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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAAAACTTCATTCAGGAGGGTGCACTTTCTGAGCTGATTGTTGCCTTCTCTCGTGAAGGACCAGCCAAAGAATACGTGCAGCATAAGATGACAGAGAAGgttagttcgatacacgctccacatttctaccgcactatgctgcttttcttgaacttctatacagaatttccccacacatggctatactcaatgaggttttctgctgatatcag

Basic information

species Oryza sativa
transcript LOC_Os04g55960.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g55960.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G104294_T02 (Zea mays), 5'ss of exon 10
GCAAAACTTCATTCAGGAGGGTGCACTTTCTGAGCTGATTGTTGCCTTCTCTCGTGAAGGACCAGCCAAAGAATACGTGCAGCATAAGATGACAGAGAAGgttagtt-cgatacacgctccacatttctaccgcactatgctgcttttcttgaacttcta-tacagaatttccccacacatg-gctatactcaatgaggttttctgctgatatcag
|||||  ||| || ||||||| || ||||||||||| |||||||| |||||||| ||||| ||| | |||||||| |||||||||||||||   |||||||| || | | ||| || |||    |   ||    ||| |  | ||| ||  |   ||| | ||   ||| |||    |  |  |||  ||| |||    || | | |||||| |||
GCAAACTTTCCTTGAGGAGGGGGCGCTTTCTGAGCTAATTGTTGCATTCTCTCGGGAAGGGCCAACTAAAGAATATGTGCAGCATAAGATGGTGGAGAAGgtcagatacaatatacactct---tccttaatatactgt--tacttctcgagtgtttcaaatattcaatgtcctagaaggtttgctcaactaaatttacttcttt-ctgataccag

upper sequence: LOC_Os04g55960.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G377451_T01 (Zea mays), 5'ss of exon 13
GCAAAACTTCATTCAGGAGGGTGCACTTTCTGAGCTGATTGTTGCCTTCTCTCGTGAAGGACCAGCCAAAGAATACGTGCAGCATAAGATGACAGAGAAGgttagttcgatacacgctccacatttctaccgcactatgctgcttttcttgaacttcta-tacagaatttccccacacatggctatactcaatgaggttttctgct----gatatcag
|||||  ||| || ||||||| || ||||||||||| |||||||| |||||||| ||||| ||| | |||||||| |||||||||||||||   || ||||| ||    |||||   | |||  |||      |   ||   ||||||  |   ||| | ||   ||| |||  ||     | | | |||||  || ||| || ||    | || |||
GCAAACTTTCCTTGAGGAGGGGGCGCTTTCTGAGCTAATTGTTGCATTCTCTCGGGAAGGGCCAACAAAAGAATATGTGCAGCATAAGATGGTGGAAAAGgtcag----atacaacatacacccttccttaatatactgtcacttttcaagtgtttcgagtattcaatgtcc--actagaagatgtgctcaactagatttacttctttttgttaccag

upper sequence: LOC_Os04g55960.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G086489_T01 (Zea mays), 5'ss of exon 16
GCAAAACTTCATTCAGGAGGGTGCACTTTCTGAGCTGATTGTTGCCTTCTCTCGTGAAGGACCAGCCAAAGAATACGTGCAGCATAAGATGACAGAGAAGgttagtt-cgatacacgctccacatttctaccgcactatgctgcttttcttgaacttcta-tacagaatttccccacacatggctatactcaatgaggttttctgct----gatatcag
|||||  ||| || ||||||| || ||||||||||| |||||||| |||||||| ||||| ||| | |||||||| |||||||||||||||   || ||||| || | | |||||   | |||  |||      |   ||   ||||||  |   ||  | ||   ||| ||  |||     | | | |||||  || ||| || ||    | || |||
GCAAACTTTCCTTGAGGAGGGGGCGCTTTCTGAGCTAATTGTTGCATTCTCTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAGgtcagatacaatacaacatacacccttccttaatatactgtcacttttcaagtgttttgagtattcaatgtc--cactagaagatgtgctcaactagatttacttctttttgttaccag

upper sequence: LOC_Os04g55960.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G480134_T01 (Zea mays), 5'ss of exon 6
GCAAAACTTCATTCAGGAGGGTGCACTTTCTGAGCTGATTGTTGCCTTCTCTCGTGAAGGACCAGCCAAAGAATACGTGCAGCATAAGATGACAGAGAAGgttagttcgatacacgctccacatttctaccgcactatgctgcttttcttgaacttcta-tacagaatttccccacacatggctatactcaatgaggttttctgct----gatatcag
|||||  ||| || ||||||| || ||||||||||| |||||||| |||||||| ||||| ||| | |||||||| |||||||||||||||   || ||||| ||    |||||   | |||  |||      |   ||   ||||||  |   ||| | ||   ||| |||  ||     | | | |||||  || ||| || ||    | || |||
GCAAACTTTCCTTGAGGAGGGGGCGCTTTCTGAGCTAATTGTTGCATTCTCTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAGgtcag----atacaacatacacccttccttaatatactgtcacttttcaagtgtttcgagtattcaatgtcc--actagaagatgtgctcaactagatttacttctttttgttaccag

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|15855705|gb|BI808517.1|BI808517
EST:     AGAATACGTGCAGCATAAGATGACAGAGAA-                         GCCACAGAAATTTGGAACATCGTCTCACAAGGTGGTTACATATATGTGTGC
genomic: AGAATACGTGCAGCATAAGATGACAGAGAAGgttagttcga ... ctgatatcagGCCACAGAAATTTGGAACATCGTCTCACAAGGTGGTTACATATATGTGTGC
EST: gi|27577335|gb|CB000030.1|CB000030
EST:     CTCGTGAAGGACCAGCCAAAGAATACGTGCAGCATAAGATGACAGAGAAG                         GCCACAGAAATTTGGAACATCATCTCACAAGGTGGTTACATA
genomic: CTCGTGAAGGACCAGCCAAAGAATACGTGCAGCATAAGATGACAGAGAAGgttagttcga ... ctgatatcagGCCACAGAAATTTGGAACATCGTCTCACAAGGTGGTTACATA
EST: gi|58666486|gb|CK055172.1|CK055172
EST:     CTCGTGAAGGACCAGCCAAAGAATACGTGCAGCATAAGATGACAGAGAAG                         GCCACAGAAATTTGGAACATCGTCTCACAAGGTGGTTACATATATGTGTGC
genomic: CTCGTGAAGGACCAGCCAAAGAATACGTGCAGCATAAGATGACAGAGAAGgttagttcga ... ctgatatcagGCCACAGAAATTTGGAACATCGTCTCACAAGGTGGTTACATATATGTGTGC
EST: gi|88272817|gb|CI386077.1|CI386077
EST:     AGAATACG-GCCAGCATAAGATGACAGAGAAG                         GCCACAGAAATTTTGAACATCGTCTCACAAGGTGGTTACATATATGTGTGC
genomic: AGAATACGTG-CAGCATAAGATGACAGAGAAGgttagttcga ... ctgatatcagGCCACAGAAATTTGGAACATCGTCTCACAAGGTGGTTACATATATGTGTGC
EST: gi|29674228|gb|CB670503.1|CB670503
EST:     CTCGTGAAGGACCAGCCAAAGAATACGTGCAGCATAAGATGACAGAGAAG                         GCCACAGAAATTTGGAACATCGTCTCACAAGGTGGTTACATATATGTGTGC
genomic: CTCGTGAAGGACCAGCCAAAGAATACGTGCAGCATAAGATGACAGAGAAGgttagttcga ... ctgatatcagGCCACAGAAATTTGGAACATCGTCTCACAAGGTGGTTACATATATGTGTGC
EST: gi|163929241|gb|EG712694.1|EG712694
EST:     CTCGTGAAGGACCAGCCAAAGAATACGTGCAGCATAAGATGACAGAGAAG                         GCCACAGAAATTTGGAACATCGTCTCACAAGGTGGTTACATATATGTGTGC
genomic: CTCGTGAAGGACCAGCCAAAGAATACGTGCAGCATAAGATGACAGAGAAGgttagttcga ... ctgatatcagGCCACAGAAATTTGGAACATCGTCTCACAAGGTGGTTACATATATGTGTGC
EST: gi|25800626|gb|CA756587.1|CA756587
EST:     CAAAGAATACGTGCAGCATAAGATGACAGAGAAG                         GCCACAGAAATTTGGAACATCGTCTCACAAGGTGGTTACATATATGTGTGC
genomic: CAAAGAATACGTGCAGCATAAGATGACAGAGAAGgttagttcga ... ctgatatcagGCCACAGAAATTTGGAACATCGTCTCACAAGGTGGTTACATATATGTGTGC
EST: gi|66917610|gb|CX104458.1|CX104458
EST:     CTCGTGAAGGACCAGCCAAAGAATACGTGCAGCATAAGATGACAGAGAAG                         GCCACAGAAATTTGGAACATCGTCTCACAAGGTGGTTACATATATGTGTGC
genomic: CTCGTGAAGGACCAGCCAAAGAATACGTGCAGCATAAGATGACAGAGAAGgttagttcga ... ctgatatcagGCCACAGAAATTTGGAACATCGTCTCACAAGGTGGTTACATATATGTGTGC
EST: gi|33793723|gb|CF322744.1|CF322744
EST:     CTCGTGAAGGACCAGCCAAAGAATACGTGCAGCATAAGATGACAGAGAAG                         GCCACAGAAATTTGGAACATCGTCTCACAAGGTGGTTACATATATGTGTGC
genomic: CTCGTGAAGGACCAGCCAAAGAATACGTGCAGCATAAGATGACAGAGAAGgttagttcga ... ctgatatcagGCCACAGAAATTTGGAACATCGTCTCACAAGGTGGTTACATATATGTGTGC
EST: gi|38480582|gb|CF964671.1|CF964671
EST:     CTCGTGAAGGACCAGCCAAAGAATACGTGCAGCATAAGATGACAGAGAAT                         GCCACAGAAATTTGGAACATCGTCTCACAAGGTGGTTACATATATGTGTGC
genomic: CTCGTGAAGGACCAGCCAAAGAATACGTGCAGCATAAGATGACAGAGAAGgttagttcga ... ctgatatcagGCCACAGAAATTTGGAACATCGTCTCACAAGGTGGTTACATATATGTGTGC
EST: gi|58673422|gb|CK062108.1|CK062108
EST:     CTCGTGAAGGACCAGCCAAAGAATACGTGCAGCATAAGATGACAGAGAAG                         GCCACAGAAATTTGGAACATCGTCTCACAAGGTGGTTACATATATGTGTGC
genomic: CTCGTGAAGGACCAGCCAAAGAATACGTGCAGCATAAGATGACAGAGAAGgttagttcga ... ctgatatcagGCCACAGAAATTTGGAACATCGTCTCACAAGGTGGTTACATATATGTGTGC
EST: gi|22307634|gb|BQ908856.1|BQ908856
EST:     CTCGTGAAGGACCAGCCAAAGAATACGTGCAGCATAAGATGACAGAGAAG                         GCCACAGAAATTTGGAACATCGTCTCACAAGGTGGTTACATATATGTGTGC
genomic: CTCGTGAAGGACCAGCCAAAGAATACGTGCAGCATAAGATGACAGAGAAGgttagttcga ... ctgatatcagGCCACAGAAATTTGGAACATCGTCTCACAAGGTGGTTACATATATGTGTGC

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: 74 (upstream exon), 62 (downstream exon)
Score: 78

GCAAAACTTCATTCAGGAGGGTGCACTTTCTGAGCTGATTGTTGCCTTCTCTCGTGAAGGACCAGCCAAAGAATACGTGCAGCATAAGATGACAGAGAAGgttagttcga ... ctgatatcagGCCACAGAAATTTGGAACATCGTCTCACAAGGTGGTTACATATATGTGTGCGGTGATGCCAAGGGTATGGCAAGAGACGTACACAGAGCTCTTCATACAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAAAACTTCATTCAGGAGGGTGCACTTTCTGAGCTGATTGTTGCCTTCTCTCGTGAAGGACCAGCCAAAGAATACGTGCAGCATAAGATGACAGAGAAGgttagttcgatacacgctccacatttctaccgcactatgctgcttttcttgaacttctatacagaatttccccacacatggctatactcaatgaggttttctgctgatatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG