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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acccgatgttctatttcccacattttcagttttctgataggtactagttggtaagtttccattgcaacttctctaatgctattactcttttgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTCGATCTGTGTATGTTGGAAAT

Basic information

species Oryza sativa
transcript LOC_Os02g52140.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g52140.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G108919_T05 (Zea mays), 3'ss of exon 2
acccgatgttctatttc-ccacattttcagttttctgataggtactagttggtaagtttccattgcaac-ttctctaatgctattactcttttgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTCGATCTGTGTATGTTGGAAAT-----------------------------
   |  |  |   |||    |    || |  ||  |  ||  |  |  ||| | ||||     |||||  ||  || |    ||| ||||| ||||||| |||||| || |||||    |||||||||||||| ||||||||||||||||| || ||||||||||||||||||                             
taacattacttggtttggttaagggtttacattaatttta--tcttgcttgtttagttcaagatgcaaggtttcctgacagaattgctcttctgttttgcagGAGGTGACCCTAGTATATCTACAGCTGAGGCGAAGGAGCAGGTGGATGCCCGGTCTGTGTATGTTGGAAATGTAAGAATTTATAATCTCTCTTTATTGTG

upper sequence: LOC_Os02g52140.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G108919_T02 (Zea mays), 3'ss of exon 2
acccgatgttctatttc-ccacattttcagttttctgataggtactagttggtaagtttccattgcaac-ttctctaatgctattactcttttgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTCGATCTGTGTATGTTGGAAAT
   |  |  |   |||    |    || |  ||  |  ||  |  |  ||| | ||||     |||||  ||  || |    ||| ||||| ||||||| |||||| || |||||    |||||||||||||| ||||||||||||||||| || ||||||||||||||||||
taacattacttggtttggttaagggtttacattaatttta--tcttgcttgtttagttcaagatgcaaggtttcctgacagaattgctcttctgttttgcagGAGGTGACCCTAGTATATCTACAGCTGAGGCGAAGGAGCAGGTGGATGCCCGGTCTGTGTATGTTGGAAAT

upper sequence: LOC_Os02g52140.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G862331_T02 (Zea mays), 3'ss of exon 2
-acccgatgttctatttcccacattttcagttttctgataggtactagttggtaagtttccattgcaacttctct-aatgctattactcttttgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTCGATCTGTGTATGTTGGAAAT-----------------------------
 | |  || ||   ||   ||    || | ||   |  ||| |  |  ||  | |||||    |||||  | |||  |    ||| ||||| ||||||| |||||| || ||||| || |||||||||||||||||||||||||||||||| || ||||||||||||||||||                             
taacatatcttggtttggtcaagggtttacttcagttttagct--tgcttatttagtttaagatgcaaggtttcttgaaataattgctcttctgttttgcagGAGGTGACCCTAGTGCATCTACAGCTGAGGCAAAGGAGCAGGTGGATGCCCGTTCTGTGTATGTTGGAAATGTAAGAATTTATAATAATCTCCCTCTCTT

upper sequence: LOC_Os02g52140.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G862331_T04 (Zea mays), 3'ss of exon 2
-acccgatgttctatttcccacattttcagttttctgataggtactagttggtaagtttccattgcaacttctct-aatgctattactcttttgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTCGATCTGTGTATGTTGGAAAT
 | |  || ||   ||   ||    || | ||   |  ||| |  |  ||  | |||||    |||||  | |||  |    ||| ||||| ||||||| |||||| || ||||| || |||||||||||||||||||||||||||||||| || ||||||||||||||||||
taacatatcttggtttggtcaagggtttacttcagttttagct--tgcttatttagtttaagatgcaaggtttcttgaaataattgctcttctgttttgcagGAGGTGACCCTAGTGCATCTACAGCTGAGGCAAAGGAGCAGGTGGATGCCCGTTCTGTGTATGTTGGAAAT

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|32948090|gb|BP184662.1|BP184662
EST:     GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAG                         GAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
genomic: GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGgtggtccgcc ... tgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
EST: gi|86830660|gb|CI293677.1|CI293677
EST:     GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAG                         GAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
genomic: GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGgtggtccgcc ... tgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
EST: gi|88326696|gb|CI658422.1|CI658422
EST:     GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAG                         GAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
genomic: GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGgtggtccgcc ... tgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
EST: gi|88376927|gb|CI639252.1|CI639252
EST:     GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAG                         GAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
genomic: GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGgtggtccgcc ... tgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
EST: gi|88353264|gb|CI654530.1|CI654530
EST:     GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAG                         GAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
genomic: GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGgtggtccgcc ... tgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
EST: gi|66926559|gb|CX113407.1|CX113407
EST:     GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAG                         GAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
genomic: GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGgtggtccgcc ... tgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
EST: gi|88351377|gb|CI627393.1|CI627393
EST:     GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAG                         GAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
genomic: GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGgtggtccgcc ... tgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
EST: gi|33664619|gb|CF295586.1|CF295586
EST:     GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAG                         GAGGAGATCCTAGTGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
genomic: GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGgtggtccgcc ... tgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
EST: gi|218499461|gb|FG958244.1|FG958244
EST:     GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAG                         GAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
genomic: GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGgtggtccgcc ... tgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
EST: gi|88587501|gb|CI705252.1|CI705252
EST:     GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAG                         GAGGAGATCCTAGCGCGTCTACAGCTGAGGCCAAGGAGCAGGTGGATGCTC
genomic: GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGgtggtccgcc ... tgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
EST: gi|32948232|gb|BP184804.1|BP184804
EST:     GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAG                         GAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
genomic: GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGgtggtccgcc ... tgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
EST: gi|88327844|gb|CI648241.1|CI648241
EST:     GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAG                         GAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
genomic: GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGgtggtccgcc ... tgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttggtaagtttccattgcaacttctctaatgctattactcttttgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTCGATCTGTGTATGTTGGAAAT
                         ctctaat  putative branch site (score: 3)
                                    ttactcttttgtttt  putative PPT
                                          ttttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acccgatgttctatttcccacattttcagttttctgataggtactagttggtaagtttccattgcaacttctctaatgctattactcttttgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTCGATCTGTGTATGTTGGAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - -ttctgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cattgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctaatgc