Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtacaacatagttaactcacttattacctcttgttacagaagtatatacagtgtacataacattacataacaacaatgttttgaattattttcatgcttcagCTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCCTGTGACAGGAACGAGCAACTCGCAGCAAATTACCTTCTTGAACATGCTG

Basic information

species Oryza sativa
transcript LOC_Os02g08300.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g08300.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G143462_T06 (Zea mays), 3'ss of exon 11
gtatgtacaacatagtt-aactcacttattacctcttgttacagaagtatatacagtgtacataacattacataacaacaatgttttgaattattttcatgcttcagCTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCCTGTGACAGGAACGAGCAACTCGCAGCAAATTACCTTCTTGAACATGCTG
||| | |    || | | |||||    ||  ||||    | || |  ||| |  ||   ||||||   | | |   | |  ||||||       ||| ||  ||||||||||   |||||| || ||||||||||| || || ||||||||||| ||||| || ||||||||| | || |||||||| || || ||||| |||||||
gtaagcatgtaattgctgaactctgccat--cctcccacttcatagatatttg-agatcacataattatcctttggatc--tgtttt-------ttttata-ttcagCTTGAGTCCATGGGGTTCGACAGAGCACGCGTTATTGAAGCATTCTTAGCCTGCGATAGGAACGAGGAGCTAGCAGCAAACTATCTCCTTGAGCATGCTG
















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|88967884|gb|CI098126.1|CI098126
EST:     TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGG                         CTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
genomic: TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGGgtatgtacaa ... catgcttcagCTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
EST: gi|40486995|gb|BX898244.1|BX898244
EST:     TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGG                         CTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
genomic: TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGGgtatgtacaa ... catgcttcagCTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
EST: gi|88261283|gb|CI364859.1|CI364859
EST:     TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATT-GACGG                         CTTGAAGGCATGGGATTTGACAGAGCACCTGTCATCGAAGCATTCTTCGCC
genomic: TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGGgtatgtacaa ... catgcttcagCTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
EST: gi|86871825|gb|CI331997.1|CI331997
EST:     TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGG                         CTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
genomic: TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGGgtatgtacaa ... catgcttcagCTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
EST: gi|88976735|gb|CI257507.1|CI257507
EST:     TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGG                         CTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
genomic: TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGGgtatgtacaa ... catgcttcagCTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
EST: gi|89168138|gb|CI109342.1|CI109342
EST:     TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGG                         CTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
genomic: TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGGgtatgtacaa ... catgcttcagCTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
EST: gi|88276832|gb|CI395995.1|CI395995
EST:     TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGG                         CTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
genomic: TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGGgtatgtacaa ... catgcttcagCTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
EST: gi|88266856|gb|CI368632.1|CI368632
EST:     TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGG                         CTTGAAGGCATGGGATTTGACAGAGCACCTGTCATCGAAGCATTCTTCGCC
genomic: TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGGgtatgtacaa ... catgcttcagCTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
EST: gi|88267177|gb|CI379112.1|CI379112
EST:     TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGG                         CTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
genomic: TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGGgtatgtacaa ... catgcttcagCTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
EST: gi|86503859|gb|CI146492.1|CI146492
EST:     AAGAGGCGATTGGACGG                         CTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
genomic: AAGAGGCGATTGGACGGgtatgtacaa ... catgcttcagCTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
EST: gi|88838256|gb|CI373616.1|CI373616
EST:     ATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGG                         CTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
genomic: ATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGGgtatgtacaa ... catgcttcagCTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
EST: gi|88831799|gb|CI369481.1|CI369481
EST:     TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGG                         CTTGAAGGCATGGGATGTGACAGAGCACGTGTCATCGAACCATTCTTCGCC
genomic: TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGGgtatgtacaa ... catgcttcagCTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
EST: gi|89178685|gb|CI391683.1|CI391683
EST:     TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGG                         CTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
genomic: TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGGgtatgtacaa ... catgcttcagCTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
EST: gi|86490040|gb|CI132673.1|CI132673
EST:     TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGGTTGGACGG                         CTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
genomic: TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGGgtatgtacaa ... catgcttcagCTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
EST: gi|88980844|gb|CI022534.1|CI022534
EST:     TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGG                         CTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
genomic: TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGGgtatgtacaa ... catgcttcagCTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
EST: gi|66923978|gb|CX110826.1|CX110826
EST:     TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGG                         CTTGAAGGCATGGGATTTGACAGAGCACGTGTCA
genomic: TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGGgtatgtacaa ... catgcttcagCTTGAAGGCATGGGATTTGACAGAGCACGTGTCA
EST: gi|88975027|gb|CI023278.1|CI023278
EST:     TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGG                         CTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
genomic: TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGGgtatgtacaa ... catgcttcagCTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
EST: gi|88966384|gb|CI119519.1|CI119519
EST:     TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGG                         CTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
genomic: TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGGgtatgtacaa ... catgcttcagCTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
EST: gi|88991630|gb|CI019808.1|CI019808
EST:     TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGG                         CTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
genomic: TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGGgtatgtacaa ... catgcttcagCTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
EST: gi|27547445|gb|CA765529.2|CA765529
EST:     TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGG                         CTTGAAGGCATGGGATTTGACAGAGCACGNGTCATCGAAGCATTCTTCGCC
genomic: TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGGgtatgtacaa ... catgcttcagCTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
EST: gi|86833994|gb|CI340133.1|CI340133
EST:     TTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGG                         CTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
genomic: TTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGGgtatgtacaa ... catgcttcagCTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
EST: gi|58676620|gb|CK065307.1|CK065307
EST:     TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGG                         CTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
genomic: TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGGgtatgtacaa ... catgcttcagCTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC
EST: gi|86490031|gb|CI132664.1|CI132664
EST:     TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGGTTGGACGG                         CTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTTTTCGCC
genomic: TGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGGgtatgtacaa ... catgcttcagCTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCC

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: 69 (upstream exon), 74 (downstream exon)
Score: 17

GGACTTCTTAGACCAACCTGACCAGGATGAGATGCCCCATTCTATCAATGTCACACCTGAAGAGCAAGAGGCGATTGGACGGgtatgtacaa ... catgcttcagCTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCCTGTGACAGGAACGAGCAACTCGCAGCAAATTACCTTCTTGAACATGCTG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagtgtacataacattacataacaacaatgttttgaattattttcatgcttcagCTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCCTGTGACAGGAACGAGCAACTCGCAGCAAATTACCTTCTTGAACATGCTG
                 acataac  putative branch site (score: 17)
                                      ttattttc  putative PPT
                        aacaatgttttgaatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtacaacatagttaactcacttattacctcttgttacagaagtatatacagtgtacataacattacataacaacaatgttttgaattattttcatgcttcagCTTGAAGGCATGGGATTTGACAGAGCACGTGTCATCGAAGCATTCTTCGCCTGTGACAGGAACGAGCAACTCGCAGCAAATTACCTTCTTGAACATGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG