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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctatttcctcccattcttcatcatatccgcaatattagattcttccgagttaataggataagtaagaacaatttttttttacaagataatatgcttttaatagGTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAG

Basic information

species Oryza sativa
transcript LOC_Os02g07760.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07760.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G119482_T01 (Zea mays), 3'ss of exon 9
gttctatttcctcccattcttcatcatatccgcaatattagattcttccgagttaataggataagtaagaacaatttttttttacaagataatatg-cttttaat-agGTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAG
||| |||||||||||||  |   |   ||| ||| | ||    | |  |    ||||| |  ||||| ||| | || |  || |||  |||||||  |||||  | |||||||||||||||||||||| || |||||||||||||| |||||||||||||||||||| |||||||||||||| |||
gttttatttcctcccatcttgtcttgcatctgcagtttt---ctttgtctttataatatgtcaagtaggaatacttgtggttgacactataatataacttttggttagGTCAGAAAGATTACATTCACTGGATCAACAGCTGTTGGGAAAAAACTGATGGCTGGATCTGCAAATACTGTGAAAAAG

upper sequence: LOC_Os02g07760.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G128114_T03 (Zea mays), 3'ss of exon 8
gttctatttcctcccattcttcatcatatccgcaatattagattcttccgagttaataggataagtaagaacaatttttttttacaagataatatg-cttttaat-agGTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAG
  ||| |||||||||||  |   |   ||| | | | ||    | |  |    ||||| |  ||||| ||| | |  |  || |||  |||||||  ||||| || |||||||||||||||| ||||| || ||||||||||||||||||||||||||||||| ||| |||||||||||||| |||
-gtctgtttcctcccatcttgtcttgcatctgtactttt---ctttgtctttataatatgtcaagtaggaatactagtggttgacactataatataacttttgattagGTCAGAAAGATTACGTTCACTGGATCAACAGCTGTTGGCAAAAAACTGATGGCTGAATCTGCAAATACTGTGAAAAAG

upper sequence: LOC_Os02g07760.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA15G41690.1 (Glycine max), 3'ss of exon 9
gttctatttcctcccattcttcatcatatccgcaatattagattcttccgagttaataggataagtaagaacaatt---tttttttacaagataatat--gcttttaatagGTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAG
                            || |  |   ||   | || |||   |||    |  || |    ||||     | |    |||| | |||   | ||   ||||| || ||||| ||||||||||| || || |||||||| || ||| |||||||||| |||||  | || || || || 
--------------------------gttctgtgaccatattattttacgaagcaattacctt-gtgaatgtaattgaacatctgagaaagaaattatcaaccttatttagGTAAGGAAGATCACATTCACAGGCTCGACGGCTGTTGGGAAGAAATTGATGGCTGGTTCAGCTGAAACAGTTAAAAAA

upper sequence: LOC_Os02g07760.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA08G17450.1 (Glycine max), 3'ss of exon 9
gttctatttcctcccattcttcatcatatccgcaatattagattcttccgagttaataggataagtaagaacaatttttttttaca-agataatatgcttttaatagGTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAG
                       |  | |   | || |||  ||     |   | |     | | |   |   |     |   | | | || ||   | ||   ||||| || ||||| ||||||||||| || ||||| ||||| || ||| |||||||||| |||||  | || || || || 
----------------------gttctgtt-accatgttattttacgaagcaattaccttgtgaatgtaattgagcgcctgaaaaagaaattatcaaccttatttagGTAAGGAAGATCACATTCACAGGCTCGACAGCAGTTGGGAAGAAATTGATGGCTGGTTCAGCTGAAACAGTTAAAAAA

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|218498176|gb|FG949780.1|FG949780
EST:     TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAG                         GTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGC-AAAAACTGATG
genomic: TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAGgttctatttc ... cttttaatagGTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATG
EST: gi|218492832|gb|FG951181.1|FG951181
EST:     TGATGGGTAATGCTCCTGAGATAGGTGATGCTCGACTCCAGAGTACACAG                         GTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATG
genomic: TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAGgttctatttc ... cttttaatagGTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATG
EST: gi|88288968|gb|CI520298.1|CI520298
EST:     TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAG                         GTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATG
genomic: TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAGgttctatttc ... cttttaatagGTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATG
EST: gi|218492318|gb|FG946726.1|FG946726
EST:     TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAG                         GTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATG
genomic: TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAGgttctatttc ... cttttaatagGTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATG
EST: gi|88519470|gb|CI447124.1|CI447124
EST:     TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAG                         GTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATG
genomic: TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAGgttctatttc ... cttttaatagGTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATG
EST: gi|218490731|gb|FG966180.1|FG966180
EST:     TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAG                         GTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATG
genomic: TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAGgttctatttc ... cttttaatagGTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATG
EST: gi|66918914|gb|CX105762.1|CX105762
EST:     TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAG                         GTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATG
genomic: TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAGgttctatttc ... cttttaatagGTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATG
EST: gi|218488132|gb|FG951352.1|FG951352
EST:     TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAG                         GTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATG
genomic: TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAGgttctatttc ... cttttaatagGTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATG
EST: gi|58694576|gb|CK083263.1|CK083263
EST:     TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAG                         GTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCNNNNNNNCTGAT
genomic: TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAGgttctatttc ... cttttaatagGTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGC-AAAAAACTGAT
EST: gi|218491346|gb|FG955033.1|FG955033
EST:     TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAG                         GTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATG
genomic: TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAGgttctatttc ... cttttaatagGTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttaataggataagtaagaacaatttttttttacaagataatatgcttttaatagGTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAG
 agttaat  putative branch site (score: 4)
                                           tgctttt  putative PPT
                  aacaatttttttttac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttctatttcctcccattcttcatcatatccgcaatattagattcttccgagttaataggataagtaagaacaatttttttttacaagataatatgcttttaatagGTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG