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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgttcagatggtatatgttgcactccactcctttttctgcacaaatgaatatatggagtatctgatgacaatgatatatttgtgtatccattgacagATGCTGCTATCCAACAAGTGAAATGGGACCCATCAAAAATTAAGGATAAGCTTAAGCGTGACATTGAGGCGCATGTGGCATCAGTTCGTGCCAAAAAACT

Basic information

species Oryza sativa
transcript LOC_Os01g39310.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g39310.1 (Oryza sativa), 3'ss of exon 15
lower sequence: AC196426.3_FGT007 (Zea mays), 3'ss of exon 14
ttttgttcagatgg--tatatgttgcactccactccttttt-ctgcacaaatgaatata-tggagtatctgatgacaatgatatatttgtgtatccattgacagATGCTGCTATCCAACAAGTGAAATGGGACCCATCAAAAATTAAGGATAAGCTTAAGCGTGACATTGAGGCGCATGTGGCATCAGTTCGTGCCAAAAAACT
|   ||||  | ||  |  | | |||  |   |   |||   |    |   |  || || | |  | ||| ||||    ||| | |   ||||| | ||||||||||||||||| ||||||||||| |||||| | |||||| | | |||||||||||  |||||||||||||| ||||| || |||||||| ||    ||| |
tcgcgttcgaaaggactgaaggatgctatttgccagtttgcaccctccctttccatgtaattgtatgtcttatga----gatgtgtgcatgtattctttgacagATGCTGCTATTCAACAAGTGAATTGGGACACCTCAAAAGTGAGGGATAAGCTTAGACGTGACATTGAGGCTCATGTAGCTTCAGTTCGGGCTGCTAAATT

upper sequence: LOC_Os01g39310.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM5G838579_T01 (Zea mays), 3'ss of exon 4
-ttttgttcagatggtatatgttgcactccactcctttttctgcacaaatgaatatatggagtatctgatgacaatgatatatttgtgtatccattgacagATGCTGCTATCCAACAAGTGAAATGGGACCCATCAAAAATTAAGGATAAGCTTAAGCGTGACATTGAGGCGCATGTGGCATCAGTTCGTGCCAAAAAACT
 | |  |||  | || ||         |     ||  |||   | |              | | | || |   |  ||| | |   | ||| | ||||||||||||||||| ||||||||||| |||||| | |||||| | |||||||||||||  |||||||||||||| ||||| || |||||||| ||    ||| |
ctctccttccaaaggaatgaaggatgatatttgccactttgcaccctccctttccacccaaatgtatg-tcttacagatgtgtgcatatattctttgacagATGCTGCTATTCAACAAGTGAATTGGGACACCTCAAAAGTGAAGGATAAGCTTAGACGTGACATTGAGGCTCATGTAGCTTCAGTTCGAGCTGCTAAATT
















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|571771|gb|D41282.1|D41282
EST:     TCGTGACTGTACTAAGGTTTTCTTGGAGAAGTTTGACAAAGGATCCGAAG                         ATGCTGCTATCCAACAAGTGAAATGGGACCCATCAAAAATTAAGGATAAGC
genomic: TCGTGACTGTACTAAGGTTTTCTTGGAGAAGTTTGACAAAGGATCCGAAGgtatgttttc ... ccattgacagATGCTGCTATCCAACAAGTGAAATGGGACCCATCAAAAATTAAGGATAAGC
EST: gi|29641074|gb|CB646081.1|CB646081
EST:     GTTTGACAAAGGATCCGAAG                         ATGCTGCTATCCAACAAGTGAAATGGGACCCATCAAAAATTAAGGATAAGC
genomic: GTTTGACAAAGGATCCGAAGgtatgttttc ... ccattgacagATGCTGCTATCCAACAAGTGAAATGGGACCCATCAAAAATTAAGGATAAGC
EST: gi|218488553|gb|FG950540.1|FG950540
EST:     TCGTGACTGTACTAAGGTTTTCTTGGAGAAGTTTGACAAAGGATCCGAAG                         ATGCTGCTATCCAACAAGTGAAATGGGACCCATCAAAAATTAAGGATAAGC
genomic: TCGTGACTGTACTAAGGTTTTCTTGGAGAAGTTTGACAAAGGATCCGAAGgtatgttttc ... ccattgacagATGCTGCTATCCAACAAGTGAAATGGGACCCATCAAAAATTAAGGATAAGC
EST: gi|58665350|gb|CK054036.1|CK054036
EST:     TCGTGACTGTACTAAGGTTTTCTTGGAGAAGTTTGACAAAGGATCCGAAG                         ATGCTGCTATCCAACAAGTGAAATGGGACCCATCAAAAATTAAGGATAAGC
genomic: TCGTGACTGTACTAAGGTTTTCTTGGAGAAGTTTGACAAAGGATCCGAAGgtatgttttc ... ccattgacagATGCTGCTATCCAACAAGTGAAATGGGACCCATCAAAAATTAAGGATAAGC
EST: gi|58661464|gb|CK050144.1|CK050144
EST:     TCGTGACTGTAGTAAGGTTTTCTTGGAGAAGTTTGACAAAGGATCCGAAG                         ATGCTGCTATCCAACAAGTGAAATGGGACCCATCAAAAATTAAGGATAAGC
genomic: TCGTGACTGTACTAAGGTTTTCTTGGAGAAGTTTGACAAAGGATCCGAAGgtatgttttc ... ccattgacagATGCTGCTATCCAACAAGTGAAATGGGACCCATCAAAAATTAAGGATAAGC
EST: gi|5003388|gb|AU068537.1|AU068537
EST:     TCGTGACTGTACTAAGGTTTTCTTGGAGAAGTTTGACAAAGGATCCGAAG                         ATGCTGCTATCCAACAAGTGAAATGGGACCCATCAAAAATTAAGGATAAGC
genomic: TCGTGACTGTACTAAGGTTTTCTTGGAGAAGTTTGACAAAGGATCCGAAGgtatgttttc ... ccattgacagATGCTGCTATCCAACAAGTGAAATGGGACCCATCAAAAATTAAGGATAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatgaatatatggagtatctgatgacaatgatatatttgtgtatccattgacagATGCTGCTATCCAACAAGTGAAATGGGACCCATCAAAAATTAAGGATAAGCTTAAGCGTGACATTGAGGCGCATGTGGCATCAGTTCGTGCCAAAAAACT
                 atctgat  putative branch site (score: 4)
                         acaatgatatattt  TA-rich tract