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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAATTTCAGAAACAATGGACTTTGAGATTAAGCGATGGGCTGCTGGAAAAGAAGGCAATTTGCGTGCATTGCTATCAACTTTGCAATATgtaagtccttattcctgatgctgctaaaaattgaatcaattatccttgtcttctcaatttttctattcattctctcggtgttattcttgcaaagaaagtt...

Basic information

species Oryza sativa
transcript LOC_Os12g36180.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g36180.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM5G839757_T01 (Zea mays), 5'ss of exon 6
AGAATTTCAGAAACAATGGACTTTGAGATTAAGCGATGGGCTGCTGGAAAAGAAGGCAATTTGCGTGCATTGCTATCAACTTTGCAATATgtaagtc---cttattcctgatgctgctaaaaattgaatcaattatccttgtcttctcaatttttctattcattctctcggtgttattcttgcaaagaaagtt
||  || | |||||| ||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||| |||||||| |||     | |  | |    ||   |   |||  |  | || ||| |    |    |||   || |          ||  |||   |    |        
AGGCTTGCGGAAACACTGGACTTTGAGATTAAGCGCTGGGCTGCTGGAAAAGAAGGCAATTTGCGTGCATTGCTATCAACTTTACAATATgtgagttagattgaagcatttcactctcattcattttactagttctccgttatgtgggcattacactttgataggaactggcattaaggtctttagctgt---
















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|88693872|gb|CI735449.1|CI735449
EST:     GGCAATTTGCGTGCATTGCTATCAACTTTGCAATAT                         GTACTTTGGCCAGAATGTGGATGGCAACCTGTATCCCTGACTGACTTGATT
genomic: GGCAATTTGCGTGCATTGCTATCAACTTTGCAATATgtaagtcctt ... tttctgacagGTACTTTGGCCAGAATGTGGATGGCAACCTGTATCCCTGACTGACTTGATT
EST: gi|38473501|gb|CF957633.1|CF957633
EST:     CTGCTGGAAAAGAAGGCAATTTGCGTGCATTGCTATCAACTTTGCAATAT                         GTACTTTGGCCAGAATGTGGATGGCAACCTGTATCCCTGACTGACTTGATT
genomic: CTGCTGGAAAAGAAGGCAATTTGCGTGCATTGCTATCAACTTTGCAATATgtaagtcctt ... tttctgacagGTACTTTGGCCAGAATGTGGATGGCAACCTGTATCCCTGACTGACTTGATT
EST: gi|29669275|gb|CB665550.1|CB665550
EST:     CTGCTGAAAAAGAAGGCAATTTGCGTGCATTGCTATCAACTTTGCAATAT                         GTACTTTGGCCAGAATGTGGATGGCAACCTGTATCCCTGACTGACTTGATT
genomic: CTGCTGGAAAAGAAGGCAATTTGCGTGCATTGCTATCAACTTTGCAATATgtaagtcctt ... tttctgacagGTACTTTGGCCAGAATGTGGATGGCAACCTGTATCCCTGACTGACTTGATT
EST: gi|88690893|gb|CI734972.1|CI734972
EST:     GGCAATTTGCGTGCATTGCTATCAACTTTGCAATAT                         GTACTTTGGCCAGAATGTGGATGGCAACCTGTATCCCTGACTGACTTGATT
genomic: GGCAATTTGCGTGCATTGCTATCAACTTTGCAATATgtaagtcctt ... tttctgacagGTACTTTGGCCAGAATGTGGATGGCAACCTGTATCCCTGACTGACTTGATT
EST: gi|58601859|gb|CK012387.1|CK012387
EST:     CTGCTGGAAAAGAAGGCAATTTGCGTGCATTGCTATCAACTTTGCAATAT                         GTACTTTGGCCAGAATGTGGATGGCAACCTGTATCCCTGACTGACTTGATT
genomic: CTGCTGGAAAAGAAGGCAATTTGCGTGCATTGCTATCAACTTTGCAATATgtaagtcctt ... tttctgacagGTACTTTGGCCAGAATGTGGATGGCAACCTGTATCCCTGACTGACTTGATT
EST: gi|58586924|gb|CF985232.1|CF985232
EST:     CTGCTGGAAAAGAAGGCAATTTGCGTGCATTGCTATCAACTTTGCAATAT                         GTACTTTGGCCAGAATGTGGATGGCAACCTGTA
genomic: CTGCTGGAAAAGAAGGCAATTTGCGTGCATTGCTATCAACTTTGCAATATgtaagtcctt ... tttctgacagGTACTTTGGCCAGAATGTGGATGGCAACCTGTA
EST: gi|88232794|gb|CI232038.1|CI232038
EST:     TTTGCGTGCATTGCTATCAACTTTGCAATAT                         GTACTTTGGCCAGAATGTGGATGGCAACCTGTATCCCTGACTGACTTGATT
genomic: TTTGCGTGCATTGCTATCAACTTTGCAATATgtaagtcctt ... tttctgacagGTACTTTGGCCAGAATGTGGATGGCAACCTGTATCCCTGACTGACTTGATT
EST: gi|88691955|gb|CI735530.1|CI735530
EST:     GGCAATTTGCGTGCATTGCTATCAACTTTGCAATAT                         GTACTTTGGCCAGAATGTGGATGGCAACCTGTATCCCTGACTGACTTGATT
genomic: GGCAATTTGCGTGCATTGCTATCAACTTTGCAATATgtaagtcctt ... tttctgacagGTACTTTGGCCAGAATGTGGATGGCAACCTGTATCCCTGACTGACTTGATT
EST: gi|88689066|gb|CI732642.1|CI732642
EST:     GGCAATTTGCGTGCATTGCTATCAACTTTGCAATAT                         GTACTTTGGCCAGAATGTGGATGGCAACCTGTATCCCTGACTGACTTGATT
genomic: GGCAATTTGCGTGCATTGCTATCAACTTTGCAATATgtaagtcctt ... tttctgacagGTACTTTGGCCAGAATGTGGATGGCAACCTGTATCCCTGACTGACTTGATT
EST: gi|33683328|gb|CF311567.1|CF311567
EST:     CTGCTGGAAAAGAAGGCAATTTGCGTGCATTGCTATCAACTTTGCAATAT                         GTACTTTGGCCAGAATGTGGATGGCAACCTGTATCCCTGACTGACTTGATT
genomic: CTGCTGGAAAAGAAGGCAATTTGCGTGCATTGCTATCAACTTTGCAATATgtaagtcctt ... tttctgacagGTACTTTGGCCAGAATGTGGATGGCAACCTGTATCCCTGACTGACTTGATT
EST: gi|29669274|gb|CB665549.1|CB665549
EST:     CTGCTGGAAAAGAAGGCAATTTGCGTGCATTGCTATCAACTTTGCAATAT                         GTACTTTGGCCAGAATGTGGATGGCAACCTGTATCCCTGACTGACTTGATT
genomic: CTGCTGGAAAAGAAGGCAATTTGCGTGCATTGCTATCAACTTTGCAATATgtaagtcctt ... tttctgacagGTACTTTGGCCAGAATGTGGATGGCAACCTGTATCCCTGACTGACTTGATT
EST: gi|38469324|gb|CF953455.1|CF953455
EST:     CTGCTGGAAAAGAAGGCAATTTGCGTGCATTGCTATCAACTTTGCAATAT                         GTACTTTGGCTAGAATGTGGATGGCAACCTGTATCCCTNACTGACTTGATT
genomic: CTGCTGGAAAAGAAGGCAATTTGCGTGCATTGCTATCAACTTTGCAATATgtaagtcctt ... tttctgacagGTACTTTGGCCAGAATGTGGATGGCAACCTGTATCCCTGACTGACTTGATT
EST: gi|88689029|gb|CI732605.1|CI732605
EST:     GGCAATTTGCGTGCATTGCTATCAACTTTGCAATAT                         GTACTTTGGCCAGAATGTGGATGGCAACCTGTATCCCTGACTGACTTGATT
genomic: GGCAATTTGCGTGCATTGCTATCAACTTTGCAATATgtaagtcctt ... tttctgacagGTACTTTGGCCAGAATGTGGATGGCAACCTGTATCCCTGACTGACTTGATT
EST: gi|58678718|gb|CK067405.1|CK067405
EST:     CTGCTGGAAAAGAAGGCAATTTGCGTGCATTGCTATCAACTTTGCAATAT                         GTACTTTGGCCAGAATGTGGATGGCAACCTGTATCCCTGACTGACTTGATT
genomic: CTGCTGGAAAAGAAGGCAATTTGCGTGCATTGCTATCAACTTTGCAATATgtaagtcctt ... tttctgacagGTACTTTGGCCAGAATGTGGATGGCAACCTGTATCCCTGACTGACTTGATT

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: 72 (upstream exon), 75 (downstream exon)
Score: 30

AGAATTTCAGAAACAATGGACTTTGAGATTAAGCGATGGGCTGCTGGAAAAGAAGGCAATTTGCGTGCATTGCTATCAACTTTGCAATATgtaagtcctt ... tttctgacagGTACTTTGGCCAGAATGTGGATGGCAACCTGTATCCCTGACTGACTTGATTACTGCTGCTGCGGTTAAAAAGGTATATAGAAAGGCAACATTGTGCATAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAATTTCAGAAACAATGGACTTTGAGATTAAGCGATGGGCTGCTGGAAAAGAAGGCAATTTGCGTGCATTGCTATCAACTTTGCAATATgtaagtccttattcctgatgctgctaaaaattgaatcaattatccttgtcttctcaatttttctattcattctctcggtgttattcttgcaaagaaagtt

- - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaagaaa