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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagccacccacgcgccgtagccaccctcatctcaggcgctaggttttggagccgaggggatctcgcagagcttgtgattttcctattcgttgtggagttattttttttaattttttgtgtgggttgatttggttctgatgtcgtttgcttgtcatgtctggtacgattttgcagACCGGATGACACGCCGTGGGATGGAG

Basic information

species Oryza sativa
transcript LOC_Os03g57790.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g57790.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G007260_T01 (Zea mays), 3'ss of exon 1
gtagccacccacgcgccgtagccaccctcatctcaggcgctaggttttggagccgaggggatctcgcagagcttgtgattttcctattcgttgtggagttattttttttaattttttgtgtgggttgatttggttctgatgtcgtttgcttgtcatgtctggtacgattttgcagACCGGATGACACGCCGTGGGATGGAG
            |       ||| ||    |||  |  | ||||||    |||| | ||                      ||  ||  | || |  | |    |     | ||   |||  |  ||   || || || | | ||           || || | ||||| ||||| |||||||||||||||||||| ||||
------------gtaatcaggccgcctatttctgtgatgttaggttagctagcctaagga---------------------tctgatgaggtgcgaggctgcaat-----acttacggtgctgactg---tgcttttgctattgtc----------gtttgttgcgattctgcagGCCGGATGACACGCCGTGGGACGGAG

upper sequence: LOC_Os03g57790.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G007260_T05 (Zea mays), 3'ss of exon 1
--------gtagcc-acccacgcgccgt------agccaccctca---tctca---ggcgctaggttttggagccgaggggatctcgcagagcttgtgattttcctattcgttgtggagttattttttt--taattttttgtgtgggttgatttggttctgatgtcgttt-gcttgtcatgtctggtacgattttgcagACCGGATGACACGCCGTGGGATGGAG--
        |  ||| |     | |  ||      ||| | ||| |   ||| |   || || ||| |      |  | ||   ||  | | |||| || | ||    || |||| |    |          | |      ||| ||   ||  ||   |  ||    ||| | ||| |  |    |||     |      | || |    | |  |||| |   |  
gtaatcaggccgcctatttctgtgatgttaggttagctagcctaaggatctgatgaggtgcgaggctgcaatacttacggtg-ctgactgtgcttttgctattgtcgtttgttgcgattctgcagGCCGGATGACACGCCGTG-GGACGGAGGTGAGACCCATCCGATTTAGTTTGCCTCGATCTGTAATTGCTCAATAGCTGGCTTCTGCACTTTGGG-TACTGCC

upper sequence: LOC_Os03g57790.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G120674_T01 (Zea mays), 3'ss of exon 1
gtagccacccacgcgccgtagccaccctcatctcaggcgctaggttttggagccgaggggatctcgcagagcttgtgattttcctattcgttgtggagttattttttttaattttttgtgtgggttgatttggttctgatgtcgtttgcttgtcatgtctggtacgattttgcagACCGGATGACACGCCGTGGGATGGAG
            |   |    || ||    |||  |  | ||||||    |||| | || |||| |    || || |       || |  | ||||         |||||||           | ||| |  | |         ||| ||  |  ||| || | ||||| ||||| |||||||||||||||||||||||||
------------gtatca-gcccgcctatttctgtgatgttaggttagctagcctaagg-atctagtgaggcgtgaggccgcgatacttttggtggg--------ttttaat-----------gctgactgtgct---------ttttctcttggtgtttgttgcgattctgcagGCCGGATGACACGCCGTGGGATGGAG

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|11025772|gb|AU162373.1|AU162373
EST:     ACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: ACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|58688873|gb|CK077560.1|CK077560
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|38469192|gb|CF953323.1|CF953323
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|4716198|gb|AU057314.1|AU057314
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|38468844|gb|CF952975.1|CF952975
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|218505167|gb|FG956727.1|FG956727
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|38469613|gb|CF953744.1|CF953744
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|58590675|gb|CF988983.1|CF988983
EST:     GGGGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|42592241|gb|CK738727.1|CK738727
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|218485740|gb|FG958740.1|FG958740
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|27576883|gb|CA999577.1|CA999577
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|38468296|gb|CF952427.1|CF952427
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|38474625|gb|CF958758.1|CF958758
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|86419732|gb|CI054533.1|CI054533
EST:     GCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|38480664|gb|CF964753.1|CF964753
EST:     GCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|58677295|gb|CK065982.1|CK065982
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|29666285|gb|CB662560.1|CB662560
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|33797775|gb|CF324747.1|CF324747
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|218500669|gb|FG957555.1|FG957555
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgggttgatttggttctgatgtcgtttgcttgtcatgtctggtacgattttgcagACCGGATGACACGCCGTGGGATGGAG
             ttctgat  putative branch site (score: 3)
                                              atttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagccacccacgcgccgtagccaccctcatctcaggcgctaggttttggagccgaggggatctcgcagagcttgtgattttcctattcgttgtggagttattttttttaattttttgtgtgggttgatttggttctgatgtcgtttgcttgtcatgtctggtacgattttgcagACCGGATGACACGCCGTGGGATGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA