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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaaacagtttagcatttttttcaagtcactttgacaatttgagcagggccatatatgacctctctcttctgttattactagGTGCGTGAGGTTGGCTAGATTTGAGAATGATAGAACTATATCCTTCATACCTCCTGACGGATCTTTCGATCTAATGACATACAGACTTAGCACCCAG

Basic information

species Oryza sativa
transcript LOC_Os01g50770.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g50770.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G162145_T01 (Zea mays), 3'ss of exon 6
gtaagtaaacagtttagcatttttttcaagtcactttgacaatttgagcagggccatatatgacctctctcttctgttattactagGTGCGTGAGGTTGGCTAGATTTGAGAATGATAGAACTATATCCTTCATACCTCCTGACGGATCTTTCGATCTAATGACATACAGACTTAGCACCCAG
||||| ||| | | |  |  |||| |  |   | |  |     |    |     ||   ||||||  ||||     || ||  |||||| ||  | || |||||||| |||||||||||||||||||| |||||||||||||| |||||||| ||||||||||||||||| |||||||| |||
gtaagcaaaaaatatttctcttttcttcaccaaatccgttgcatc--actaattca-gcatgaccattctccc---ttctttttagGTGTGTACGTTTAGCTAGATTCGAGAATGATAGAACTATATCGTTCATACCTCCTGATGGATCTTTTGATCTAATGACATACAGGCTTAGCACTCAG

upper sequence: LOC_Os01g50770.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G436835_T02 (Zea mays), 3'ss of exon 7
gtaagtaaacagtttagcatttttttcaagtcactttgacaatttgagcagggccata-tatgacctctctcttctgttattactagGTGCGTGAGGTTGGCTAGATTTGAGAATGATAGAACTATATCCTTCATACCTCCTGACGGATCTTTCGATCTAATGACATACAGACTTAGCACCCAG
    |||| ||   ||    | ||||   | ||||    |  ||  | ||       | | |||||  ||||     || ||  |||||| ||  | |||||||||||||||||||||||||||||||| |||||||||||||| |||||||| ||||||||||||||||| |||||||| |||
----gtaagcaaaatactgctcttttt--ggcactaaatctgttgcatcactaattcagtgtgaccattctccc---ttctttttagGTGTGTACGTTTGGCTAGATTTGAGAATGATAGAACTATATCGTTCATACCTCCTGATGGATCTTTTGATCTAATGACATACAGGCTTAGCACTCAG

upper sequence: LOC_Os01g50770.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv00s0225g00220.t01 (Vitis vinifera), 3'ss of exon 6
----------------------------------------------------------------------------gtaagtaaacagtttagcatttttttcaagtcactttgacaatttga--gcagggccatatatgacctctctcttctgttattactagGTGCGTGAGGTTGGCTAGATTTGAGAATGATAGAACTATATCCTTCATACCTCCTGACGGATCTTTCGATCTAATGACATACAGACTTAGCACCCAG
                                                                             |  | |||      ||   |  |||   |  |  ||   | | | |  ||| |  |  | |  |  | |   |  | || ||  ||| || ||  | |||||| |||||||||||||| |||| |||||||| || ||||| || |||||||| ||||| |||||||| || || || || |||
gtatgtagtcaaacttttttgtgtagttgtaatctgctgctggtaattaatttttattttttttctgataattatcatgtgcaaaactgcaagggctgatttattgcaaactttctattcttactgcaagatctcaaactaaatgtgcttatttttgtt-ttagATGTGTTCGTTTGGCTCGATTTGAGAATGATCGAACAATATCCTTTATTCCTCCAGATGGATCTTTTGATCTCATGACATATAGGCTCAGTACTCAG

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|163923569|gb|EG713310.1|EG713310
EST:     CGAGCTACTAAAGGAAAAGCAATAGATCTTGATGATATTAAATTTCACCA                         GTGCGTGAGGTTGGCTAGATTTGAGGATGATAGAACTATATCCTTCATACC
genomic: CGAGCTACTAAAGGAAAAGCAATAGATCTTGATGATATTAAATTTCACCAgtaagtaaac ... ttattactagGTGCGTGAGGTTGGCTAGATTTGAGAATGATAGAACTATATCCTTCATACC
EST: gi|58589259|gb|CF987567.1|CF987567
EST:     CGAGCTACTAAAGGAAAAGCAATAGATCTTGATGATATTAAATTTCACCA                         GTGCGTGAGGTTGGCGAGATTTGAGAATGATAGAACTATATCCTTCATACC
genomic: CGAGCTACTAAAGGAAAAGCAATAGATCTTGATGATATTAAATTTCACCAgtaagtaaac ... ttattactagGTGCGTGAGGTTGGCTAGATTTGAGAATGATAGAACTATATCCTTCATACC
EST: gi|27554506|gb|CA998406.1|CA998406
EST:     CGAGCTACTAAAGGAAAAGCAATAGATCTTGATGATATTAAATTTCACCA                         GTGCGTGAGGTTGGCTAGATTTGAGAATGATAGAACTATATCCTTCATACC
genomic: CGAGCTACTAAAGGAAAAGCAATAGATCTTGATGATATTAAATTTCACCAgtaagtaaac ... ttattactagGTGCGTGAGGTTGGCTAGATTTGAGAATGATAGAACTATATCCTTCATACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactttgacaatttgagcagggccatatatgacctctctcttctgttattactagGTGCGTGAGGTTGGCTAGATTTGAGAATGATAGAACTATATCCTTCATACCTCCTGACGGATCTTTCGATCTAATGACATACAGACTTAGCACCCAG
  ctttgac  putative branch site (score: 4)
                                cctctctcttctgtta  putative PPT
                                             ttattacta  TA-rich tract