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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGACGGACTGTGAAGTGGACTTTGCACCTCCTCTTGATTACAAAGAACCTGAAAATCCGCAGCAACCATCAGTTCCTGCAAGTGAGGCAACTGCTGAAGgtttgtctttagattaagtgcactttagttttcagatgaacttgtattgaaaggctgaattttatcctcctcttctatagcaatttttcaagtgtgctgc...

Basic information

species Oryza sativa
transcript LOC_Os04g48770.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g48770.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G114220_T02 (Zea mays), 5'ss of exon 8
GAGACGGACTGTGAAGTGGACTTTGCACCTCCTCTTGATTACAAAGAACCTGAAAATCCGCAGCAACCATCAGTTCCTGCAAGTGAGGCAACTGCTGAAGgtttgtctttaga---ttaagtgcactttagttttcagatgaacttgtattgaaaggctgaattttatcctcctcttctatagcaatttttcaagtgtgctgc
||||| |||||||||||||||||||| |||||||||||||| ||||||||||| || || |  |||||| |||||||||||||  ||||| ||||||||||||||| |||||    ||      |   | |  |    ||    |||  |||  |       || | |     |      || |  |  |     | |     
GAGACAGACTGTGAAGTGGACTTTGCGCCTCCTCTTGATTATAAAGAACCTGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAGgtttgtatttagcatcttggagaaatcatggcctatgaattctgttgatttgttacatgtgcttgttttacagttgatcttatcgttcctatttatatag---

upper sequence: LOC_Os04g48770.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA08G05030.1 (Glycine max), 5'ss of exon 8
---GAGACGGACTGTGAAGTGGACTTTGCACCTCCTCTTGATTACAAAGAACCTGAAAATCCGCAGCAACCATCAGTTCCTGCAAGTGAGGCAACTGCTGAAGgtttgtctttagattaagtgcactt----tagttttcagatgaacttgtattgaaaggctgaattttatcctcctcttctatagcaatttttcaagtgtgctgc
   ||||| |||||||| ||||||||||| |||||  | |||||||| ||||||||||| || ||     || |  || ||||  |  ||||| | |  |  ||| ||   ||   |||  |    ||     || | ||   |     ||| | |   |    ||| |    |||    ||| |   |  | ||   || |     
ATTGAGACTGACTGTGAGGTGGACTTTGCTCCTCCCTTGGATTACAAGGAACCTGAAAAACC-CATTG--CACCCCTTTCTGCCGGAAAGGCAGCAGTGGCTGgtatgcacttgacttacttatgtttgtcacagatgtctcttttctctgtctggtcggatgaaatctctctctctctctctctgtgacatgtttctgtata----

upper sequence: LOC_Os04g48770.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA05G34630.2 (Glycine max), 5'ss of exon 8
---GAGACGGACTGTGAAGTGGACTTTGCACCTCCTCTTGATTACAAAGAACCTGAAAATCCGCAGCAACCATCAGTTCCTGCAAGTGAGGCAACTGCTGAAGgtttgtctttagattaagtgcactttagttttcagatgaacttgtattgaaaggctgaattttatcctcctcttctatagcaatttttcaagtgtgctgc-
   ||||| |||||||| ||||||||||| |||||  | |||||||| ||||||||||| || ||     || |  || ||||  |  ||||| | |  |  ||| ||   || || | | ||   |||    |  |  |    ||    ||   ||  | || |    |||    ||| |  |  | | ||       ||   
ATTGAGACTGACTGTGAGGTGGACTTTGCTCCTCCCTTGGATTACAAGGAACCTGAAAAACC-CACTG--CACCCCTTTCTGCTGGGAAGGCAGCAGTGGCTGgtatgcactt-gacttactgatttttgtcatagatgtctcttttctctgtctggtcggatctctctctctctctctctctctctctctctctctctctctg

upper sequence: LOC_Os04g48770.2 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv03s0038g00750.t01 (Vitis vinifera), 5'ss of exon 8
---GAGACGGACTGTGAAGTGGACTTTGCACCTCCTCTTGATTACAAAGAACCTGAAAATCCGCAGCAACCATCAGTTCCTGCAAGTGAGGCAACTGCTGAAGgtttgtctttagattaagtgcactttagttttcagatgaacttgtattgaaaggctga-attttatcctcctcttctatagcaattttt-caagtgtgctgc
   ||||| |||||||| ||||| ||||||||||||||||||| ||||||||| ||||| ||   |   | | | |||||     |  ||||| | |||||||||     | |        |         | ||    | |  |   ||||     ||   |||  ||| |  |  |   |  | |||    ||||    ||  
ATTGAGACAGACTGTGAGGTGGATTTTGCACCTCCTCTTGATTTCAAAGAACCAGAAAAGCCT--GTTGC-ACCTGTTCCCCTGGGCAAGGCAGCAGCTGAAGgtgaacatctcatcagcttatttagctatgtttcatttatttcacattgtctttctttcattccatcatagttctaggtttccattccaacaagcccact--

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|427856|gb|D23997.1|D23997
EST:     TGAAAATCCGCAGCAACCATCAGTTCCTGCAAGTGAGGCAACTGCTGAAG                         ATGAAAATGCTAAAGTTGAAGATGAACTGAAATTCAAGCCGTTTACTGGTT
genomic: TGAAAATCCGCAGCAACCATCAGTTCCTGCAAGTGAGGCAACTGCTGAAGgtttgtcttt ... ttcccaccagATGAAAATGCTAAAGTTGAAGATGAACTGAAATTCAAGCCGTTTACTGGTT
EST: gi|58687667|gb|CK076354.1|CK076354
EST:     TGAAAATCCGCAGCAACCATCAGTTCCTGCAAGTGAGGCAACTGCTGAAG                         ATGAAAATGCTAAAGTTGGAGATGAACTGAAATTCAGGCCGTTTACTGGTT
genomic: TGAAAATCCGCAGCAACCATCAGTTCCTGCAAGTGAGGCAACTGCTGAAGgtttgtcttt ... ttcccaccagATGAAAATGCTAAAGTTGAAGATGAACTGAAATTCAAGCCGTTTACTGGTT
EST: gi|11173107|gb|AU164616.1|AU164616
EST:     TGAAAATCNGCAGCAACCATCAGTTCCTGCAAGTGAGGCAACTGCTGAAG                         ATGAAAATGCTAAAGTTGAAGATGAACTGAAATTCAAGCCGTTTACTGGTT
genomic: TGAAAATCCGCAGCAACCATCAGTTCCTGCAAGTGAGGCAACTGCTGAAGgtttgtcttt ... ttcccaccagATGAAAATGCTAAAGTTGAAGATGAACTGAAATTCAAGCCGTTTACTGGTT
EST: gi|58603204|gb|CK013732.1|CK013732
EST:     TGAAAATCCGCAGCAACCATCAGTTCCTGCAAGTGAGGCAACTGCTGAAG                         ATGAAAATGCTAAAGTTGGAGATGAACTGAAATTCAGGCCGTTTACTGGTT
genomic: TGAAAATCCGCAGCAACCATCAGTTCCTGCAAGTGAGGCAACTGCTGAAGgtttgtcttt ... ttcccaccagATGAAAATGCTAAAGTTGAAGATGAACTGAAATTCAAGCCGTTTACTGGTT
EST: gi|86498019|gb|CI140652.1|CI140652
EST:     TGAAAATCCGCAGCAACCATCAGTTCCTGCTAGTGAGGCAACTGCTGAAG                         ATGAAAATGCTAAAGTTGAAGATGAACTGAAATTCAAGCCGTTTACTGGTT
genomic: TGAAAATCCGCAGCAACCATCAGTTCCTGCAAGTGAGGCAACTGCTGAAGgtttgtcttt ... ttcccaccagATGAAAATGCTAAAGTTGAAGATGAACTGAAATTCAAGCCGTTTACTGGTT
EST: gi|86430668|gb|CI083091.1|CI083091
EST:     CAAGTGAGGCAACTGCTGAAG                         ATGAAAATGCTAAAGTTGAAGATGAACTGAAATTCAAGCCGTTTACTGGTT
genomic: CAAGTGAGGCAACTGCTGAAGgtttgtcttt ... ttcccaccagATGAAAATGCTAAAGTTGAAGATGAACTGAAATTCAAGCCGTTTACTGGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGACGGACTGTGAAGTGGACTTTGCACCTCCTCTTGATTACAAAGAACCTGAAAATCCGCAGCAACCATCAGTTCCTGCAAGTGAGGCAACTGCTGAAGgtttgtctttagattaagtgcactttagttttcagatgaacttgtattgaaaggctgaattttatcctcctcttctatagcaatttttcaagtgtgctgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctcctc