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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGGACACAACTTCTCTGGGATCAACAACATCAAGTGCCTTTGATGTGAGAAGCAACATGATTGGAGAGATTGAGAATAGATCAACATTCCTCTTAGCTgtaagttattcaagatgatgcttcctttcagaaatatatatactaccgaattcccttagtccattagtaattcaggtagattattatgaggactgactttttatataaaaaaatggatttgtttcag

Basic information

species Oryza sativa
transcript LOC_Os11g01439.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g01439.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G062738_T01 (Zea mays), 5'ss of exon 4
GAAGGACACAACTTCTCTGGGATCAACAACATCAAGTGCCTTTGATGTGAGAAGCAACATGATTGGAGAGATTGAGAATAGATCAACATTCCTCTTAGCTgtaagttattcaagatgatgcttcctttcagaaatatat----atactaccgaattccc---ttagtccattagtaattcaggta----gatt---attatgaggactgact--ttttatataaaaaaatggatttgtttcag
 ||       || ||| | || |||| | |||| | ||  | |||||  ||||| || |||||||||||||||||||| |||||||||||||||||||||||||||  ||   | ||   |   |||  | ||| ||      | | |   || ||||    ||| | ||| | |||  |  |||    ||||   || ||||  | ||||   | || |||||||| ||||| | |||||||
AAAAAGGGAGACATCTTTAGGGTCAATATCATCCAATGTATCTGATGCCAGAAGTAATATGATTGGAGAGATTGAGAACAGATCAACATTCCTCTTAGCTgtaagtattttctgctggcaccatcttgaacaaaaatcctgtgaaatttatgagttccactattaatgcataattaaaactagtaatcagatttcaataatgaaaagtgacaaatgttttataaaaacatggaat-gtttcag

upper sequence: LOC_Os11g01439.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G396927_T01 (Zea mays), 5'ss of exon 1
GAAGGACACAACTTCTCTGGGATCAACAACATCAAGTGCCTTTGATGTGAGAAGCAACATGATTGGAGAGATTGAGAATAGATCAACATTCCTCTTAGCTgtaagttattcaagatgatgcttcctttcagaaatatat----atactaccgaattccc---ttagtccatta--gtaatt--caggtagatt---attatgaggactgact--ttttatataaaaaaatggatttgtttcag
                         |   |||| | ||  | |||||  ||||| ||||||||||||||||| ||||| |||||||||||||||||||||||||||  ||   |  |   |  |||  || ||  ||      | | |   || ||||    ||| | ||| |   ||| |   |   | |||   || |||   | ||||   | || |||||||| ||||| | | | |||
-------------------------ATGTCATCCAATGTTTATGATGCCAGAAGTAACATGATTGGAGAGATCGAGAACAGATCAACATTCCTCTTAGCTgtaagtattttttgccggcaccacctggcacaagaatcctgccaaatttatgagttccactattaatacataattataactagtaaccaaattttaataatgcaaagtgacaaatgttttataaaaacatggaat-gctccag

upper sequence: LOC_Os11g01439.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA01G22620.1 (Glycine max), 5'ss of exon 4
GAAGGACACAACTTCTCTGGGATCAACAACATCAAGT---GCCTTTGATGTGAGAAGCAACATGATTGGAGAGATTGAGAATAGATCAACATTCCTCTTAGCTgtaagttattcaagatgatgcttcctttcagaaatatatatactaccgaattcccttagtccattagtaattcaggtagattattatgaggactgactttttatataaaaaaatggatttgtttcag
   ||| ||  | || ||   |   ||  |  |||||   || | |||||  || |||||||||||||| || ||||||||||||||| ||||||||||||||||| |||         || ||||||        || ||| |  |      |  | ||  | || |      | |      || | |  |  | |    || | | ||| ||   |            
---GGATACTTCATCACTATTAGTTACTTCTGCAAGTAATGCATCTGATGCTAGGAGCAACATGATTGGTGAAATTGAGAATAGATCATCATTCCTCTTAGCTgtatgtt---------gaagcttcc--------atctattttgttatttttctcatttttacactgaagtcttaacacatttttgaaaaatatttctcttctgtgtaacaatcag------------

upper sequence: LOC_Os11g01439.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA20G32630.1 (Glycine max), 5'ss of exon 3
GAAGGACACAACTTCTCTGGGATCAACAACATCAAGTGCCTTTGATGTGAGAAGCAACATGATTGGAGAGATTGAGAATAGATCAACATTCCTCTTAGCTgtaagttattcaagatgatgcttcctttcagaaatatatatactaccgaattcccttagtccattagtaattcaggtagattattatgaggactgactttttatataaaaaaatggatttgtttcag
 ||| |    |||||  |   |||| ||||| |   | | |||||||  || |||||||||||||| |||||||||||||||||| |||||||||||||||||  |||    | ||    || |  ||  |  || | |  ||    | ||||  |     |||||  ||||     |  || |||   |  ||                                 
AAAGAAGGATACTTCATTAATATCATCAACAACTTATCCATTTGATGCTAGGAGCAACATGATTGGGGAGATTGAGAATAGATCATCATTCCTCTTAGCTgtacatta----aaatttccctccagttttgttattttttcacattggcattctat-----cattacaaattttataacctttttaatggatctag-------------------------------

upper sequence: LOC_Os11g01439.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA02G11260.1 (Glycine max), 5'ss of exon 4
GAAGGACACAACTTCTCTGGGAT-CAACAACATCAAGTGCCTTTGATGTGAGAAGCAACATGATTGGAGAGATTGAGAATAGATCAACATTCCTCTTAGCTgtaagttattcaagatgatgcttcctttcagaaatatatatactaccgaattcccttagtccattagt--aattcaggtagattattatgaggactgactttttatataaaaaaatggatttgtttcag
  |   ||  |   || |  | | |  || ||   | ||| | |||||  || |||||||||||||| || ||||||||||||||| |||||||| |||||||| |||         || || ||| |       ||| | |  ||     ||  || | |  |  | |  | |  ||  | ||| ||   |  |      |  | | |  || |||             
-TACTTCATCATCACTATTAGTTACTTCAGCAAGTAATGCATCTGATGCTAGGAGCAACATGATTGGTGAAATTGAGAATAGATCATCATTCCTCCTAGCTgtatgtt---------gaagcctccatc------tatttttgttatt---ttttctcattttaagactcaagtctagacacatttttg-aaaaatatttctcctctgtctaacaatcag----------

upper sequence: LOC_Os11g01439.2 (Oryza sativa), 5'ss of exon 3
lower sequence: AT3G25690.2 (Arabidopsis thaliana), 5'ss of exon 5
GAAGGACACAACTTCTCTGGGATCAACAACATCAAGTGCCTTT---GATGTGAGAAGCAACATGATTGGAGAGATTGAGAATAGATCAACATTCCTCTTAGCTgtaagttattcaagatgatgcttcctttcagaaatatatatactaccgaattccct-tagtccattagtaattcagg-tagattattatgaggactgactttttatataaaaaaatggatttgtttcag
    |   || ||||| ||   ||  ||  | |  ||   | |   |  |  || | ||| |||||||| || || |||||  ||||||||||||||||||| |||||||          |  ||| |  |   |  | || || | |  | |||      |    || | |  || |   | |||||                                            
---AGGTGCACCTTCTTTGATCTCTTCAGGAACTGGTAATTCTTCAGCAGCTAGGAACAATATGATTGGGGAAATCGAGAACCGATCAACATTCCTCTTAGCAgtaagttc---------acactttcaatataatgt-taaatgcaattggatttgaaacaaagaatcaattgtttaaacttgattacag-----------------------------------------

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|29667941|gb|CB664216.1|CB664216
EST:     GAAGCAACATGATTGGAGAGATTGAGAATAGATCAACATTCCTCTTAGCT                         GTCAAAGCGGATGTGGAGACACAAGGAGACTTTGTCGAGTCTCTAGCAAAT
genomic: GAAGCAACATGATTGGAGAGATTGAGAATAGATCAACATTCCTCTTAGCTgtaagttatt ... tttgtttcagGTCAAAGCGGATGTGGAGACACAAGGAGACTTTGTCGAGTCTCTAGCAAAT
EST: gi|29612722|gb|CB617735.1|CB617735
EST:     GAAGCAACATGATTGGAGAGATTGAGAATAGATCAACATTCCTCTTAGCT                         GTCAAAGCGGAT
genomic: GAAGCAACATGATTGGAGAGATTGAGAATAGATCAACATTCCTCTTAGCTgtaagttatt ... tttgtttcagGTCAAAGCGGAT
EST: gi|29615363|gb|CB620375.1|CB620375
EST:     GAAGCAACATGATTGGAGAGATTGAGAATAGATCAACATTCCTCTTAGCT                         GTCAAAGCGGATGT
genomic: GAAGCAACATGATTGGAGAGATTGAGAATAGATCAACATTCCTCTTAGCTgtaagttatt ... tttgtttcagGTCAAAGCGGATGT
EST: gi|157651193|gb|EX450827.1|EX450827
EST:     GAAGCAATATGATTGGAGAGATTGAGAATAGATCAACATTCCTCTTAGCT                         GTCAAAGCGGATGTGGAGACACAAGGAGACTTTGTCGAGTCTCTAGCAAAT
genomic: GAAGCAACATGATTGGAGAGATTGAGAATAGATCAACATTCCTCTTAGCTgtaagttatt ... tttgtttcagGTCAAAGCGGATGTGGAGACACAAGGAGACTTTGTCGAGTCTCTAGCAAAT
EST: gi|38475765|gb|CF959898.1|CF959898
EST:     GAAGCAACATGATTGGAGAGATTGAGAATAGATCAACATTCCTCTTAGCT                         GTCAAAGCGGATGTGGAGACACAAGGAGACTTTGTCGAGTCGCGAGCAAAT
genomic: GAAGCAACATGATTGGAGAGATTGAGAATAGATCAACATTCCTCTTAGCTgtaagttatt ... tttgtttcagGTCAAAGCGGATGTGGAGACACAAGGAGACTTTGTCGAGTCTCTAGCAAAT
EST: gi|29668095|gb|CB664370.1|CB664370
EST:     ATAGATCANCATTCCTCTTAGCT                         GTCAAAGCGGATGTGGAGACACAAGGAGACTTTGTCGAGTCTCTAGCAAAT
genomic: ATAGATCAACATTCCTCTTAGCTgtaagttatt ... tttgtttcagGTCAAAGCGGATGTGGAGACACAAGGAGACTTTGTCGAGTCTCTAGCAAAT

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), 72 (downstream exon)
Score: 74

GAAGGACACAACTTCTCTGGGATCAACAACATCAAGTGCCTTTGATGTGAGAAGCAACATGATTGGAGAGATTGAGAATAGATCAACATTCCTCTTAGCTgtaagttatt ... tttgtttcagGTCAAAGCGGATGTGGAGACACAAGGAGACTTTGTCGAGTCTCTAGCAAATGAGGTCCGAGCAGCAAGTTTTGTAAATATCGACGATGTTGTTGCATTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGGACACAACTTCTCTGGGATCAACAACATCAAGTGCCTTTGATGTGAGAAGCAACATGATTGGAGAGATTGAGAATAGATCAACATTCCTCTTAGCTgtaagttattcaagatgatgcttcctttcagaaatatatatactaccgaattcccttagtccattagtaattcaggtagattattatgaggactgactttttatataaaaaaatggatttgtttcag

- - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA