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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCGAACAGCATCCTCGTCGTCACCATCAACGGCATCGGTCTCATTGTCGAGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGCgtatatacgcttttccctccctcttgatatatctatatatccatatttcctcgatttaatttcgaaatttgaatctatctgaaatataatcttgacattaattcattgttgcag

Basic information

species Oryza sativa
transcript LOC_Os01g42090.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g42090.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G157675_T02 (Zea mays), 5'ss of exon 2
CCCGAACAGCATCCTCGTCGTCACCATCAACGGCATCGGTCTCATTGTCGAGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGCgtatatacgcttttccctccctcttgatatatctatatatccatatttcctcgatttaatttcgaaatttgaatctatctgaaatataatcttgacattaattcattgttgcag
||| |||||||| |||||||||||||||||||||||||| ||| |  |||||| |  |||||||   |||||||||||||| |||  || | ||||||||||   |  |   | || |     | |    ||| ||  |||  |   | ||    ||    || |  | | | | |||||   || |  |  ||   ||    | ||  |||||
CCCCAACAGCATTCTCGTCGTCACCATCAACGGCATCGGCCTCGTCATCGAGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagt--gtcgtgccatgttgttcgcccgatccatg-atctgtccctgctgttgtttccctccacgtgt-agtgtatctctcatctggtggtggtttttgagc-ttaatgcag

upper sequence: LOC_Os01g42090.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G416965_T01 (Zea mays), 5'ss of exon 3
CCCGAACAGCATCCTCGTCGTCACCATCAACGGCATCGGTCTCATTGTCGAGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGCgtatatacgcttttccctccctcttgatatatctatatatccatatttcctcgatttaatttcgaaatttgaatctatctgaaatataatcttgacattaattcattgttgcag
||| |||||||||||||||||||||||||||||| |||| ||| |  |||||| || |||||||  |||||||||||| |||||      |  ||| |||||   | | |    |  |  | ||  | | ||        || | | | | |  ||    |   |  |||||   |  |       ||  | |   ||||||||    | ||||
CCCTAACAGCATCCTCGTCGTCACCATCAACGGCGTCGGGCTCGTCATCGAGGCCATCTACCTCACCATCTTCTTCCTTTACTCTGATGGCCCGAAACGCgtgagtgc-cacggcgatggcgctgcacaaatgc---cggccgtgtgttccctcttcggatct-agttttgagcttgacgatcccttacgcct--tattaattctcgttcgcag
















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|88668966|gb|CI719923.1|CI719923
EST:     AGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAANAAGAAGCGC                         CTGAGGATGTTGGCTGTG
genomic: AGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGCgtatatacgc ... attgttgcagCTGAGGATGTTGGCTGTG
EST: gi|88905343|gb|CI712642.1|CI712642
EST:     AGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGC                         CTGAGGATGTTGGCTGTGCTGGGCGTGGAG
genomic: AGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGCgtatatacgc ... attgttgcagCTGAGGATGTTGGCTGTGCTGGGCGTGGAG
EST: gi|88983988|gb|CI723553.1|CI723553
EST:     AGGGCCCCTACCTCTTCATCTTCTTCCTCTACTCCCC-AACAAGAAGCGC                         CTGAGGATGTTGGCTGTGCTGGGCGTGGAGTTGGTGTCCATG
genomic: AGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGCgtatatacgc ... attgttgcagCTGAGGATGTTGGCTGTGCTGGGCGTGGAGTTGGTGTTCATG
EST: gi|88672630|gb|CI726746.1|CI726746
EST:     AGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCAAACAAGAAGCGC                         CTGAGGATGTTGGCTGTGCTGGGCGTGGAGTTGGTGTT
genomic: AGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGCgtatatacgc ... attgttgcagCTGAGGATGTTGGCTGTGCTGGGCGTGGAGTTGGTGTT
EST: gi|88669647|gb|CI723763.1|CI723763
EST:     AGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGC                         CTGAGGATGTTG
genomic: AGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGCgtatatacgc ... attgttgcagCTGAGGATGTTG
EST: gi|88594265|gb|CI714223.1|CI714223
EST:     AGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGC                         CTGAGGATGTTGGCTGTGCTGGGC
genomic: AGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGCgtatatacgc ... attgttgcagCTGAGGATGTTGGCTGTGCTGGGC
EST: gi|88905608|gb|CI712907.1|CI712907
EST:     AGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGC                         CTGAGGATGTTGGCTGTGCTGGGCGTGGA
genomic: AGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGCgtatatacgc ... attgttgcagCTGAGGATGTTGGCTGTGCTGGGCGTGGA
EST: gi|88904481|gb|CI711789.1|CI711789
EST:     AGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGC                         CTGAGGATGTTGGCTGTGCTGGGCGTGGAGTTGGTGTTCATGC
genomic: AGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGCgtatatacgc ... attgttgcagCTGAGGATGTTGGCTGTGCTGGGCGTGGAGTTGGTGTTCATGC
EST: gi|88674354|gb|CI728467.1|CI728467
EST:     AGGGCACCTANCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGC                         CTGAGGATGTTGGCTGTGC
genomic: AGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGCgtatatacgc ... attgttgcagCTGAGGATGTTGGCTGTGC
EST: gi|88904560|gb|CI711859.1|CI711859
EST:     AGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGC                         CTGAGGATGTTGGCTGTGCTGGGCGTGGAGTTGGTGTTCATGCTGGCGGTG
genomic: AGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGCgtatatacgc ... attgttgcagCTGAGGATGTTGGCTGTGCTGGGCGTGGAGTTGGTGTTCATGCTGGCGGTG
EST: gi|89172658|gb|CI721717.1|CI721717
EST:     AGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGC                         CTGAGGATGTTGG
genomic: AGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGCgtatatacgc ... attgttgcagCTGAGGATGTTGG
EST: gi|88593573|gb|CI713527.1|CI713527
EST:     AGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGC                         CTGAGGATGTTGGCTGTGCT
genomic: AGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGCgtatatacgc ... attgttgcagCTGAGGATGTTGGCTGTGCT
EST: gi|88666200|gb|CI716356.1|CI716356
EST:     AGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGC                         CTGAGGATGTTGGCTGTGCTGGG
genomic: AGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGCgtatatacgc ... attgttgcagCTGAGGATGTTGGCTGTGCTGGG
EST: gi|89172310|gb|CI721369.1|CI721369
EST:     AGGGCACCTACCTCTTNATCTTCTTCCTCTACTCCCCCAANAAGAAGCGC                         CTGAGGATGTTGGCTGTGCTGGGCGTGGAGTTGGTGTTCATGCTGGCG
genomic: AGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGCgtatatacgc ... attgttgcagCTGAGGATGTTGGCTGTGCTGGGCGTGGAGTTGGTGTTCATGCTGGCG
EST: gi|88673232|gb|CI726007.1|CI726007
EST:     AGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGC                         CTGAGGATGTTGGCTGTGCTGGGCGTGGAGTTGGTGTTCATGCTGGC
genomic: AGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGCgtatatacgc ... attgttgcagCTGAGGATGTTGGCTGTGCTGGGCGTGGAGTTGGTGTTCATGCTGGC
EST: gi|88671009|gb|CI725125.1|CI725125
EST:     GGGCACCTACCTCTTCATCTTCCTTCCTCTACTCCCCCAANAAGAAGCGC                         CTGAGGATGTCGGCTGCGCTGGGCGTGGAGTTGGTGT
genomic: GGGCACCTACCTCTTCATCTTC-TTCCTCTACTCCCCCAACAAGAAGCGCgtatatacgc ... attgttgcagCTGAGGATGTTGGCTGTGCTGGGCGTGGAGTTGGTGT
EST: gi|88670105|gb|CI724221.1|CI724221
EST:     AGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGC                         CTGAGGATGTTGGCTGTGCTGGGCGTGGAGTTGGTGTTCATGCTGG
genomic: AGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGCgtatatacgc ... attgttgcagCTGAGGATGTTGGCTGTGCTGGGCGTGGAGTTGGTGTTCATGCTGG
EST: gi|88954484|gb|CI718463.1|CI718463
EST:     AGGGCACCTACCTCTTCATCTTCTTCCTCTAATCCCCCAACAAGAAGCGC                         CTGAGGATGTTGGCTGTGCTG
genomic: AGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGCgtatatacgc ... attgttgcagCTGAGGATGTTGGCTGTGCTG
EST: gi|88668994|gb|CI719951.1|CI719951
EST:     AGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAANAAGAAGCGC                         CTGAGGATGTTGG
genomic: AGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGCgtatatacgc ... attgttgcagCTGAGGATGTTGG
EST: gi|88676759|gb|CI730872.1|CI730872
EST:     AGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGC                         CTGAGGGATGTTGGCTGTGCTGGGCGTGGA
genomic: AGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGCgtatatacgc ... attgttgcagCTGAGG-ATGTTGGCTGTGCTGGGCGTGGA
EST: gi|88984145|gb|CI723701.1|CI723701
EST:     AGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGC                         CTGAGGATGTTGGC
genomic: AGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGCgtatatacgc ... attgttgcagCTGAGGATGTTGGC

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: 70 (upstream exon), 44 (downstream exon)
Score: 6

CCCGAACAGCATCCTCGTCGTCACCATCAACGGCATCGGTCTCATTGTCGAGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGCgtatatacgc ... attgttgcagCTGAGGATGTTGGCTGTGCTGGGCGTGGAGTTGGTGTTCATGCTGGCGGTGATTCTGGGCGTGCTTCTGAGCGCGCACACGCACAAGAAGCGTTCCATGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCGAACAGCATCCTCGTCGTCACCATCAACGGCATCGGTCTCATTGTCGAGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGCgtatatacgcttttccctccctcttgatatatctatatatccatatttcctcgatttaatttcgaaatttgaatctatctgaaatataatcttgacattaattcattgttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC