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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattatgcgccttatgtcctaaatcttttctgtcaaaaccaatcataaatactttggtccttaaatggtgcaagttattatttatttcttatctaaatacataattttgtaatctgattccaatattcatctatggtatgttcatgtgtttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGAAGTGCGGATAGCGGCTGCAGGGAAAGTTACTAAGTTCTGTAGGATTTTA

Basic information

species Oryza sativa
transcript LOC_Os09g07510.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 5
gtattatgcgccttatgtcctaaatcttttctgtcaaaaccaatcataaatactttggtccttaaatggtgcaagttattatttatttcttatctaaatacataattttgtaatctgattccaatattcatcta-tggtatgttcat-gtgtttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGAAGTGCGGATAGCGGCTGCAGGGAAAGTTACTAAGTTCTGTAGGATTTTA
                ||  | |||||| | | |  |    ||    ||||     | | |||   ||    || ||  |  ||  ||  ||  |  | | || | |    ||  | || |||  | || | || |  |  |  ||| |  |||  ||||||||   |  ||||| | || |||||||| || ||  ||||||||||||| ||||||||||| || ||||| || |||||||| || ||||| |  || |||
----------------gtgttcaatcttctttctttatgttaa----aaat-----gattctt---tgacataaattgattattgctttatacatggaaagattaat---caacataatgccatgactcgtttactattgagaccattgccttttataatagGGGTGATCTGGTGTCAGCGTATGTTCGCCTTCTCTGTGACAATGAGGCTGAAGTGCGGATTGCAGCTGCTGGAAAAGTTACAAAATTCTGCAAAATATTA

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 4
gtattatgcgccttatgtcctaaatcttttctgtcaaaaccaatcataaatactttggtccttaaatggtgcaagttattatttatttcttatctaaatacata----attttgtaatctgattccaat-attcatctatggtatgttcatgtgtttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGAAGTGCGGATAGCGGCTGCAGGGAAAGTTACTAAGTTCTGTAGGATTTTA
                                                             | |  |  | | | ||  |  ||  |   |  |   ||  |||    ||||  |  ||  |||| | |      | |||   ||| | |||   |||    ||||    | ||||| || |||||||||||||| || ||||| |||||||| ||||| || || || ||||| |||||||| |||||||| |   | ||||||
-------------------------------------------------------------tgacttcatactaatttcttcttggtctatgacatgatttatagtgtatttgtttctcacattctagttgactgtttatataatggtgatgcacttg----tagGTCAGAATTGGTCCCTGCATATGTTCGTCTGCTGCGTGATAATGAGGCTGAAGTACGTATTGCTGCTGCTGGGAAAGTAACTAAGTTTTCCCGCATTTTA

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA09G31760.1 (Glycine max), 3'ss of exon 5
gtattatgcgccttatgtcctaaatcttttctgtcaaaaccaatcataaatactttggtccttaaatggtgcaagttattatttatttcttatctaaatacataattttgtaatctgattccaatattcatctatggtatgttcatgtgtttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGAAGTGCGGATAGCGGCTGCAGGGAAAGTTACTAAGTTCTGTAGGATTTTA
                                                   |  ||  |   |   ||||  | |  || ||||||    ||| |  ||   | |  || |||| ||| |          | |||   ||| | |||   |||   ||  | |    ||||| || |||||||||||||| || ||||| |||||||| ||||| || || || ||||| |||||||| |||||||| |   | || |||
--------------------------------------------tgacttcatattaatttcttcttggtctatgacatgatttatagtgtattt--atttctcacattctaat-tgactt---------tttatatgatggtgatgcacttgcagATCAGAA----TTGGTCCCTGCATATGTTCGTCTGCTGCGTGATAATGAGGCTGAAGTACGTATTGCTGCTGCTGGGAAAGTAACTAAGTTTTCCCGCATATTA

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 6
gtattatgcgccttatgtcctaaatcttttctgtcaaaaccaatcataaatactttggtccttaaatggtgcaagttattatttatttct-tatctaaatacataattttgtaatctgattccaatattcatctatggt--atgttcatgtgtttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGAAGTGCGGATAGCGGCTGCAGGGAAAGTTACTAAGTTCTGTAGGATTTTA
                                                          |  ||  || |    | |  | || | | ||  | | | || | || ||||    || | |||   || || |  |||| |  ||  | || || |   |   |||    | ||||| || |||||||||||  | ||||||||||||||||| ||||| || ||||| |||||||| ||||| || || || ||  ||||||| 
----------------------------------------------------------tttttggattggtttattcctgatctgtgtccattttttaacaaattattt----atataattgttat-ttgacttatgattgataattatttgatattttgcagGTCAGACTTGGTTCCTGCATATGTTCGGTTGCTTCGTGACAATGAGGCTGAAGTACGCATAGCAGCTGCAGGAAAAGTAACAAAATTTTGCCGGATTTTG

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|300215963|gb|HO088589.1|HO088589
EST:     GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG                         GGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCTGA
genomic: GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAGgtattatgcg ... ttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
EST: gi|58654414|gb|CK043094.1|CK043094
EST:     GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG                         GGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
genomic: GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAGgtattatgcg ... ttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
EST: gi|86904336|gb|CI306754.1|CI306754
EST:     CAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG                         GGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
genomic: CAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAGgtattatgcg ... ttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
EST: gi|58652709|gb|CK041389.1|CK041389
EST:     GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG                         GGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
genomic: GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAGgtattatgcg ... ttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
EST: gi|38474762|gb|CF958895.1|CF958895
EST:     GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG                         GGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
genomic: GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAGgtattatgcg ... ttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
EST: gi|33654809|gb|CF277423.1|CF277423
EST:     GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG                         GGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
genomic: GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAGgtattatgcg ... ttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
EST: gi|58593044|gb|CF991352.1|CF991352
EST:     GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG                         GGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCTGA
genomic: GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAGgtattatgcg ... ttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
EST: gi|33796143|gb|CF323937.1|CF323937
EST:     GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG                         GGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
genomic: GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAGgtattatgcg ... ttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
EST: gi|29635602|gb|CB640611.1|CB640611
EST:     GGCAGTTGGTCCTGAACATTCTAG                         GGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
genomic: GGCAGTTGGTCCTGAACATTCTAGgtattatgcg ... ttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
EST: gi|58598714|gb|CK009242.1|CK009242
EST:     GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG                         GGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
genomic: GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAGgtattatgcg ... ttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
EST: gi|218487576|gb|FG960599.1|FG960599
EST:     GAGCTCTGCGAGGCAGGTTGGTCCTGAACATTCTAG                         GGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
genomic: GAGCTCTGCGAGGCA-GTTGGTCCTGAACATTCTAGgtattatgcg ... ttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
EST: gi|300215769|gb|HO088395.1|HO088395
EST:     GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG                         GGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCTGA
genomic: GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAGgtattatgcg ... ttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
EST: gi|3768380|gb|AU032407.1|AU032407
EST:     GGTCCTGAACATTCTAG                         GGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
genomic: GGTCCTGAACATTCTAGgtattatgcg ... ttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
EST: gi|58655438|gb|CK044118.1|CK044118
EST:     GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG                         GGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
genomic: GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAGgtattatgcg ... ttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
EST: gi|33676187|gb|CF304426.1|CF304426
EST:     GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG                         GGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
genomic: GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAGgtattatgcg ... ttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
EST: gi|58678838|gb|CK067525.1|CK067525
EST:     GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG                         GGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA
genomic: GCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAGgtattatgcg ... ttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgtaatctgattccaatattcatctatggtatgttcatgtgtttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGAAGTGCGGATAGCGGCTGCAGGGAAAGTTACTAAGTTCTGTAGGATTTTA
       atctgat  putative branch site (score: 4)
                 aatattcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattatgcgccttatgtcctaaatcttttctgtcaaaaccaatcataaatactttggtccttaaatggtgcaagttattatttatttcttatctaaatacataattttgtaatctgattccaatattcatctatggtatgttcatgtgtttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGAAGTGCGGATAGCGGCTGCAGGGAAAGTTACTAAGTTCTGTAGGATTTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG