Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGAAAGTGAGGAAATTTGTGGAGTTGTTGCTAGTGTCCGCCAGAGAGGAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAGgttggttttttgaaaaatactgtagtataacaatatgagtgtatttgctcatatatttgatgtagcaagcaatttaatctgtagtacattgttttcccac...

Basic information

species Oryza sativa
transcript LOC_Os10g32970.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g32970.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G022019_T01 (Zea mays), 5'ss of exon 3
TGATGAAAGTGAGGAAATTTGTGGAGTTGTTGCTAGTGTCCGCCAGAGAGGAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAGgttggttttttgaaaaatactgtagtataacaatatgagtgtatttgctcatatatttgatgtagcaagcaatttaatctgtagtacattgttttcccac--
||||||||  ||||| ||||||||| ||||||||||||||||    |||||||| ||||| ||||| |||||||||||||||||||||||||| || ||||||||||||  |||||  | | ||          |||    ||| | ||  |     |  |          || ||   ||    |    ||   ||     
TGATGAAACAGAGGACATTTGTGGAATTGTTGCTAGTGTCCGTGCAAGAGGAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAGgttggtttt--gaaaaccattctaacgagtttcaatgctgatatcttcttgtcatcatagtaccttggttcatatatattgataaagggggtgaaccggtga
















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|3767396|gb|AU031506.1|AU031506
EST:     AGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAANCCGTTCCAG                         GTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGAT
genomic: AGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTT-CAGgttggttttt ... tgctttgcagGTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGAT
EST: gi|5667210|gb|AU077496.1|AU077496
EST:     AGACAAGCTNGCATTGTGGACTAGGACTGCCCAGCAATGAAGCCGTTCAG                         GTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTANAATGATAAGATG
genomic: AGACAAGCTTGCATTGTGGACTAGGACTG-CCAGCAATGAAGCCGTTCAGgttggttttt ... tgctttgcagGTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
EST: gi|88418154|gb|CI501679.1|CI501679
EST:     AGGACTGCCAGCAATGAAGCCGTTCAG                         GTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
genomic: AGGACTGCCAGCAATGAAGCCGTTCAGgttggttttt ... tgctttgcagGTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
EST: gi|88287006|gb|CI500066.1|CI500066
EST:     CATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAG                         GTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
genomic: CATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAGgttggttttt ... tgctttgcagGTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
EST: gi|86522564|gb|CI162770.1|CI162770
EST:     GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAG                         GTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
genomic: GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAGgttggttttt ... tgctttgcagGTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
EST: gi|88565841|gb|CI496558.1|CI496558
EST:     CCAGCAATGAAGCCGTTCAG                         GTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
genomic: CCAGCAATGAAGCCGTTCAGgttggttttt ... tgctttgcagGTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
EST: gi|88460719|gb|CI534591.1|CI534591
EST:     AGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAG                         GTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
genomic: AGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAGgttggttttt ... tgctttgcagGTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
EST: gi|88284371|gb|CI405817.1|CI405817
EST:     GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAG                         GTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
genomic: GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAGgttggttttt ... tgctttgcagGTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
EST: gi|88200110|gb|CI199960.1|CI199960
EST:     GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAG                         GTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
genomic: GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAGgttggttttt ... tgctttgcagGTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
EST: gi|88509260|gb|CI436766.1|CI436766
EST:     GAGACAAGCTTGCATTGTTGACTAGGACTGCCAGCAATGAACCCGTTCAG                         GTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
genomic: GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAGgttggttttt ... tgctttgcagGTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
EST: gi|8860119|gb|AU097437.1|AU097437
EST:     GAGACAAGCTTGNATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAG                         GTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
genomic: GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAGgttggttttt ... tgctttgcagGTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
EST: gi|89165097|gb|CI255154.1|CI255154
EST:     GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAG                         GTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
genomic: GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAGgttggttttt ... tgctttgcagGTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
EST: gi|88286887|gb|CI520197.1|CI520197
EST:     GAGACAAGCTTGCATTTTGGACTAGGACTGCCAGCAATGAAGCCGTTCAG                         GTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
genomic: GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAGgttggttttt ... tgctttgcagGTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
EST: gi|86525895|gb|CI166101.1|CI166101
EST:     GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAG                         GTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
genomic: GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAGgttggttttt ... tgctttgcagGTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
EST: gi|88435008|gb|CI504350.1|CI504350
EST:     GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAG                         GTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
genomic: GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAGgttggttttt ... tgctttgcagGTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
EST: gi|86597282|gb|CI280419.1|CI280419
EST:     GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAG                         GTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
genomic: GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAGgttggttttt ... tgctttgcagGTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
EST: gi|218493197|gb|FG958056.1|FG958056
EST:     GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAG                         GTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
genomic: GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAGgttggttttt ... tgctttgcagGTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
EST: gi|88568661|gb|CI499378.1|CI499378
EST:     CAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCNTTCAG                         GTAAACATTGGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGAT
genomic: CAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAGgttggttttt ... tgctttgcagGTAAACATT-GGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGAT
EST: gi|89161806|gb|CI102154.1|CI102154
EST:     GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAG                         GTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
genomic: GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAGgttggttttt ... tgctttgcagGTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
EST: gi|218485786|gb|FG945172.1|FG945172
EST:     GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAG                         GTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATTAGATG
genomic: GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAGgttggttttt ... tgctttgcagGTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
EST: gi|88281177|gb|CI402375.1|CI402375
EST:     GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAG                         GTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
genomic: GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAGgttggttttt ... tgctttgcagGTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
EST: gi|88842763|gb|CI371663.1|CI371663
EST:     GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAG                         GTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
genomic: GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAGgttggttttt ... tgctttgcagGTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
EST: gi|86501861|gb|CI144494.1|CI144494
EST:     GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAG                         GTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
genomic: GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAGgttggttttt ... tgctttgcagGTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
EST: gi|86522556|gb|CI162762.1|CI162762
EST:     GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAG                         GTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
genomic: GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAGgttggttttt ... tgctttgcagGTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
EST: gi|27576343|gb|CA999037.1|CA999037
EST:     GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAG                         GTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
genomic: GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAGgttggttttt ... tgctttgcagGTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
EST: gi|88284235|gb|CI405681.1|CI405681
EST:     GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAG                         GTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
genomic: GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAGgttggttttt ... tgctttgcagGTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
EST: gi|29665281|gb|CB661556.1|CB661556
EST:     GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAG                         GTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
genomic: GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAGgttggttttt ... tgctttgcagGTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
EST: gi|58681185|gb|CK069872.1|CK069872
EST:     AGGACTGCCAGCAATGAAGCCGTTCAG                         GTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
genomic: AGGACTGCCAGCAATGAAGCCGTTCAGgttggttttt ... tgctttgcagGTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
EST: gi|218483813|gb|FG965939.1|FG965939
EST:     GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAG                         GTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
genomic: GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAGgttggttttt ... tgctttgcagGTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
EST: gi|88471338|gb|CI408609.1|CI408609
EST:     GCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAG                         GTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
genomic: GCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAGgttggttttt ... tgctttgcagGTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
EST: gi|33796941|gb|CF324334.1|CF324334
EST:     CCAGCAATGAACCCGTTCGG                         GTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
genomic: CCAGCAATGAAGCCGTTCAGgttggttttt ... tgctttgcagGTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
EST: gi|88434999|gb|CI504341.1|CI504341
EST:     CTTGCATTGTGGAGTAGGACTGCCAGCAATGAAGCCGTTCAG                         GTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
genomic: CTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAGgttggttttt ... tgctttgcagGTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
EST: gi|88373901|gb|CI508520.1|CI508520
EST:     GAGACAAGCTTGCATTGTGNACTAGGACTNCCAGCAATGAAGCCGTTCAG                         GTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
genomic: GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAGgttggttttt ... tgctttgcagGTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
EST: gi|86507489|gb|CI150122.1|CI150122
EST:     GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAG                         GTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
genomic: GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAGgttggttttt ... tgctttgcagGTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
EST: gi|88263461|gb|CI367235.1|CI367235
EST:     GAGACAAGCTTCCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAG                         GTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG
genomic: GAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAGgttggttttt ... tgctttgcagGTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATG

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: 68 (upstream exon), 66 (downstream exon)
Score: 24

TGATGAAAGTGAGGAAATTTGTGGAGTTGTTGCTAGTGTCCGCCAGAGAGGAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAGgttggttttt ... tgctttgcagGTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATGGTCTACAGCTTCCAT




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATGAAAGTGAGGAAATTTGTGGAGTTGTTGCTAGTGTCCGCCAGAGAGGAGACAAGCTTGCATTGTGGACTAGGACTGCCAGCAATGAAGCCGTTCAGgttggttttttgaaaaatactgtagtataacaatatgagtgtatttgctcatatatttgatgtagcaagcaatttaatctgtagtacattgttttcccac

- - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaata