCGCGGCGCAGCTCATCCCCCGCTTCTTCCGGAGCT

Basic information

species Oryza sativa
transcript LOC_Os02g20930.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g20930.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G059039_T01 (Zea mays), 3'ss of exon 1
gtgcgcctccgctcccccctccgccgcctgctccattcgccgctacgggccccgccgccgccgcctagggttttgac-ggggtttcgttttgctcggggggcg-gccttccgcatcgcagCACGCGGCGGACTACGAGGCGATCATATCGGCCGTGAAGGGGCAGAGCGTGAAGGCGAAGCAGCTCGCGGCGCAGCTCATCCCCCGCTTCTTCCGGAGCT
                            |||  |     || |  ||      |     || |    | |||  | |  |||||| |  |  |  || |     |  ||| | || |||||| |||||||||||||||||||| ||  | || |||||||| ||||| |  ||||||||||||||||| |||||||| |||||| | |||||||||||||
---------------------------gtgcctcgaatccctcc-cgtagtttgttaaggctggtctgcgttcaggctagggttttgggtgacgtggagttttcggtttcggaattgcagCATGCGGCGGACTACGAGGCGATTATTGCAGCGGTGAAGGGACAGAGTGCCAAGGCGAAGCAGCTCGCAGCGCAGCTTATCCCCAGGTTCTTCCGGAGCT

upper sequence: LOC_Os02g20930.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G014577_T01 (Zea mays), 3'ss of exon 1
gtgcgcctccgctcccccctccgccgcctgctccattcgccgctacgggccccgccgccgccgcctagggttttgac-ggggtttcgttttgctcggggggcg-gccttccgcatcgcagCACGCGGCGGACTACGAGGCGATCATATCGGCCGTGAAGGGGCAGAGCGTGAAGGCGAAGCAGCTCGCGGCGCAGCTCATCCCCCGCTTCTTCCGGAGCT
                            |||| |   |||     | |     |  |  ||||    | |||  | |  |||||| |  |  |  ||||     |  ||| | || |||||  |||||||||||||||||||| ||  | || |||||||||||||| || ||||||||||||||||| ||||||||||||||  | |||||||||||||
---------------------------gtgcttc-cccgctctcccagattttgttgaggccggtccgtgttcaggctagggttttgagtgacgtggggttttcggtttcggaattgcagCTTGCGGCGGACTACGAGGCGATTATTGCAGCAGTGAAGGGGCAGAGTGTCAAGGCGAAGCAGCTCGCAGCGCAGCTCATCCCGAGGTTCTTCCGGAGCT

upper sequence: LOC_Os02g20930.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA13G24090.2 (Glycine max), 3'ss of exon 1
gtgcgcctccgctcccccctccgc-cgcctgctccattcgccgctacgggccccgccgccgccgcctagggttttgacggggtttcgttttgctcggggggcggccttccgcatcgcagCACGCGGCGGACTACGAGGCGATCATATCGGCCGTGAAGGGGCAGAGCGTGAAGGCGAAGCAGCTCGCGGCGCAGCTCATCCCCCGCTTCTTCCGGAGCT---
          | ||     | ||| |  |   |   ||    | |  ||     |  |     |  | |  ||      |||||| |  ||| |        |   ||  |    |||| | | |  ||| ||| |||  ||||||   || | ||||  |   || |||||||||||||||||||| |||||||| || |||   ||||||  |  ||   
----------gttcggaatttcgctcttcaaattgttttagggttttggattgtgatgttcgagtttggaatt-----agggttttgaattgttttt----tgttgttttg----gcagAATGTGCAGGATTACCAGGGAATCATAGATGCGGCGAAGACG---AGTGTGAAGGCGAAGCAGCTCGCCGCGCAGCTGATTCCCAAGTTCTTCAAGTTCTTCC

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|29640658|gb|CB645667.1|CB645667
EST:     GGCTCTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAAGGACAAGTCCCAG                         CACGCGGCGGACTACGAGGCGATCATATCGGCCGTGAAGGGGCAGAGCGTG
genomic: GGCTCTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAAGGACAAGTCCCAGgtgcgcctcc ... cgcatcgcagCACGCGGCGGACTACGAGGCGATCATATCGGCCGTGAAGGGGCAGAGCGTG
EST: gi|86849950|gb|CI301813.1|CI301813
EST:     GGCTCTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAAGGACAAGTCCCAG                         CACGCGGCGGACTACGAGGCGATCATATCGGCCGTGAAGGGGCAGAGCGTG
genomic: GGCTCTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAAGGACAAGTCCCAGgtgcgcctcc ... cgcatcgcagCACGCGGCGGACTACGAGGCGATCATATCGGCCGTGAAGGGGCAGAGCGTG
EST: gi|29615477|gb|CB620489.1|CB620489
EST:     GGCTCTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAAGGACAAGTCCCAG                         CACGCGGCGGACTACGAGGCGATCATATCGGCCGTGAAGGGGCAGAGCGTG
genomic: GGCTCTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAAGGACAAGTCCCAGgtgcgcctcc ... cgcatcgcagCACGCGGCGGACTACGAGGCGATCATATCGGCCGTGAAGGGGCAGAGCGTG
EST: gi|29662176|gb|CB658451.1|CB658451
EST:     GGCTCTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAAGGACAAGTCCCAG                         CACGCGGCGGACTACGAGGCGATCATATCGGCCGTGAAGGGGCAGAGCGTG
genomic: GGCTCTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAAGGACAAGTCCCAGgtgcgcctcc ... cgcatcgcagCACGCGGCGGACTACGAGGCGATCATATCGGCCGTGAAGGGGCAGAGCGTG
EST: gi|29635298|gb|CB640307.1|CB640307
EST:     GGCTCTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAAGGACAAGTCCCAG                         CACGCGGCGGACTACGAGGCGATCATATCGGCCGTGAAGGGGCAGAGCGTG
genomic: GGCTCTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAAGGACAAGTCCCAGgtgcgcctcc ... cgcatcgcagCACGCGGCGGACTACGAGGCGATCATATCGGCCGTGAAGGGGCAGAGCGTG

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: 17 (upstream exon), 59 (downstream exon)
Score: 1

CTCCCCCGCCGCCATGGCCGCCTCCGACGCCGACGCCGCGGAGGTCGAGCGGCTCTACGAGCTCGGCGAGCGCCTCTCCTCCGCCAAGGACAAGTCCCAGgtgcgcctcc ... cgcatcgcagCACGCGGCGGACTACGAGGCGATCATATCGGCCGTGAAGGGGCAGAGCGTGAAGGCGAAGCAGCTCGCGGCGCAGCTCATCCCCCGCTTCTTCCGGAGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctagggttttgacggggtttcgttttgctcggggggcggccttccgcatcgcagCACGCGGCGGACTACGAGGCGATCATATCGGCCGTGAAGGGGCAGAGCGTGAAGGCGAAGCAGCTCGCGGCGCAGCTCATCCCCCGCTTCTTCCGGAGCT
       ttttgac  putative branch site (score: 1)
                                        ccttccgc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgcctccgctcccccctccgccgcctgctccattcgccgctacgggccccgccgccgccgcctagggttttgacggggtttcgttttgctcggggggcggccttccgcatcgcagCACGCGGCGGACTACGAGGCGATCATATCGGCCGTGAAGGGGCAGAGCGTGAAGGCGAAGCAGCTCGCGGCGCAGCTCATCCCCCGCTTCTTCCGGAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT