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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGCTAACAAACCTCCAGATAGTTGGTTTGATCTCAAAGTTAACACACATGTCTACGTTACTGGTTTGCCTGATGATGTCACAGCTGAGGAGgtaagttgcttatatctttaaaagcactttgtatgctttgaatgacctatttaacacattcatgattatgtaaatagtgtctggttttgatggtgaatttcttttgcag

Basic information

species Oryza sativa
transcript LOC_Os04g41910.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g41910.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G411893_T01 (Zea mays), 5'ss of exon 4
GAAGCTAACAAACCTCCAGATAGTTGGTTTGATCTCAAAGTTAACACACATGTCTACGTTACTGGTTTGCCTGATGATGTCACAGCTGAGGAGgtaagttgcttatatctttaaaa---gcactttgtatgctttg-----------------aatgacctatttaacacattcatgattatgt--------aaatagtgtctggttt-------tgatggtgaatttcttttgcag
||||||||||||||||| || |||||||||||||||||||| |||||||||||||| || ||||||||||||||||||||||| |  |||||||||| |||||| || |    ||     || ||  | |   ||                  ||||||| || || || || | | ||||| |        ||| |||   || | |       ||||| || |||||||||||||
GAAGCTAACAAACCTCCGGACAGTTGGTTTGATCTCAAAGTAAACACACATGTCTATGTAACTGGTTTGCCTGATGATGTCACGGTGGAGGAGgtaaattgcttctaccaactaactctacatttcatttctcttatagagataattttgtttaatgacc-atgtagcaaatgcttaattatttggttatttaaaaagtacttgttctgcacttgtgatgctggatttcttttgcag

upper sequence: LOC_Os04g41910.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G074351_T01 (Zea mays), 5'ss of exon 5
GAAGCTAACAAACCTCCAGATAGTTGGTTTGATCTCAAAGTTAACACACATGTCTACGTTACTGGTTTGCCTGATGATGTCACAGCTGAGGAGgtaagttgcttatatct-ttaaaagcactttgtatgctt-------------------tgaatgacctatttaacacattcatgatta-----------tgtaaatagt-gtctgg---ttttgatggtgaatttcttttgcag
|||||||||||||||||||| |||||||||||||||||||||||||||||||||||| | |||||||| ||||||||||| ||||  |||||||||| |||||| || |   |||    || ||  ||   |                   ||||||||| || || || |||| | ||||             ||| || | ||   |   || ||||| ||  ||||||||||||
GAAGCTAACAAACCTCCAGACAGTTGGTTTGATCTCAAAGTTAACACACATGTCTACATAACTGGTTTACCTGATGATGTTACAGTGGAGGAGgtaaattgcttctaacaactaattatacatttcatttctcttttagagatcgttttgttgaatgacc-atgtagcaaattcttaattaattggttatttcataagtacttgttccgaacttctgatgatggttttcttttgcag

upper sequence: LOC_Os04g41910.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G171660_T02 (Zea mays), 5'ss of exon 5
GAAGCTAACAAACCTCCAGATAGTTGGTTTGATCTCAAAGTTAACACACATGTCTACGTTACTGGTTTGCCTGATGATGTCACAGCTGAGGAGgtaagttgcttatatctttaaaagc---actttgtatgctttg-----------------aatgacc---tatttaacac---attcat-gattatgtaaatagtgtctggttt-------tgatggtgaatttcttttgcag
||||||||||||||||| || |||||||||||||||||||| |||||||||||||| || |||||||||||||||||||||||||  |||||||||| |||||| || |    ||  |   | ||  | |   ||                  |||||||   ||   ||| |   ||| || | |||| |||| |||   || | |       ||||| || ||| |||||||||
GAAGCTAACAAACCTCCGGACAGTTGGTTTGATCTCAAAGTAAACACACATGTCTATGTAACTGGTTTGCCTGATGATGTCACAGTGGAGGAGgtaaattgcttctaccaactaattctatatttcatttctcttatagagatcattttgtttaatgaccatgtaacaaacgcttaattaattggttatttaaaaagtacttgttctgcacttgtgatgctggattccttttgcag

upper sequence: LOC_Os04g41910.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G353114_T01 (Zea mays), 5'ss of exon 8
GAAGCTAACAAACCTCCAGATAGTTGGTTTGATCTCAAAGTTAACACACATGTCTACGTTACTGGTTTGCCTGATGATGTCACAGCTGAGGAGgtaagttgcttatatctttaaaa---gcactttgtatgctttg-----------------aatgacctatttaacacattcatgattatgt--------aaatagtgtctggttt-------tgatggtgaatttcttttgcag
||||||||||||||||| || |||||||||||||||||||| |||||||||||||| || |||||||||||| |||||||||| |  |||||||||| |||||| || |    ||     || ||  | |   ||                  ||||||| || || || || | | ||||| |        ||| |||   || | |       ||||| || |||||||||||||
GAAGCTAACAAACCTCCGGACAGTTGGTTTGATCTCAAAGTAAACACACATGTCTATGTAACTGGTTTGCCTAATGATGTCACGGTGGAGGAGgtaaattgcttctaccaactaactctacatttcatttctcttatagagataattttgtttaatgacc-atgtagcaaatgcttaattatttggttatttaaaaagtacttgttctgcacttgtgatgctggatttcttttgcag

upper sequence: LOC_Os04g41910.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv00s0499g00010.t01 (Vitis vinifera), 5'ss of exon 6
GAAGCTAACAAACCTCCAGATAGTTGGTTTGATCTCAAAGTTAACACACATGTCTACGTTACTGGTTTGCCTGATGATGTCACAGCTGAGGAGgtaagttgcttatatctttaaaagcactttgtatgctttgaatgacctatttaacacattcatgattatgtaaatagtgtctggttttgatggtgaatttcttttgcag
||||||||||||||||| ||||||||||| ||| | |||||||| |||||||| || || || || ||||| |||||||| || | ||| ||||||||  | | |  | |           | | ||    |   |   || |      ||||||  |    |  |||||   ||| || |  || ||  | |||  |    
GAAGCTAACAAACCTCCTGATAGTTGGTTCGATTTAAAAGTTAATACACATGTTTATGTGACCGGGTTGCCAGATGATGTTACTGTTGACGAGgtaagacggtcaattttgcttttatctctggaatatgattcttattctgtgactagcattcacaa----gataatagca-ctgtttctagtgttgcttatctcct----

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|32948435|gb|BP185007.1|BP185007
EST:     ACACACATGTCTACGTTACTGGTTTGCCTGATGATGTCACAGCTGAGGAG                         ATTGTGGAGGTATTTTCCAAATGTGGAATTATAAAGGAG
genomic: ACACACATGTCTACGTTACTGGTTTGCCTGATGATGTCACAGCTGAGGAGgtaagttgct ... tcttttgcagATTGTGGAGGTATTTTCCAAATGTGGAATTATAAAGGAG
EST: gi|89190588|gb|CI392441.1|CI392441
EST:     ACACACATGTGTACGTTACTGGTTTGCCTGATGATGTCACAGCTGAGGAG                         ATTGTGGAGGTATTTTCCAAATGTGGAATTATAAAGGAG
genomic: ACACACATGTCTACGTTACTGGTTTGCCTGATGATGTCACAGCTGAGGAGgtaagttgct ... tcttttgcagATTGTGGAGGTATTTTCCAAATGTGGAATTATAAAGGAG
EST: gi|88502487|gb|CI429993.1|CI429993
EST:     ACACACATGTCTACGTTACTGGTTTGCCTGATGATGTCACAGCTGAGGAG                         ATTGTGGAGGTATTTTCCAAATGTGGAATTATAAAGGAG
genomic: ACACACATGTCTACGTTACTGGTTTGCCTGATGATGTCACAGCTGAGGAGgtaagttgct ... tcttttgcagATTGTGGAGGTATTTTCCAAATGTGGAATTATAAAGGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGCTAACAAACCTCCAGATAGTTGGTTTGATCTCAAAGTTAACACACATGTCTACGTTACTGGTTTGCCTGATGATGTCACAGCTGAGGAGgtaagttgcttatatctttaaaagcactttgtatgctttgaatgacctatttaacacattcatgattatgtaaatagtgtctggttttgatggtgaatttcttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG