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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagatagatttatgtaggctagccagaccttgtaaactcttatgttgactagatggtccttaaaatatctaagtttttattattattctgtatatttgagtatttgacctgtttgtttggtgttccagGGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTGATCCCAAGGATGCTTGTTGTTGATCCAATGAAGAGAATCACAATTCGTG

Basic information

species Oryza sativa
transcript LOC_Os03g17980.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g17980.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G107867_T02 (Zea mays), 3'ss of exon 5
gtgagatagatttatgtaggctagccagaccttgtaaactcttatgttgactagatggtccttaaaatatctaagtttttattattattctgtatatttgagtatttgacctgtttgtttggtgttccagGGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTGATCCCAAGGATGCTTGTTGTTGATCCAATGAAGAGAATCACAATTCGTG
                                 | || | ||||||| || || |    ||||  || |  ||  || |        ||||| |  | |||  | |     | |   |||   |||  |||| ||||| || || || ||||||||||| |||||| ||||||| |||||||||||| | |||||||||||||| || |||||||||||||||||| | |
-----------------------------gtgagaaagcacttatgtggaatacaaa--ccttgcaacaattagattct-------gttctggagttatgaccactctctatctggttttacggttttagGGAGGTATCTACACACTTCCAAGTCATTTGTCTGCTTTGGCCAGGGATTTGATCCCACGAATGCTTGTTGTTGAGCCTATGAAGAGAATCACAATTAGGG

upper sequence: LOC_Os03g17980.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 5
gtgagatagatttatgtaggctagccagaccttgtaaactcttatgttgactagatggtccttaaaatatctaagtttttattattattctgtatatttgagtatttgacctgtttgtttggtgttccagGGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTGATCCCAAGGATGCTTGTTGTTGATCCAATGAAGAGAATCACAATTCGTG
      | ||||||   |   | |||   || |  || |  | ||||| ||  |       | || | ||||| |||||  || | ||   || ||  | | || ||   || |||        ||  ||||||| ||||| ||||| || |||||| ||||  ||   || ||||||||||| |||||||||||||| || ||||| |||||||| || || || | ||
-----ttggatttaccca---ttgcctatccctacaatcattgatgtt-accgg-------taaacagatcta-gttttgcttctgat---gtgtacctcactaatta--ctattt--------ttatagGGTGGGATATACACTCTTCCTAGTCATCTATCACCTGGTGCTAGAGATTTGATACCAAGGATGCTTGTGGTGGATCCCATGAAGAGGATGACCATACCTG

upper sequence: LOC_Os03g17980.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 5
gtgagatagatttatgtaggctagccagaccttgtaaactcttatgttgactagatg--gtccttaaaatatctaagtttttattattattctgtatatttgagtatttgacctgtttgtttggtgttccagGGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTGATCCCAAGGATGCTTGTTGTTGATCCAATGAAGAGAATCACAATTCGTG
                              ||  ||   || |||   || || ||    ||||   |||     | | |||  |   |||    || ||||     |  |||  |||  || || ||  ||||||| ||||||||||| || |||||||||||  ||   || |||||| ||||||||||||||||  | ||||| || |||||| |||| ||||||| ||
-----------------------------gctctta---tcctataaagagtacattttatcctatcaatcatatattattttctgagattaaaaatgtttgctccataaacccatttcatttgtattttagGGTGGGATATATACTCTTCCTAGTCATTTATCAACTGGTGCTAGAGATCTGATCCCAAGGATGCTCATAGTTGACCCTATGAAGCGAATGACAATTCCTG

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|58667418|gb|CK056104.1|CK056104
EST:     CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAG                         GGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTG
genomic: CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagataga ... ggtgttccagGGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTG
EST: gi|29627233|gb|CB632244.1|CB632244
EST:     CTCTTCCATATGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAG                         GGTGGTATATATACTCTCCCGAGTCATTTATCTGCTC
genomic: CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagataga ... ggtgttccagGGTGGTATATATACTCTCCCAAGTCATTTATCTGCTC
EST: gi|29663426|gb|CB659701.1|CB659701
EST:     CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAG                         GGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGG
genomic: CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagataga ... ggtgttccagGGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGG
EST: gi|117237395|gb|CT861888.1|CT861888
EST:     CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAG                         GGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCT
genomic: CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagataga ... ggtgttccagGGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCT
EST: gi|58666104|gb|CK054790.1|CK054790
EST:     CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAG                         GGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTG
genomic: CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagataga ... ggtgttccagGGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTG
EST: gi|58674982|gb|CK063669.1|CK063669
EST:     CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAG                         GGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTG
genomic: CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagataga ... ggtgttccagGGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTG
EST: gi|218482816|gb|FG952976.1|FG952976
EST:     CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAG                         GGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTG
genomic: CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagataga ... ggtgttccagGGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTG
EST: gi|218482252|gb|FG960526.1|FG960526
EST:     CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAG                         GGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTG
genomic: CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagataga ... ggtgttccagGGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTG
EST: gi|218502900|gb|FG954558.1|FG954558
EST:     CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCACAAAGATAAAG                         GGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTG
genomic: CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagataga ... ggtgttccagGGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTG
EST: gi|2317303|gb|C22357.1|C22357
EST:     CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAG                         GGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTG
genomic: CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagataga ... ggtgttccagGGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTG
EST: gi|218484843|gb|FG952392.1|FG952392
EST:     CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAG                         GGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTG
genomic: CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagataga ... ggtgttccagGGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTG
EST: gi|29616519|gb|CB621531.1|CB621531
EST:     CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAG                         GGTGGTATATATACTC
genomic: CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagataga ... ggtgttccagGGTGGTATATATACTC
EST: gi|29614995|gb|CB620008.1|CB620008
EST:     CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAG                         GGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTG
genomic: CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagataga ... ggtgttccagGGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTG
EST: gi|33381730|gb|CF197073.1|CF197073
EST:     CTCTTCCATTTGATGATGAGAATATCCCCANCCTATTCAAAAAGATAAAG                         GNTNGTATATATACTCTNNNNNGTCATTTATCTGCTCTGGCC
genomic: CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagataga ... ggtgttccagGGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCC
EST: gi|218488644|gb|FG955529.1|FG955529
EST:     CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAG                         GGTGGTATATATACTCTCC
genomic: CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagataga ... ggtgttccagGGTGGTATATATACTCTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttattattattctgtatatttgagtatttgacctgtttgtttggtgttccagGGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTGATCCCAAGGATGCTTGTTGTTGATCCAATGAAGAGAATCACAATTCGTG
                            atttgac  putative branch site (score: 4)
     attattattctgtata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagatagatttatgtaggctagccagaccttgtaaactcttatgttgactagatggtccttaaaatatctaagtttttattattattctgtatatttgagtatttgacctgtttgtttggtgttccagGGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTGATCCCAAGGATGCTTGTTGTTGATCCAATGAAGAGAATCACAATTCGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA