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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAGAGATATCCAAGCTTGGGAAACTATACCTCTTGGACCTTTCCTTGGGAAAAGTTTCAgtaagacacctgatgccttttcagttatacttatgccatgttcactaatacaccactctctgttgaaaagtttcctgcacatttattgcttagtttttac...

Basic information

species Oryza sativa
transcript LOC_Os02g10310.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g10310.3 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G029566_T02 (Zea mays), 5'ss of exon 7
CCAGAGATATCCAAGCTTGGGAAACTATACCTCTTGGACCTTTCCTTGGGAAAAGTTTCAgtaagacacctgatgccttttcagttatactt-atgccatgttcactaatac-----accactctctgttga-----aaagtt-----tcctgcacatttattgctta-gtttttac----------------------------------------------------------------------
||||||||||||| |||||||| |||||||||||||||||||||||||||||||| ||||||||||||| ||||||| ||  | | | |||| | |   | |  || |||        |||  || | |  |     ||||||     |||||||   |||     |    ||                                                                          
CCAGAGATATCCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCAgtaagacacttgatgccctt--aatgaaactttaggttttctaaacaaatcttaagggccatgctttataaacaaaaaaagttagaagtcctgcaagcttaacatatgcacttccgtcattttcccttttgggctccatatttcagttgtgacctgaaaatgtactgtgcttctacaatttctctag

upper sequence: LOC_Os02g10310.3 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G093359_T02 (Zea mays), 5'ss of exon 8
CCAGAGATATCCAAGCTTGGGAAACTATACCTCTTGGACCTTTCCTTGGGAAAAGTTTCAgtaagacacctgatgccttttcagttatact--tatgccatgttcactaatacaccactctct------gttgaaaagtttcctgcacatttattgcttagtttttac-------------------------------------------------------------------------------
|||||||||| || |||||||| |||||||||||||||||||||||||||||||| ||||||||| |||||||| || |||  |  |   |  |||  |      | || ||    | |||||      ||| ||||   |     |   |    |||||   | | |                                                                               
CCAGAGATATTCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCAgtaagccacctgataccctttatgaaactttagtatttctcaacaaatattaagatattctctttataagttaaaaaaagttagaaatcctgcaagcttaacatatgcgcttccgtcatttttccccttttggcttcatatttcaattgtgacctgaaaattctccgtgcttctacaatttctctag
















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|29660372|gb|CB656647.1|CB656647
EST:     GAAAAGTTTCA                         GTACCACAGTATCACCNTGGATCGTTACTATGGATGCCCTAAAGCCTTTCA
genomic: GAAAAGTTTCAgtaagacacc ... tgatttttagGTACCACAGTATCACCCTGGATCGTTACTATGGATGCCCTAAAGCCTTTCA
EST: gi|29672587|gb|CB668862.1|CB668862
EST:     CCAAGCTTGGGAAACTATACCTCTTGGACCTTTCCTTGGGAAAAGTTTCA                         GTACCACAGTATCACCCTGGATCGTTACTATGGATGCCCTAAAGCCTTTCA
genomic: CCAAGCTTGGGAAACTATACCTCTTGGACCTTTCCTTGGGAAAAGTTTCAgtaagacacc ... tgatttttagGTACCACAGTATCACCCTGGATCGTTACTATGGATGCCCTAAAGCCTTTCA
EST: gi|29612852|gb|CB617865.1|CB617865
EST:     CCAAGCTTGGGAAACTATACCTCTTGGACCTTTCCTTGGGAAAAGTTTCA                         GTACCACAGTATCACCCTGGATCGTTACTATGGATGCCCTAAAGCCTTTCA
genomic: CCAAGCTTGGGAAACTATACCTCTTGGACCTTTCCTTGGGAAAAGTTTCAgtaagacacc ... tgatttttagGTACCACAGTATCACCCTGGATCGTTACTATGGATGCCCTAAAGCCTTTCA
EST: gi|29657905|gb|CB654180.1|CB654180
EST:     CCAAGCTTGGGAAACTATACCTCTTGGACCTTTCCTTGGGAAAAGTTTCA                         GTACCACAGTATCACCCTGGATCGTTACTATGGATGCCCTAAAGCCTTTCA
genomic: CCAAGCTTGGGAAACTATACCTCTTGGACCTTTCCTTGGGAAAAGTTTCAgtaagacacc ... tgatttttagGTACCACAGTATCACCCTGGATCGTTACTATGGATGCCCTAAAGCCTTTCA
EST: gi|29672586|gb|CB668861.1|CB668861
EST:     CCAAGCTTGGGAAACTATACCTCTTGGACCTTTCCTTGGGAAAAGTTTCA                         GTACCACAGTATCACCCTGGATCGTTACTATGGAT
genomic: CCAAGCTTGGGAAACTATACCTCTTGGACCTTTCCTTGGGAAAAGTTTCAgtaagacacc ... tgatttttagGTACCACAGTATCACCCTGGATCGTTACTATGGAT
EST: gi|29671043|gb|CB667318.1|CB667318
EST:     CCAAGCTTGGGAAACTATACCTCTTGGACCTTTCCTTGGGAAAAGTTTCA                         GTACCACAGTATCACCCTGGATCGTTACTATGGATGCCCTAAAGCCTTTCA
genomic: CCAAGCTTGGGAAACTATACCTCTTGGACCTTTCCTTGGGAAAAGTTTCAgtaagacacc ... tgatttttagGTACCACAGTATCACCCTGGATCGTTACTATGGATGCCCTAAAGCCTTTCA
EST: gi|163929432|gb|EG713401.1|EG713401
EST:     CCAAGCTTGGGAAACTATACCTCTTGGACCTTTCCTTGGGAAAAGTTTCA                         GTACCACAGTATCACCCTGGATCGTTACTATGGATGCCCTAAAGCCTTTCA
genomic: CCAAGCTTGGGAAACTATACCTCTTGGACCTTTCCTTGGGAAAAGTTTCAgtaagacacc ... tgatttttagGTACCACAGTATCACCCTGGATCGTTACTATGGATGCCCTAAAGCCTTTCA
EST: gi|117232667|gb|CT861058.1|CT861058
EST:     CCAAGCTTGGGAAACTATACCTCTTGGACCTTTCCTTGGGAAAAGTTTCA                         GTACCACAGTATCACCCTGGATCGTTACTATGGATGCCCTAAAGCCTTTCA
genomic: CCAAGCTTGGGAAACTATACCTCTTGGACCTTTCCTTGGGAAAAGTTTCAgtaagacacc ... tgatttttagGTACCACAGTATCACCCTGGATCGTTACTATGGATGCCCTAAAGCCTTTCA
EST: gi|29637362|gb|CB642371.1|CB642371
EST:     CCAAGCTTGGGAAACTATACCTCTTGGACCTTTCCTTGGGAAAAGTTTCA                         GTACCACAGTATCACCCTGGATCGTTACTATGGATGCCCTAAAGCCTTTCA
genomic: CCAAGCTTGGGAAACTATACCTCTTGGACCTTTCCTTGGGAAAAGTTTCAgtaagacacc ... tgatttttagGTACCACAGTATCACCCTGGATCGTTACTATGGATGCCCTAAAGCCTTTCA
EST: gi|29672144|gb|CB668419.1|CB668419
EST:     CCAAGCTTGGGAAACTATACCTCTTGGACCTTTCCTTGGGAAAAGTTTCA                         GTACCACAGTATCACCCTGGATCGTTACTATGGATGCCCTAAAGCCTTTCA
genomic: CCAAGCTTGGGAAACTATACCTCTTGGACCTTTCCTTGGGAAAAGTTTCAgtaagacacc ... tgatttttagGTACCACAGTATCACCCTGGATCGTTACTATGGATGCCCTAAAGCCTTTCA
EST: gi|88691997|gb|CI735572.1|CI735572
EST:     CCAAGCTTGGGAAACTATACCTCTTGGACCTTTCCTTGGGAAAAGTTTCA                         GTACCACAGTATCACCCTGGATCGTTACTATGGATGCCCTAAAGCCTTTCA
genomic: CCAAGCTTGGGAAACTATACCTCTTGGACCTTTCCTTGGGAAAAGTTTCAgtaagacacc ... tgatttttagGTACCACAGTATCACCCTGGATCGTTACTATGGATGCCCTAAAGCCTTTCA
EST: gi|29643533|gb|CB648540.1|CB648540
EST:     CCAAGCTTGGGAAACTATACCTCTTGGACCTTTCCTTGGGAAAAGTTTCA                         GTACCACAGTATCACCCTGGATCGTTACTATGGATGCCCTAAAGCCTTTCA
genomic: CCAAGCTTGGGAAACTATACCTCTTGGACCTTTCCTTGGGAAAAGTTTCAgtaagacacc ... tgatttttagGTACCACAGTATCACCCTGGATCGTTACTATGGATGCCCTAAAGCCTTTCA
EST: gi|29636552|gb|CB641561.1|CB641561
EST:     GGGAAAAGTTTCA                         GTACCACAGTATCACCCTGGATCGTTACTATGGATGCCCTAAAGCCTTTCA
genomic: GGGAAAAGTTTCAgtaagacacc ... tgatttttagGTACCACAGTATCACCCTGGATCGTTACTATGGATGCCCTAAAGCCTTTCA
EST: gi|29636597|gb|CB641606.1|CB641606
EST:     CTTGGGAAAAGTTTCA                         GTACCACAGTATCACCCTGGATCGTTACTATGGATGCCCTAAAGCCTTTCA
genomic: CTTGGGAAAAGTTTCAgtaagacacc ... tgatttttagGTACCACAGTATCACCCTGGATCGTTACTATGGATGCCCTAAAGCCTTTCA
EST: gi|88324389|gb|CI566202.1|CI566202
EST:     CCAAGCTTGGGAAACTATACCTCTTGGACCTTTCCTTGGGAAAAGTTTCA                         GTACCACAGTATCACCCTGGATCGTTACTATGG
genomic: CCAAGCTTGGGAAACTATACCTCTTGGACCTTTCCTTGGGAAAAGTTTCAgtaagacacc ... tgatttttagGTACCACAGTATCACCCTGGATCGTTACTATGG
EST: gi|29664840|gb|CB661115.1|CB661115
EST:     CCAAGCTTGGGAAACTATACCTCTTGGACCTTTCCTTGGGAAAAGTTTCA                         GTACCACAGTATCACCCTGGATCGTTACTATGGATGCCCTAAAGCCTTTCA
genomic: CCAAGCTTGGGAAACTATACCTCTTGGACCTTTCCTTGGGAAAAGTTTCAgtaagacacc ... tgatttttagGTACCACAGTATCACCCTGGATCGTTACTATGGATGCCCTAAAGCCTTTCA
EST: gi|88690598|gb|CI734677.1|CI734677
EST:     CCAAGCTTGGGAAACTATACCTCTTGGACCTTTCCTTGGGAAAAGTTTCA                         GTACCACAGTATCACCCTGGATCGTTACTATGGATGCCCTAAAGCCTTTCA
genomic: CCAAGCTTGGGAAACTATACCTCTTGGACCTTTCCTTGGGAAAAGTTTCAgtaagacacc ... tgatttttagGTACCACAGTATCACCCTGGATCGTTACTATGGATGCCCTAAAGCCTTTCA
EST: gi|27548667|gb|CA766758.2|CA766758
EST:     CCAAGCTTGGGAAACTATACCTCTTGGACCTTTCCTTGGGAAAAGTTTCA                         GTACCACAGTATCACCCTGGATCGTTACTATGGATGCCCTAAAGCCTTTCA
genomic: CCAAGCTTGGGAAACTATACCTCTTGGACCTTTCCTTGGGAAAAGTTTCAgtaagacacc ... tgatttttagGTACCACAGTATCACCCTGGATCGTTACTATGGATGCCCTAAAGCCTTTCA

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: 58 (upstream exon), 74 (downstream exon)
Score: 39

CCAGAGATATCCAAGCTTGGGAAACTATACCTCTTGGACCTTTCCTTGGGAAAAGTTTCAgtaagacacc ... tgatttttagGTACCACAGTATCACCCTGGATCGTTACTATGGATGCCCTAAAGCCTTTCACCTGTGAAGCTCCTAAGCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAGAGATATCCAAGCTTGGGAAACTATACCTCTTGGACCTTTCCTTGGGAAAAGTTTCAgtaagacacctgatgccttttcagttatacttatgccatgttcactaatacaccactctctgttgaaaagtttcctgcacatttattgcttagtttttac

- - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccactctc