Skip to another splice site:
1  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccttcttcctcgatcatatcgatggatcgattgagttggtcgttcggtcaattgctactggttaattaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACCGCAAGTACCCCAACGGAATCCGGCCGAACCGCGCCGCCGGGTCGGGGTA

Basic information

species Oryza sativa
transcript LOC_Os07g48450.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g48450.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G042494_T01 (Zea mays), 3'ss of exon 2
---------------------------------------------------------gtaagccttcttc-ctcgatcatatcgatggatcgattgagttggtcgttcg--gtcaattgcta-ctggttaattaat-----------tgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACCGCAAGTACCCCAACGGAATCCGGCCGAACCGCGCCGCCGGGTCGGGGTA
                                                         || | ||    || |  |  |||  ||   ||||||  ||| |   || ||    |   | |||| || | | ||| ||           |||||| | ||| | ||||||||| |  |||||||| |||||||||||||| |||||||||||||| |||||  |||||||||||||||| || || ||||| ||
gttagtacccgcgccgcgcgcgcctgcactcagactcagctcgcatcacatatcgctgtgatccccgctcacatgcacatgacgcgtgatcgaccgagatccccgctcacaatttctagctagctagctgattgatgtgtatattattgcagCCAGGGCTGCGTACGGGGACAAGGAGTGGTACTTCTTCAGCCCGCGCGACCGCAAGTACCCAAACGGGGTCCGGCCGAACCGCGCGGCAGGATCGGGTTA

upper sequence: LOC_Os07g48450.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G011598_T01 (Zea mays), 3'ss of exon 1
-----------------------------------------------------------gtaagccttcttcctcgatcatatcgatggatcgattgagttggtcgttcggtcaattgctactggttaattaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACCGCAAGTACCCCAACGGAATCCGGCCGAACCGCGCCGCCGGGTCGGGGTA
                                                           | || |  ||||  |  |    | |||| |||   |||   |  |  ||   |  ||   |||||  | || | ||||||| | ||| | ||||||||| |  |||||||| ||||||||||| || |||||||||||||| ||||| ||||||||||||||||| || ||||| || ||
gttagtagtactacccgccgtgcgcgcgcgcgcctgcactcgcatcgatcgatctgcagggaaactctcttttttaac---accgatagatt--ttgccctaattatt-aattgatgtgtactgtattatca-ttgcagCCAGGGCTGCGTACGGGGACAAGGAGTGGTACTTCTTCAGCCCCCGCGACCGCAAGTACCCGAACGGGATCCGGCCGAACCGCGCGGCGGGGTCCGGCTA

upper sequence: LOC_Os07g48450.3 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv01s0026g02710.t01 (Vitis vinifera), 3'ss of exon 1
------------------gtaagccttctt-cctcgatcatatcgatggatcgattgagttg-gtcgttcggtcaattgctactggttaattaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACCGCAAGTACCCCAACGGAATCCGGCCGAACCGCGCCGCCGGGTCGGGGTA
                  ||| |  | | |  ||| |  ||    |||  ||   | | | | ||    |  | ||||  ||||   |      | |||| ||||||||  |  || || | ||||||||||||||| |||||||| ||||| ||||| ||||| ||     | || ||||| ||  | | ||| || ||
gtgagtttcatttcattggtaggagtacatatctcaactatgctcatgc-tcatgtaactcgtgtttaacctttaatttttactatatgggctgt-gcagAGAAGGCGGAATTTGGAGAAAATGAGTGGTATTTCTTTAGCCCGCGTGACCGTAAGTATCCCAATGGGGCTAGACCCAACCGAGCTACAGTGTCCGGCTA

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|88343042|gb|CI641568.1|CI641568
EST:     CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCAT                         CGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
genomic: CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttc ... ttaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
EST: gi|88340880|gb|CI637040.1|CI637040
EST:     CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCAT                         CGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCCGCGAGAA
genomic: CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttc ... ttaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCC-GCGAGAC
EST: gi|88306193|gb|CI636575.1|CI636575
EST:     CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCAT                         CGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
genomic: CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttc ... ttaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
EST: gi|88734147|gb|CI757655.1|CI757655
EST:     -ATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCAT                         CGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTNTTCAGCCCGCGAGACC
genomic: CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttc ... ttaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
EST: gi|88349457|gb|CI653736.1|CI653736
EST:     CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCAT                         CGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
genomic: CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttc ... ttaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
EST: gi|88592662|gb|CI710781.1|CI710781
EST:     CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGAACTGCCAT                         CGAAGGCGGTGTANGGGGAGAGTGAGTGGTATTTCTTCAGCCCCGCGAGAC
genomic: CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttc ... ttaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCC-GCGAGAC
EST: gi|88726289|gb|CI749944.1|CI749944
EST:     CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCAT                         CGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
genomic: CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttc ... ttaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
EST: gi|88336492|gb|CI656763.1|CI656763
EST:     CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCAT                         CGAAGGGGGTGTACGGGGAGAGTGAGTGGTATTTCTCCAGCCCCGCGAG
genomic: CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttc ... ttaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCC-GCGAG
EST: gi|88340558|gb|CI659764.1|CI659764
EST:     CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCAT                         CGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCCGCGAGAC
genomic: CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttc ... ttaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCC-GCGAGAC
EST: gi|86901187|gb|CI306376.1|CI306376
EST:     CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCAT                         CGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
genomic: CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttc ... ttaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
EST: gi|88340456|gb|CI659662.1|CI659662
EST:     CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCAT                         CGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
genomic: CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttc ... ttaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
EST: gi|58593345|gb|CF991653.1|CF991653
EST:     CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCAT                         CGAAGGCGGTGTACGGGGAGAGCGAGTGGTATTTCTTCAGCCCGCGAGAAC
genomic: CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttc ... ttaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
EST: gi|88336172|gb|CI647366.1|CI647366
EST:     CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCAT                         CGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
genomic: CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttc ... ttaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
EST: gi|88583081|gb|CI700538.1|CI700538
EST:     CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCAT                         CGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
genomic: CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttc ... ttaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
EST: gi|88336530|gb|CI656801.1|CI656801
EST:     CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCAT                         CGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
genomic: CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttc ... ttaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
EST: gi|88734408|gb|CI757916.1|CI757916
EST:     CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCAT                         CGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCA
genomic: CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttc ... ttaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCA
EST: gi|88296187|gb|CI667577.1|CI667577
EST:     CATCATCGCCGANGTCGACATCTACAAGTTCGATCCATGGGACCTGCCAT                         CGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
genomic: CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttc ... ttaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC
EST: gi|58592461|gb|CF990769.1|CF990769
EST:     CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCAT                         CGAAGGCGGTGTACGGGGAGAGCGAGTGGTATTTCTTCAGCCCGCGAGACC
genomic: CATCATCGCCGACGTCGACATCTACAAGTTCGATCCATGGGACCTGCCATgtaagccttc ... ttaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatggatcgattgagttggtcgttcggtcaattgctactggttaattaattgcagCGAAGGCGGTGTACGGGGAGAGTGAGTGGTATTTCTTCAGCCCGCGAGACCGCAAGTACCCCAACGGAATCCGGCCGAACCGCGCCGCCGGGTCGGGGTA
                                           aattaat  putative branch site (score: 3)
                                         ttaattaatt  TA-rich tract