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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGAAGCTAGCGATCACACGTGATAAATACAGACAGACCAGATTAGATCAGTACAAGAATTATGAGAACATGCCTAATTCTGGAGAAGCAGCCGCAAAGgtgcgtccttttgaaagctcactgtgtagaactgtctgtgtttgtgcttgacagttgacacttgtgtacag

Basic information

species Oryza sativa
transcript LOC_Os02g48964.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g48964.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G109039_T03 (Zea mays), 5'ss of exon 3
GGAGAAGCTAGCGATCACACGTGATAAATACAGACAGACCAGATTAGATCAGTACAAGAATTATGAGAACATGCCTAATTCTGGAGAAGCAGCCGCAAAGgtgcg--------tccttttgaaagctca-ctgtgtagaactgtctgt--gtttgtgcttgacagttgacacttgtgtacag
|||| || ||   || || ||| | |||||||||||| |||||||||| |||||||| |||||||||||  | ||||| |||||||||| |||    |||||  |        |||| ||| ||| |   || |||| || | ||| |  |  |||| |||||| |||   | |  | | ||
GGAGCAGATAAACATAACCCGTAAAAAATACAGACAGTCCAGATTAGAACAGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctcttactcctgttggaagtttggctttgtaaaattttctatccgcatgtgtttgacacttg---ccttggaatag

upper sequence: LOC_Os02g48964.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G048045_T01 (Zea mays), 5'ss of exon 3
GGAGAAGCTAGCGATCACACGTGATAAATACAGACAGACCAGATTAGATCAGTACAAGAATTATGAGAACATGCCTAATTCTGGAGAAGCAGCCGCAAAGgtgcgtccttttgaaagctcactgtgtagaactgtctgtgtttgtgcttgaca----gttgacacttgtgtacag----
|||| |||||   || || ||| | ||||| |||||| |||||||||| |||||||| |||||||||||  | ||||| |||||||||| |||    |||||  | ||| ||      |   |  ||  | || | |   |||    |  |||    ||||||| |||| |        
GGAGCAGCTAAACATAACCCGTAAAAAATATAGACAGTCCAGATTAGAACAGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttg-cctcttactctttttgtaagttaagctttgtaaattttctatccacatgttgttgacaattgtcttggaatag

upper sequence: LOC_Os02g48964.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA15G12980.2 (Glycine max), 5'ss of exon 3
GGAGAAGCTAGCGATCACACGTGATAAATACAGACAGACCAGATTAGATCAGTACAAGAATTATGAGAACATGCCTAATTCTGGAGAAGCAGCCGCAAAGgtg----cgtccttttgaaagctca-------ctgtgtagaactgtc--------tgtgt---ttgtgcttgacagttgacacttgtgtacag
||| | | |    || |  ||||| ||||| ||||| || ||| |||| ||||||||||||||||| ||||| ||  | || || |||    | |  |||||      ||  |  | | || |          ||  |||   | |         |||||   || | |||     |   | ||||| |||||
GGATAGGTTGAGCATTAGTCGTGAGAAATATAGACAAACTAGACTAGACCAGTACAAGAATTATGAAAACATACCACAATCAGGGGAAATGTCAGAGAAGgtaaatatgttttgcttagagtttggatgcatttgattagtgattttgaaaatattgtgtaccttatactttttcttcttctcttgtctacag

upper sequence: LOC_Os02g48964.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT3G13340.2 (Arabidopsis thaliana), 5'ss of exon 3
GGAGAAGCTAGCGATCACACGTGATAAATACAGACAGACCAGATTAGATCAGTACAAGAATTATGAGAACATGCCTAATTCTGGAGAAGCAGCCGCAAAGgtgcg-----tccttttgaaagctcactgtgtagaactgtctgtgtttgtgcttgacagttgacac----ttgtgtacag------
||| |  ||    ||  |  | || ||||||||||| || |||||||| ||||| ||||||||||| ||  | ||||||||||||||| || | | ||||||  |     |    |   |  |||  | ||||  | |||    ||| |     | ||  | | ||    || ||||  |      
GGACAGACTTAATATTTCTAGAGAGAAATACAGACAAACTAGATTAGAACAGTATAAGAATTATGAAAATGTCCCTAATTCTGGAGAATCATCAGAAAAGgtaagggttatatcctctgatcctctatttgtattagtgttcaggttagc-tcagtcacctaatacatcattttgtatggattcag

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|29671102|gb|CB667377.1|CB667377
EST:     AGTACAAGAATTATGAGAACATGCCTAATTCTGGAGAAGCAGCCGCAAAG                         GAATGCAAACCGACTGAAAAAGGCGGGATGTATTATGAATTTAGGCGAAAT
genomic: AGTACAAGAATTATGAGAACATGCCTAATTCTGGAGAAGCAGCCGCAAAGgtgcgtcctt ... ttgtgtacagGAATGCAAACCGACTGAAAAAGGCGGGATGTATTATGAATTTAGGCGAAAT
EST: gi|58685929|gb|CK074616.1|CK074616
EST:     AGTACAAGAATTATGAGAACATGCCTAATTCTGGAGAAGCAGCCGCAAAG                         GAATGCAAACCGACTGCAAAAGGCGGGATGTATTATGAATTTAGGCGAAAT
genomic: AGTACAAGAATTATGAGAACATGCCTAATTCTGGAGAAGCAGCCGCAAAGgtgcgtcctt ... ttgtgtacagGAATGCAAACCGACTGAAAAAGGCGGGATGTATTATGAATTTAGGCGAAAT
EST: gi|218482945|gb|FG948107.1|FG948107
EST:     AGTACAAGAATTATGAGAACATGCCTAATTCTGGAGAAGCAGCCGCAAAG                         GAATGCAAACCGACTGCAAAAGGCGGGATGTATTATGAATTTAGGCGAAAT
genomic: AGTACAAGAATTATGAGAACATGCCTAATTCTGGAGAAGCAGCCGCAAAGgtgcgtcctt ... ttgtgtacagGAATGCAAACCGACTGAAAAAGGCGGGATGTATTATGAATTTAGGCGAAAT
EST: gi|218504711|gb|FG953266.1|FG953266
EST:     AGTACAAGAATTATGAGAACATGCCTAATTCTGGAGAAGCAGCCGCAAAG                         GAATGCAAACCGACTGCAAAAGGCGGGATGTATTATGAATTTAGGCGAAAT
genomic: AGTACAAGAATTATGAGAACATGCCTAATTCTGGAGAAGCAGCCGCAAAGgtgcgtcctt ... ttgtgtacagGAATGCAAACCGACTGAAAAAGGCGGGATGTATTATGAATTTAGGCGAAAT
EST: gi|29619648|gb|CB624660.1|CB624660
EST:     AGTACAAGAATTATGAGAACATGCCTAATTCTGGAGAAGCAGCCGCAAAG                         GAATGCAAACCGACTGCAAAAGGCGGGATGTATTATGAATTTAGGCGAAAT
genomic: AGTACAAGAATTATGAGAACATGCCTAATTCTGGAGAAGCAGCCGCAAAGgtgcgtcctt ... ttgtgtacagGAATGCAAACCGACTGAAAAAGGCGGGATGTATTATGAATTTAGGCGAAAT
EST: gi|29672638|gb|CB668913.1|CB668913
EST:     AGTACAAGAATTATGAGAACATGCCTAATTCTGGAGAAGCAGCCGCAAAG                         GAATGCAAACCGACTGAAAAAGGCGGGATGTATTATGAATTTACGCGAAAT
genomic: AGTACAAGAATTATGAGAACATGCCTAATTCTGGAGAAGCAGCCGCAAAGgtgcgtcctt ... ttgtgtacagGAATGCAAACCGACTGAAAAAGGCGGGATGTATTATGAATTTAGGCGAAAT

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: 75 (upstream exon), 74 (downstream exon)
Score: 37

GGAGAAGCTAGCGATCACACGTGATAAATACAGACAGACCAGATTAGATCAGTACAAGAATTATGAGAACATGCCTAATTCTGGAGAAGCAGCCGCAAAGgtgcgtcctt ... ttgtgtacagGAATGCAAACCGACTGAAAAAGGCGGGATGTATTATGAATTTAGGCGAAATACTAGATCAGTAAAATCAACTATACTACATTTTCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGAAGCTAGCGATCACACGTGATAAATACAGACAGACCAGATTAGATCAGTACAAGAATTATGAGAACATGCCTAATTCTGGAGAAGCAGCCGCAAAGgtgcgtccttttgaaagctcactgtgtagaactgtctgtgtttgtgcttgacagttgacacttgtgtacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG