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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgttgcctaaactttggaaattatactctttttacttaacatgctacattctgcaactgtcacatcattttccttaaccatcttgtgatgtagTCCGTGTCCAACCGAACACTGGATCAACAATGTACAGTAACACGGCCTGGATTGTCCTCCATTACATCTGGCTGTGCGGCAGACCTCTTCACAAGAATGT

Basic information

species Oryza sativa
transcript LOC_Os01g42850.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g42850.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G005304_T01 (Zea mays), 3'ss of exon 17
gtaatgttgcctaaactttggaaattatactc-tttttactt--aacatgctacattctgcaactgtcacatcattttccttaaccatcttgtgatgtagTCCGTGTCCAACCGAACACTGGATCAACAATGTACAGTAACACGGCCTGGATTGTCCTCCATTACATCTGGCTGTGCGGCAGACCTCTTCACAAGAATGT
|||||||| | |    |||||||||| ||||  ||||| |||  || ||| |||   || |||   |  | | || ||              || || |||| || ||||| || ||||||||||||||||||||||| ||||| || || ||| |||| ||| |||| ||  | || ||||||||||||| ||||||||
gtaatgttccatgc-ttttggaaattgtacttgtttttgcttttaatatgttaccgactacaatcatggcgttatgtt--------------tggtgcagTCAGTTTCCAATCGGACACTGGATCAACAATGTACAGTGACACGACCGGGGTTGGCCTCTATTGCATCAGGACGCGCTGCAGACCTCTTCAGAAGAATGT
















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|29677767|gb|CB674042.1|CB674042
EST:     GTCAGAGACTAGGATGTTATTTCTGCAATGACGTCGTTGCTCCTGTTGAT                         TCCGTGTCCAACCGAACACTGGATCAACAATGTACAGTAACACGGCCTGGA
genomic: GTCAGAGACTAGGATGTTATTTCTGCAATGACGTCGTTGCTCCTGTTGATgtaatgttgc ... tgtgatgtagTCCGTGTCCAACCGAACACTGGATCAACAATGTACAGTAACACGGCCTGGA
EST: gi|29672225|gb|CB668500.1|CB668500
EST:     GTCAGAGACTAGGATGTTATTTCTGCAATGACGTCGTTGCTCCTGTTGAT                         TCCGTGTCCAACCGAACACTGGATCAACAATGTACAGTAACACGGCCTGGA
genomic: GTCAGAGACTAGGATGTTATTTCTGCAATGACGTCGTTGCTCCTGTTGATgtaatgttgc ... tgtgatgtagTCCGTGTCCAACCGAACACTGGATCAACAATGTACAGTAACACGGCCTGGA
EST: gi|29667791|gb|CB664066.1|CB664066
EST:     GTCAGAGACTAGGATGTTATTTCTGCAATGACGTCGTTGCTCCTGTTGAT                         TCCGTGTCCAACCGAACACTGGATCAACAATGTACAGTAACACGGCCTGGA
genomic: GTCAGAGACTAGGATGTTATTTCTGCAATGACGTCGTTGCTCCTGTTGATgtaatgttgc ... tgtgatgtagTCCGTGTCCAACCGAACACTGGATCAACAATGTACAGTAACACGGCCTGGA
EST: gi|29641126|gb|CB646133.1|CB646133
EST:     GTCAGAGACTAGGATGTTATTTCTGCAATGACGTCGTTGCTCCTGTTGAT                         TCCGTGTCCAACCGAACACTGGATCAACAATGTACAGTAACACGGCCTGGA
genomic: GTCAGAGACTAGGATGTTATTTCTGCAATGACGTCGTTGCTCCTGTTGATgtaatgttgc ... tgtgatgtagTCCGTGTCCAACCGAACACTGGATCAACAATGTACAGTAACACGGCCTGGA
EST: gi|33682080|gb|CF310319.1|CF310319
EST:     TCAGA-ACTNANGATGTTATTTCTGCAATGACGTCGTTGCTCCTGTTGAT                         TCCGTGTCCAACCGAACACTGGATCAACAATGTACAGTAACACGGCCCTGG
genomic: TCAGAGACT-AGGATGTTATTTCTGCAATGACGTCGTTGCTCCTGTTGATgtaatgttgc ... tgtgatgtagTCCGTGTCCAACCGAACACTGGATCAACAATGTACAGTAACACGGCC-TGG
EST: gi|29674598|gb|CB670873.1|CB670873
EST:     GTCAGAGACTAGGATGTTATTTCTGCAATGACGTCGTTGCTCCTGTTGAT                         TCCGTGTCCAACCGAACACTGGATCAACAATGTACAGTAACACGGCCTGGA
genomic: GTCAGAGACTAGGATGTTATTTCTGCAATGACGTCGTTGCTCCTGTTGATgtaatgttgc ... tgtgatgtagTCCGTGTCCAACCGAACACTGGATCAACAATGTACAGTAACACGGCCTGGA
EST: gi|29640245|gb|CB645254.1|CB645254
EST:     GTCAGAGACTAGGATGTTATTTCTGCAATGACGTCGTTGCTCCTGTTGAT                         TCCGTGTCCAACCGAACACTGGATCAACAATGTACAGTAACACGGCCTGGA
genomic: GTCAGAGACTAGGATGTTATTTCTGCAATGACGTCGTTGCTCCTGTTGATgtaatgttgc ... tgtgatgtagTCCGTGTCCAACCGAACACTGGATCAACAATGTACAGTAACACGGCCTGGA
EST: gi|29627979|gb|CB632990.1|CB632990
EST:     GTCAGAGACTAGGATGTTATTTCTGCAATGACGTCGTTGCTCCTGTTGAT                         TCCGTGTCCAACCGAACACTGGATCAACAATGTACAGTAACACGGCCTGGA
genomic: GTCAGAGACTAGGATGTTATTTCTGCAATGACGTCGTTGCTCCTGTTGATgtaatgttgc ... tgtgatgtagTCCGTGTCCAACCGAACACTGGATCAACAATGTACAGTAACACGGCCTGGA
EST: gi|29629460|gb|CB634469.1|CB634469
EST:     GTCAGAGACTAGGATGTTATTTCTGCAATGACGTCGTTGCTCCTGTTGAT                         TCCGTGTCCAACCGAACACTGGATCAACAATGTACAGTAACACGGCCTGGA
genomic: GTCAGAGACTAGGATGTTATTTCTGCAATGACGTCGTTGCTCCTGTTGATgtaatgttgc ... tgtgatgtagTCCGTGTCCAACCGAACACTGGATCAACAATGTACAGTAACACGGCCTGGA
EST: gi|29674600|gb|CB670875.1|CB670875
EST:     GTCAGAGACTAGGATGTTATTTCTGCAATGACGTCGTTGCTCCTGTTGAT                         TCCGTGTCCAACCGAACACTGGATCAACAATGTACAGTAACACGGCCTGGA
genomic: GTCAGAGACTAGGATGTTATTTCTGCAATGACGTCGTTGCTCCTGTTGATgtaatgttgc ... tgtgatgtagTCCGTGTCCAACCGAACACTGGATCAACAATGTACAGTAACACGGCCTGGA
EST: gi|29642677|gb|CB647684.1|CB647684
EST:     GTCAGAGACTAGGATGTTATTTCTGCAATGACGTCGTTGCTCCTGTTGAT                         TCCGTGTCCAACCGAACACTGGATCAACAATGTACAGTAACACGGCCTGGA
genomic: GTCAGAGACTAGGATGTTATTTCTGCAATGACGTCGTTGCTCCTGTTGATgtaatgttgc ... tgtgatgtagTCCGTGTCCAACCGAACACTGGATCAACAATGTACAGTAACACGGCCTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatgctacattctgcaactgtcacatcattttccttaaccatcttgtgatgtagTCCGTGTCCAACCGAACACTGGATCAACAATGTACAGTAACACGGCCTGGATTGTCCTCCATTACATCTGGCTGTGCGGCAGACCTCTTCACAAGAATGT
                                 ccttaac  putative branch site (score: 3)
                                       ccatctt  CT-rich tract
                         atcatttt  TA-rich tract