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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacagtggtacacacactacagattcttaagctactgaaactatggtcctatggacctatggttaccaaggtatgatcagtagttttctgtcgagtccatgattcatgcagtagcattaccatccttgatttgcagACTGCAGCAGCGACGTCTTCGTTTATGGTCCTTTTCTGCGCATCCATGTCGATGGTTCAGTTCATCCTGCTAGGCATGCAAGGCATCGGAGAAGCTTCTG

Basic information

species Oryza sativa
transcript LOC_Os01g57710.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g57710.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G116670_T01 (Zea mays), 3'ss of exon 3
gtacagtggtacacacactacagattcttaagctactgaaactatggtcctatggacctatggttaccaaggtatgatcagtagttttctgtcgagtccatgattcatgcagtagcattaccatccttgatttgcagACTGCAGCAGCGACGTCTTCGTTTATGGTCCTTTTCTGCGCATCCATGTCGATGGTTCAGTTCATCCTGCTAGGCATGCAAGGCATCGGAGAAGCTTCTG
||     |||||||| || ||     |    ||      |     | ||||    |  | | | | | |||     ||   |||     |  ||   |  ||| |||| || |   ||           || ||||||| || ||||||||||||||||| |||||||| ||||| || |||||||| ||||| |||||||||||||| ||| || ||||| ||||  | || |  |
gtcgtacggtacaca-acaacgacgccccgggc------attcgcgttcctccctaa-tgttgctgcaaagtccatatatatag----gtaccgtaccagtgaatcattcaattctatgt---------atctgcagACCGCGGCAGCGACGTCTTCGTTCATGGTCCTGTTCTGTGCGTCCATGTCCATGGTCCAGTTCATCCTGCTGGGCGTGGAAGGCGTCGGGCAGGCCTGCG

upper sequence: LOC_Os01g57710.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G116670_T02 (Zea mays), 3'ss of exon 3
gtacagtggtacacacactacagattcttaagctactgaaactatggtcctatggacctatggttaccaaggtatgatcagtagttttctgtcgagtccatgattcatgcagtagcattaccatccttgatttgcagACTGCAGCAGCGACGTCTTCGTTTATGGTCCTTTTCTGCGCATCCATGTCGATGGTTCAGTTCATCCTGCTAGGCATGCAAGGCATCGGAGAAGCTTCTG
        ||||||| || ||     |    ||      |     | ||||    |  | | | | | |||     ||   |||     |  ||   |  ||| |||| || |   ||           || ||||||| || ||||||||||||||||| |||||||| ||||| || |||||||| ||||| |||||||||||||| ||| || ||||| ||||  | || |  |
--------gtacaca-acaacgacgccccgggc------attcgcgttcctccctaa-tgttgctgcaaagtccatatatatag----gtaccgtaccagtgaatcattcaattctatgt---------atctgcagACCGCGGCAGCGACGTCTTCGTTCATGGTCCTGTTCTGTGCGTCCATGTCCATGGTCCAGTTCATCCTGCTGGGCGTGGAAGGCGTCGGGCAGGCCTGCG
















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|86505990|gb|CI148623.1|CI148623
EST:     GAGGCCTACTTCTGAACCCTGTTCTTCTTCAGATTGGAATACCACCGCAG                         ACTGCAGCAGCGACGTCTTCGTTTATGGTCCTTTTCTGCGCATCCATGTCG
genomic: GAGGCCTACTTCTGAACCCTGTTCTTCTTCAGATTGGAATACCACCGCAGgtacagtggt ... tgatttgcagACTGCAGCAGCGACGTCTTCGTTTATGGTCCTTTTCTGCGCATCCATGTCG
EST: gi|87015232|gb|CI275422.1|CI275422
EST:     GAGGCCTACTTCTGAACCCTGTTCTTCTTCAGATTGGAATACCACCGCAG                         ACTGCAGCAGCGACGTCTTCGTTTATGGTCCTTTTCTGCGCATCCATGTCG
genomic: GAGGCCTACTTCTGAACCCTGTTCTTCTTCAGATTGGAATACCACCGCAGgtacagtggt ... tgatttgcagACTGCAGCAGCGACGTCTTCGTTTATGGTCCTTTTCTGCGCATCCATGTCG
EST: gi|86539782|gb|CI179988.1|CI179988
EST:     GAGGCCTACTTCTGAACCCTGTTCTTCTTCAGATTGGAATACCACCGCAG                         ACTGCAGCAGCGACGTCTTCGTTTATGGTCCTTTTCTGCGCATCCATGTCG
genomic: GAGGCCTACTTCTGAACCCTGTTCTTCTTCAGATTGGAATACCACCGCAGgtacagtggt ... tgatttgcagACTGCAGCAGCGACGTCTTCGTTTATGGTCCTTTTCTGCGCATCCATGTCG
EST: gi|86597951|gb|CI276737.1|CI276737
EST:     GAGGCCTACTTCTGAACCCTGTTCTTCTTCAGATTGGAATACCACCGCAG                         ACTGCAGCAGCGACGTCTTCGTTTATGGTCCTTTTCTGCGCATCCATGTCG
genomic: GAGGCCTACTTCTGAACCCTGTTCTTCTTCAGATTGGAATACCACCGCAGgtacagtggt ... tgatttgcagACTGCAGCAGCGACGTCTTCGTTTATGGTCCTTTTCTGCGCATCCATGTCG
EST: gi|88984478|gb|CI015029.1|CI015029
EST:     GAGGCCTACTTCTGAACCCTGTTCTTCTTCAGATTGGAATACCACCGCAG                         ACTGCAGCAGCGACGTCTTCGTTTATGGTCCTTTTCTGCGCATCCATGTCG
genomic: GAGGCCTACTTCTGAACCCTGTTCTTCTTCAGATTGGAATACCACCGCAGgtacagtggt ... tgatttgcagACTGCAGCAGCGACGTCTTCGTTTATGGTCCTTTTCTGCGCATCCATGTCG
EST: gi|86496301|gb|CI138934.1|CI138934
EST:     GAGGCCTACTTCTGAACCCTGTTCTTCTTCAGATTGGAATACCACCGCAG                         ACTGCAGCAGCGACGTCTTCGTTTATGGTCCTTTTCTGCGCATCCATGTCG
genomic: GAGGCCTACTTCTGAACCCTGTTCTTCTTCAGATTGGAATACCACCGCAGgtacagtggt ... tgatttgcagACTGCAGCAGCGACGTCTTCGTTTATGGTCCTTTTCTGCGCATCCATGTCG
EST: gi|86435520|gb|CI106753.1|CI106753
EST:     GAGGCCTACTTCTGAACCCTGTTCTTCTTCAGATTGGAATACCACCGCAG                         ACTGCAGCAGCGACGTCTTCGTTTATGGTCCTTTTCTGCGCATCCATGTCG
genomic: GAGGCCTACTTCTGAACCCTGTTCTTCTTCAGATTGGAATACCACCGCAGgtacagtggt ... tgatttgcagACTGCAGCAGCGACGTCTTCGTTTATGGTCCTTTTCTGCGCATCCATGTCG
EST: gi|88222540|gb|CI222496.1|CI222496
EST:     GAGGCCTACTTCTGAACCCTGTTCTTCTTCAGATTGGAATACCACCGCAG                         ACTGCAGCAGCGACGTCTTCGTTTATGGTCCTTTTCTGCGCATCCATGTCG
genomic: GAGGCCTACTTCTGAACCCTGTTCTTCTTCAGATTGGAATACCACCGCAGgtacagtggt ... tgatttgcagACTGCAGCAGCGACGTCTTCGTTTATGGTCCTTTTCTGCGCATCCATGTCG
EST: gi|86844209|gb|CI337596.1|CI337596
EST:     GAGGCCTACTTCTGAACCCTGTTCTTCTTCAGATTGGAATACCACCGCAG                         ACTGCAGCAGCGACGTCTTCGTTTATGGTCCTTTTCTGCGCATCCATGTCG
genomic: GAGGCCTACTTCTGAACCCTGTTCTTCTTCAGATTGGAATACCACCGCAGgtacagtggt ... tgatttgcagACTGCAGCAGCGACGTCTTCGTTTATGGTCCTTTTCTGCGCATCCATGTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttttctgtcgagtccatgattcatgcagtagcattaccatccttgatttgcagACTGCAGCAGCGACGTCTTCGTTTATGGTCCTTTTCTGCGCATCCATGTCGATGGTTCAGTTCATCCTGCTAGGCATGCAAGGCATCGGAGAAGCTTCTG
                                          ccttgat  putative branch site (score: 5)
                                      ccatcctt  CT-rich tract
                                            ttgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacagtggtacacacactacagattcttaagctactgaaactatggtcctatggacctatggttaccaaggtatgatcagtagttttctgtcgagtccatgattcatgcagtagcattaccatccttgatttgcagACTGCAGCAGCGACGTCTTCGTTTATGGTCCTTTTCTGCGCATCCATGTCGATGGTTCAGTTCATCCTGCTAGGCATGCAAGGCATCGGAGAAGCTTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC