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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcatgtcttagtattatagtatatagttaaccatattttccttgagaatcatcattttattgttctatggataaattaaattgctttgcgtggcagGAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGATATTCCTCTTGAG

Basic information

species Oryza sativa
transcript LOC_Os02g10310.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g10310.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G029566_T01 (Zea mays), 3'ss of exon 9
------------------------------------gtgagcatgtc-ttagtattatagtatata---gttaaccatattttccttgagaatcatcattttattgttctatg------gataaattaaattgctttgcgtggcagGAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGATATTCCTCTTGAG
                                     | ||    ||  |||   | ||||  | |   || |      ||    ||   ||||| |||||||| |  ||  |      | | |  ||| |  | |||| |  |||||||| || ||||| || |||||||| |||||||| ||| |||| || || ||||||||||| 
gtgaggaaacattctttaagatttatcgttggaataatcagttaatcactagcgct-tagttaacaccggtcagtttggttagtttttctaatcagcattttatagaacttcgatccatggtgacctaattctccttgcattacagGAACCCGAGCCTTTACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAA

upper sequence: LOC_Os02g10310.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G093359_T02 (Zea mays), 3'ss of exon 9
------------------------------gtgagcatgtct-tagtatta---tagtatatagttaaccatattttccttgagaatcatcattttat-------tgttctatggataaattaaattgctttgcgtggcagGAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGATATTCCTCTTGAG
                               |||     ||  |||| |||   ||  || |   | |   | ||    ||   ||||| ||||||||           | ||||  |   ||| |  |||||| |  |||||||| |||||||| || ||| ||||||||||||| ||| ||||||| || ||||||||||| 
gtgaggaaatagtgtctttaagatttattattgaaataatcaatagttttaagctaacat-tgactgattctgttagtttttctaatcagcattttatgtaacttcagcccatgggcac-ctaattctctttgcattacagGAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAA
















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:     TCGTTACTATGGATGCCCTAAAGCCTTTCACCTGTGAAGCTCCTAAGCAG                         GAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGAT
genomic: TCGTTACTATGGATGCCCTAAAGCCTTTCACCTGTGAAGCTCCTAAGCAGgtgagcatgt ... tgcgtggcagGAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGAT
EST: gi|29672587|gb|CB668862.1|CB668862
EST:     TCGTTACTATGGATGCCCTAAAGCCTTTCACCTGTGAAGCTCCTAAGCAG                         GAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGAT
genomic: TCGTTACTATGGATGCCCTAAAGCCTTTCACCTGTGAAGCTCCTAAGCAGgtgagcatgt ... tgcgtggcagGAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGAT
EST: gi|29612852|gb|CB617865.1|CB617865
EST:     TCGTTACTATGGATGCCCTAAAGCCTTTCACCTGTGAAGCTCCTAAGCAG                         GAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGAT
genomic: TCGTTACTATGGATGCCCTAAAGCCTTTCACCTGTGAAGCTCCTAAGCAGgtgagcatgt ... tgcgtggcagGAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGAT
EST: gi|29657905|gb|CB654180.1|CB654180
EST:     TCGTTACTATGGATGCCCTAAAGCCTTTCACCTGTGAAGCTCCTAAGCAG                         GAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGAT
genomic: TCGTTACTATGGATGCCCTAAAGCCTTTCACCTGTGAAGCTCCTAAGCAGgtgagcatgt ... tgcgtggcagGAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGAT
EST: gi|29671043|gb|CB667318.1|CB667318
EST:     TCGTTACTATGGATGCCCTAAAGCCTTTCACCTGTGAAGCTCCTAAGCAG                         GAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGAT
genomic: TCGTTACTATGGATGCCCTAAAGCCTTTCACCTGTGAAGCTCCTAAGCAGgtgagcatgt ... tgcgtggcagGAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGAT
EST: gi|163929432|gb|EG713401.1|EG713401
EST:     TCGTTACTATGGATGCCCTAAAGCCTTTCACCTGTGAAGCTCCTAAGCAG                         GAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGAT
genomic: TCGTTACTATGGATGCCCTAAAGCCTTTCACCTGTGAAGCTCCTAAGCAGgtgagcatgt ... tgcgtggcagGAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGAT
EST: gi|117232667|gb|CT861058.1|CT861058
EST:     TCGTTACTATGGATGCCCTAAAGCCTTTCACCTGTGAAGCTCCTAAGCAG                         GAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGAT
genomic: TCGTTACTATGGATGCCCTAAAGCCTTTCACCTGTGAAGCTCCTAAGCAGgtgagcatgt ... tgcgtggcagGAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGAT
EST: gi|29637362|gb|CB642371.1|CB642371
EST:     TCGTTACTATGGATGCCCTAAAGCCTTTCACCTGTGAAGCTCCTAAGCAG                         GAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGAT
genomic: TCGTTACTATGGATGCCCTAAAGCCTTTCACCTGTGAAGCTCCTAAGCAGgtgagcatgt ... tgcgtggcagGAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGAT
EST: gi|29672144|gb|CB668419.1|CB668419
EST:     TCGTTACTATGGATGCCCTAAAGCCTTTCACCTGTGAAGCTCCTAAGCAG                         GAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGAT
genomic: TCGTTACTATGGATGCCCTAAAGCCTTTCACCTGTGAAGCTCCTAAGCAGgtgagcatgt ... tgcgtggcagGAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGAT
EST: gi|88691997|gb|CI735572.1|CI735572
EST:     TCGTTACTATGGATGCCCTAAAGCCTTTCACCTGTGAAGCTCCTAAGCAG                         GAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGAT
genomic: TCGTTACTATGGATGCCCTAAAGCCTTTCACCTGTGAAGCTCCTAAGCAGgtgagcatgt ... tgcgtggcagGAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGAT
EST: gi|29643533|gb|CB648540.1|CB648540
EST:     TCGTTACTATGGATGCCCTAAAGCCTTTCACCTGTGAAGCTCCTAAGCAG                         GAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGAT
genomic: TCGTTACTATGGATGCCCTAAAGCCTTTCACCTGTGAAGCTCCTAAGCAGgtgagcatgt ... tgcgtggcagGAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGAT
EST: gi|29636552|gb|CB641561.1|CB641561
EST:     TCGTTACTATGGATGCCCTAAAGCCTTTCACCTGTGAAGCTCCTAAGCAG                         GAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGAT
genomic: TCGTTACTATGGATGCCCTAAAGCCTTTCACCTGTGAAGCTCCTAAGCAGgtgagcatgt ... tgcgtggcagGAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGAT
EST: gi|29636597|gb|CB641606.1|CB641606
EST:     TCGTTACTATGGATGCCCTAAAGCCTTTCACCTGTGAAGCTCCTAAGCAG                         GAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGAT
genomic: TCGTTACTATGGATGCCCTAAAGCCTTTCACCTGTGAAGCTCCTAAGCAGgtgagcatgt ... tgcgtggcagGAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGAT
EST: gi|29664840|gb|CB661115.1|CB661115
EST:     TCGTTACTATGGATGCCCTAAAGCCTTTCACCTGTGAAGCTCCTAAGCAG                         GAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGAT
genomic: TCGTTACTATGGATGCCCTAAAGCCTTTCACCTGTGAAGCTCCTAAGCAGgtgagcatgt ... tgcgtggcagGAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGAT
EST: gi|88690598|gb|CI734677.1|CI734677
EST:     TCGTTACTATGGATGCCCTAAAGCCTTTCACCTGTGAAGCTCCTAAGCAG                         GAACCTGAACCTTTGCCTTACTTACCTGAAAAGAACCACGTAAACTACGAT
genomic: TCGTTACTATGGATGCCCTAAAGCCTTTCACCTGTGAAGCTCCTAAGCAGgtgagcatgt ... tgcgtggcagGAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGAT
EST: gi|27548667|gb|CA766758.2|CA766758
EST:     TCGTTACTATGGATGCCCTAAAGCCTTTCACCTGTGAAGCTCCTAAGCAG                         GAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGAT
genomic: TCGTTACTATGGATGCCCTAAAGCCTTTCACCTGTGAAGCTCCTAAGCAGgtgagcatgt ... tgcgtggcagGAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgagaatcatcattttattgttctatggataaattaaattgctttgcgtggcagGAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGATATTCCTCTTGAG
                                       ttgcttt  CT-rich tract
            attttattgttctatg  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcatgtcttagtattatagtatatagttaaccatattttccttgagaatcatcattttattgttctatggataaattaaattgctttgcgtggcagGAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGATATTCCTCTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC