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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTCAGAAATATTTTAGACGAGGAGCGCGTCTAAATTGGCCTGAAGGTGCTGTTTCAAGAGAGAGTATCAGAGCAGTCAAAAAACTAGATCGGCTAAAGgttttggttccctcaattatgtctctttttttttgctacgtttatccccaatctaaattatatctctaaaattcaaaacaatattatgcatattcctgtt...

Basic information

species Oryza sativa
transcript LOC_Os01g40840.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g40840.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G094039_T06 (Zea mays), 5'ss of exon 9
AGCTCAGAAATATTTTAGACGAGGAGCGCGTCTAAATTGGCCTGAAGGTGCTGTTTCAAGAGAGAGTATCAGAGCAGTCAAAAAACTAGATCGGCTAAAGgttttggttccctcaattatgtctctttttttttgctacgtttatccccaatctaaattatatctctaaaattcaaaacaatattatgcatatt-cctgtt
||||||||||||||||||  ||| | | ||  ||||||||||||||||||||||||||||||| || |||||||| || |  ||||| ||||| ||||||||||| |||| |||  || |    ||||     ||||   | ||||  |   | |   | |  ||  | || |   || | | |  ||  | |   ||| |
AGCTCAGAAATATTTTAGGAGAGCAACACGATTAAATTGGCCTGAAGGTGCTGTTTCAAGAGAAAGCATCAGAGCTGTGAGGAAACTGGATCGACTAAAGgttttagttctctcgtttcttctactttggccatgct-tatctatcaacttaccacgctttgacttaagaaattttaatattttcttgtctttgatctgat

upper sequence: LOC_Os01g40840.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G366935_T08 (Zea mays), 5'ss of exon 10
AGCTCAGAAATATTTTAGACGAGGAGCGCGTCTAAATTGGCCTGAAGGTGCTGTTTCAAGAGAGAGTATCAGAGCAGTCAAAAAACTAGATCGGCTAAAGgttttggttccctcaattatgtctctttttttttgctacgtttatccccaatctaaattatatctctaaaattcaaaacaatattatgcatatt-cctgtt
       |||||||| ||  | | | | ||| ||||||||||||||||||||||||||||||| || |||||||| || || ||||| ||||| ||||||||||| ||||||||| || ||   ||||     ||||   |  |||  |   | | | | |  ||  | |  |   || | | |  ||  | |   ||| |
-------AAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGAAGGTGCTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAGgttttagttccctcatttctgctgctttggccgtgct-tatccatcaacttaccacactttgacttaagacattttaatattttcttgtctttggtctgat

upper sequence: LOC_Os01g40840.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G366935_T01 (Zea mays), 5'ss of exon 10
AGCTCAGAAATATTTTAGACGAGGAGCGCGTCTAAATTGGCCTGAAGGTGCTGTTTCAAGAGAGAGTATCAGAGCAGTCAAAAAACTAGATCGGCTAAAGgttttggttccctcaattatgtctctttttttttgctacgtttatccccaatctaaattatatctctaaaattcaaaacaatattatgcatatt-cctgtt
 |||||||||||||| ||  | | | | ||| ||||||||||||||||||||||||||||||| || |||||||| || || ||||| ||||| ||||||||||| ||||||||| || ||   ||||     ||||   |  |||  |   | | | | |  ||  | |  |   || | | |  ||  | |   ||| |
TGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGAAGGTGCTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAGgttttagttccctcatttctgctgctttggccgtgct-tatccatcaacttaccacactttgacttaagacattttaatattttcttgtctttggtctgat

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|58596016|gb|CK006544.1|CK006544
EST:     CTGTTTCAAGAGAGAGTATCAGAGCAGTCAAAAAACTAGATCGGCTAAAG                         GACTTAGTGGCGAGGAAGGCTGATCATTCAAGGGCGGTGCTGGCAGACTTG
genomic: CTGTTTCAAGAGAGAGTATCAGAGCAGTCAAAAAACTAGATCGGCTAAAGgttttggttc ... gaaacttcagGACTTAGTGGCGAGGAAGGCTGATCATTCAAGGGCGGTGCTGGCAGACTTG
EST: gi|86493399|gb|CI136032.1|CI136032
EST:     CTGTTTCAAGAGAGAGTATCAGAGCAGTCAAAAAACTAGATCGGCTAAAG                         GACTTAGTGGCGAGGAAGGCTGATCATTCAAGGGCGGTGCTGGCAGACTTG
genomic: CTGTTTCAAGAGAGAGTATCAGAGCAGTCAAAAAACTAGATCGGCTAAAGgttttggttc ... gaaacttcagGACTTAGTGGCGAGGAAGGCTGATCATTCAAGGGCGGTGCTGGCAGACTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTCAGAAATATTTTAGACGAGGAGCGCGTCTAAATTGGCCTGAAGGTGCTGTTTCAAGAGAGAGTATCAGAGCAGTCAAAAAACTAGATCGGCTAAAGgttttggttccctcaattatgtctctttttttttgctacgtttatccccaatctaaattatatctctaaaattcaaaacaatattatgcatattcctgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG