Skip to another splice site:
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAGgtatttctttatcattcggagaaaatttgcttttctagttccataatctcattaattttcatggcctattctctgcag

Basic information

species Oryza sativa
transcript LOC_Os02g21250.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g21250.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G314679_T08 (Zea mays), 5'ss of exon 3
CATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAGgtattt-ctttatcattcggagaaaatttgcttttctagttccata-atctcattaattttcatggcctattctctgcag
 || || ||||||||||||||||| |||||||| || |||||||||||||||||||||||||||||||  ||||| |||||||||||| || |||||||  ||  |  | | |     |||  ||| ||||  ||||||  |||    || |||  ||| |||||
AATCATCCTGGAAACAGATGCAAACACCATTGCTGGTAAGGTTGCAACCAATGCTGTTGATGGTTCTGTGCCCTTTTCTGAGCAGgtaattactttatccatcctatcacaata---cttcaggttgcatatgtctcat-gattgctgtgacctgctctgtgcag
















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|88517568|gb|CI445222.1|CI445222
EST:     GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAG                         ACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
genomic: GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAGgtatttcttt ... ttctctgcagACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
EST: gi|89198260|gb|CI015649.1|CI015649
EST:     GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAG                         ACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
genomic: GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAGgtatttcttt ... ttctctgcagACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
EST: gi|8955503|gb|BE229309.1|BE229309
EST:     GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAG                         ACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
genomic: GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAGgtatttcttt ... ttctctgcagACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
EST: gi|86506579|gb|CI149212.1|CI149212
EST:     GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAG                         ACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
genomic: GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAGgtatttcttt ... ttctctgcagACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
EST: gi|88485774|gb|CI423045.1|CI423045
EST:     GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAG                         ACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
genomic: GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAGgtatttcttt ... ttctctgcagACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
EST: gi|88281898|gb|CI403294.1|CI403294
EST:     GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAG                         ACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
genomic: GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAGgtatttcttt ... ttctctgcagACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
EST: gi|88277852|gb|CI398654.1|CI398654
EST:     GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAG                         ACGATATCTCAGGCTTTAGCCACTGGTAGGGAGCACCTTGCAAGATCTCTG
genomic: GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAGgtatttcttt ... ttctctgcagACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
EST: gi|86831266|gb|CI297535.1|CI297535
EST:     GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAG                         ACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACC
genomic: GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAGgtatttcttt ... ttctctgcagACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACC
EST: gi|86526502|gb|CI166708.1|CI166708
EST:     GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAG                         ACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
genomic: GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAGgtatttcttt ... ttctctgcagACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
EST: gi|88277867|gb|CI398669.1|CI398669
EST:     GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAG                         ACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
genomic: GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAGgtatttcttt ... ttctctgcagACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
EST: gi|88511151|gb|CI438657.1|CI438657
EST:     GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAG                         ACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
genomic: GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAGgtatttcttt ... ttctctgcagACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
EST: gi|88277106|gb|CI397908.1|CI397908
EST:     AAGGGTTGCAACCAATGGCTGTTGATGGTTCTGCCCCCTTCTGTGAGCAG                         ACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
genomic: AAGG-TTGCAACCAATG-CTGTTGATGGTTCTGCCCCCTTCTCTGAGCAGgtatttcttt ... ttctctgcagACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
EST: gi|88520651|gb|CI448305.1|CI448305
EST:     GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAG                         ACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
genomic: GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAGgtatttcttt ... ttctctgcagACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
EST: gi|88547773|gb|CI478095.1|CI478095
EST:     GAAGGGTGCAACCAATGGCTGTTGATGTTTCTGCCCCCTTCTCTGAGCAG                         ACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
genomic: GAAGGTTGCAACCAAT-GCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAGgtatttcttt ... ttctctgcagACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
EST: gi|88243238|gb|CI244360.1|CI244360
EST:     GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAG                         ACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
genomic: GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAGgtatttcttt ... ttctctgcagACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
EST: gi|88483987|gb|CI421258.1|CI421258
EST:     GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAG                         ACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
genomic: GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAGgtatttcttt ... ttctctgcagACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
EST: gi|86522432|gb|CI162638.1|CI162638
EST:     GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAG                         ACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
genomic: GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAGgtatttcttt ... ttctctgcagACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
EST: gi|117248583|gb|CT862782.1|CT862782
EST:     GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAG                         ACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
genomic: GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAGgtatttcttt ... ttctctgcagACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
EST: gi|88964103|gb|CI033020.1|CI033020
EST:     GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAG                         ACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCA-GATCTCTG
genomic: GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAGgtatttcttt ... ttctctgcagACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
EST: gi|88281682|gb|CI403078.1|CI403078
EST:     GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAG                         ACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
genomic: GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAGgtatttcttt ... ttctctgcagACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
EST: gi|88491507|gb|CI428779.1|CI428779
EST:     GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAG                         ACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG
genomic: GGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAGgtatttcttt ... ttctctgcagACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTG

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: 67 (upstream exon), 74 (downstream exon)
Score: 30

CATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAGgtatttcttt ... ttctctgcagACGATATCTCAGGCTTTAGCCACTGCTAGGGAGCACCTTGCAAGATCTCTGCTCAAGTAAATCATTTATCTTTTGACTCCTTAAAACTTCTCTGCGTTGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAGgtatttctttatcattcggagaaaatttgcttttctagttccataatctcattaattttcatggcctattctctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG