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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTGgtatgtatgcacactgatcgatccatccatccatcccatgggatgtggcacaccaacaagtgtcaattctccacaagtacactagcttgacacttgcatg...

Basic information

species Oryza sativa
transcript LOC_Os01g02120.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g02120.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G059358_T02 (Zea mays), 5'ss of exon 1
--------------------------------------ATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTGgtatgtatgcacactgatcgatccatccatccatc----ccatgggatgtggcacaccaacaagtgtcaattctccacaagtacactagcttgacacttgcatg
                                      |||||||||||||| || || |||||||| ||||||||  ||||||||||||  ||||||||||||| |     || |   | | | | | |   ||     |  |    |||   | ||||  |||       ||  | |  |  ||   ||   || |      
ATGCATGGATGGATTGCACAACTTGCTGCGTGTCGCAGATCATGACGGACCCAGATGCGCCTAGCCCCAGCGACCCGACCATGAGGGAGTACCTCCACTGgtatgaactgctacagcatgctacgtacttgtgtcatgatctggcagcgtgtgtcgccaaagagtagatgcactgtatatttgtacgtactactcattaa----

upper sequence: LOC_Os01g02120.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G021614_T01 (Zea mays), 5'ss of exon 2
ATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTGgtatgtatgcacactgat--cgatccatccatccatcccatgggatgtg-gcacaccaacaag-tgtcaattctc-cacaagtacactagcttgacacttgcatg---------------------------------------------------------------------------------------------
|||||||||||||| || || |||||||| ||| ||||  ||||||||||||  ||||||||||| ||||  ||     |   ||| |  | | | | |    |  | |||  ||     |  |  || ||     |  | |  || |   |  ||   |  |                                                                                                 
ATCATGACGGACCCCGATGCGCCTAGCCCCAGCAACCCGACCATGAGGGAGTACCTCCACTGgtacgtatataccgcagtactgatactactagctagctagcgctacgtgtacatgtgtatgatctggcagcatgcatatatatatatatgtatgcgtccagtccagctgatgatgcctaattttttttctcttgccacacatgtacgtatgcatgtacgtttctccttgcgtcaattcgcggcggcgtacgtgtgcag

upper sequence: LOC_Os01g02120.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G059358_T01 (Zea mays), 5'ss of exon 2
ATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTGgtatgtatgcacactgatcgatccatccatccatc----ccatgggatgtggcacaccaacaagtgtcaattctccacaagtacactagcttgacacttgcatg
|||||||||||||| || || |||||||| ||||||||  ||||||||||||  ||||||||||||| |     || |   | | | | | |   ||     |  |    |||   | ||||  |||       ||  | |  |  ||   ||   || |      
ATCATGACGGACCCAGATGCGCCTAGCCCCAGCGACCCGACCATGAGGGAGTACCTCCACTGgtatgaactgctacagcatgctacgtacttgtgtcatgatctggcagcgtgtgtcgccaaagagtagatgcactgtatatttgtacgtactactcattaa----

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|218495548|gb|FG956083.1|FG956083
EST:     CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTG                         GATCGTGGTTAACATACCGGGGGGAACAGATGCATCTAAAG
genomic: CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTGgtatgtatgc ... tcttgcacagGATCGTGGTTAACATACCGGGGGGAACAGATGCATCTAAAG
EST: gi|218495786|gb|FG965856.1|FG965856
EST:     CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTG                         GATCGTGGTTAACATACCGGGGGGAACAGATGCATCTAAAG
genomic: CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTGgtatgtatgc ... tcttgcacagGATCGTGGTTAACATACCGGGGGGAACAGATGCATCTAAAG
EST: gi|218479392|gb|FG964734.1|FG964734
EST:     CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTG                         GATCGTGGTTAACATACCGGGGGGAACAGATGCATCTAAAG
genomic: CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTGgtatgtatgc ... tcttgcacagGATCGTGGTTAACATACCGGGGGGAACAGATGCATCTAAAG
EST: gi|88585362|gb|CI702989.1|CI702989
EST:     CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTG                         GATCGTGGTTA
genomic: CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTGgtatgtatgc ... tcttgcacagGATCGTGGTTA
EST: gi|218487396|gb|FG969251.1|FG969251
EST:     CCGGACGCACCTAGCCCTAGCGACCCGTCCATGAGGGAGTTTCTCCACTG                         GATCGTGGTTAACATACCGGGGGGAACAGATGCATCTAAAG
genomic: CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTGgtatgtatgc ... tcttgcacagGATCGTGGTTAACATACCGGGGGGAACAGATGCATCTAAAG
EST: gi|66914461|gb|CX101309.1|CX101309
EST:     CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTG                         GATCGTGGTTAACATACCGGGGGGAACAGATGCATCTAAAG
genomic: CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTGgtatgtatgc ... tcttgcacagGATCGTGGTTAACATACCGGGGGGAACAGATGCATCTAAAG
EST: gi|218499952|gb|FG964309.1|FG964309
EST:     CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTG                         GATCGTGGTTAACATACCGGGGGGAACAGATGCATCTAAAG
genomic: CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTGgtatgtatgc ... tcttgcacagGATCGTGGTTAACATACCGGGGGGAACAGATGCATCTAAAG
EST: gi|218486167|gb|FG951231.1|FG951231
EST:     CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTG                         GATCGTGGTTAACATACCGGGGGGAACAGATGCATCTAAAG
genomic: CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTGgtatgtatgc ... tcttgcacagGATCGTGGTTAACATACCGGGGGGAACAGATGCATCTAAAG
EST: gi|218495072|gb|FG958772.1|FG958772
EST:     CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTG                         GATCGTGGTTAACATACCGGGGGGAACAGATGCATCTAAAG
genomic: CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTGgtatgtatgc ... tcttgcacagGATCGTGGTTAACATACCGGGGGGAACAGATGCATCTAAAG
EST: gi|88388601|gb|CI683383.1|CI683383
EST:     CCGGACGCACCTACCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTG                         GATCGTGGTTAACATACCGGGGGGAACAGATGCATCTAAAGGT
genomic: CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTGgtatgtatgc ... tcttgcacagGATCGTGGTTAACATACCGGGGGGAACAGATGCATCTAAAGGT
EST: gi|88592180|gb|CI710265.1|CI710265
EST:     CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTG                         GATCGTGGTTAACATACCG
genomic: CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTGgtatgtatgc ... tcttgcacagGATCGTGGTTAACATACCG
EST: gi|218484094|gb|FG956003.1|FG956003
EST:     CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTG                         GATCGTGGTTAACATACCGGGGGGAACAGATGCATCTAAAG
genomic: CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTGgtatgtatgc ... tcttgcacagGATCGTGGTTAACATACCGGGGGGAACAGATGCATCTAAAG
EST: gi|218483444|gb|FG953420.1|FG953420
EST:     CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTG                         GATCGTGGTTAACATACCGGGGGGAACAGATGCATCTAAAG
genomic: CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTGgtatgtatgc ... tcttgcacagGATCGTGGTTAACATACCGGGGGGAACAGATGCATCTAAAG
EST: gi|218482064|gb|FG957113.1|FG957113
EST:     CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTG                         GATCGTGGTTAACATACCGGGGGGAACAGATGCATCTAAAG
genomic: CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTGgtatgtatgc ... tcttgcacagGATCGTGGTTAACATACCGGGGGGAACAGATGCATCTAAAG
EST: gi|88352680|gb|CI678699.1|CI678699
EST:     CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTG                         GATCGTGGTTAACATACCGGGGGGAACAGATGCATCTAAAG
genomic: CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTGgtatgtatgc ... tcttgcacagGATCGTGGTTAACATACCGGGGGGAACAGATGCATCTAAAG
EST: gi|218479589|gb|FG967768.1|FG967768
EST:     CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTG                         GATCGTGGTTAACATACCGGGGGGAACAGATGCATCTAAAG
genomic: CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTGgtatgtatgc ... tcttgcacagGATCGTGGTTAACATACCGGGGGGAACAGATGCATCTAAAG
EST: gi|218491779|gb|FG963455.1|FG963455
EST:     CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTG                         GATCGTGGTTAACATACCGGGGGGAACAGATGCATCTAAAG
genomic: CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTGgtatgtatgc ... tcttgcacagGATCGTGGTTAACATACCGGGGGGAACAGATGCATCTAAAG
EST: gi|218490459|gb|FG959442.1|FG959442
EST:     CCGGACGCAGCTAGCCCTAGCGAACCATCCATGAGGGAGTTACTCCACTG                         GATCGTGGTTAACATACCGGGGGGAACAGATG
genomic: CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTGgtatgtatgc ... tcttgcacagGATCGTGGTTAACATACCGGGGGGAACAGATG
EST: gi|218493478|gb|FG952537.1|FG952537
EST:     CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTG                         GATCGTGGTTAACATACCGGGGGGAACAGATGCATCTAAAG
genomic: CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTGgtatgtatgc ... tcttgcacagGATCGTGGTTAACATACCGGGGGGAACAGATGCATCTAAAG
EST: gi|218479879|gb|FG966076.1|FG966076
EST:     CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTG                         GATCGTGGTTAACATACCGGGGGGAACAGATGCATCTAAAG
genomic: CCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTGgtatgtatgc ... tcttgcacagGATCGTGGTTAACATACCGGGGGGAACAGATGCATCTAAAG

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: 56 (upstream exon), 41 (downstream exon)
Score: 14

ATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTGgtatgtatgc ... tcttgcacagGATCGTGGTTAACATACCGGGGGGAACAGATGCATCTAAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTGgtatgtatgcacactgatcgatccatccatccatcccatgggatgtggcacaccaacaagtgtcaattctccacaagtacactagcttgacacttgcatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccatccc