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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtcttttgatttcacagttgtattttgtacgacaaaggtcccaagtttgctaatagagatgttctcttggtcctgcagGATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTATAACCACGCTTGTGCAGACTATGCCAGGCAGAAATTGTCAGCACCAAACT

Basic information

species Oryza sativa
transcript LOC_Os11g14430.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g14430.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G103430_T04 (Zea mays), 3'ss of exon 4
gtgtgtcttttgatttcacagttgtatt---ttgtacgacaaaggtcccaagtttgctaatagagatgttctcttggtcctgcagGATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTATAACCACGCTTGTGCAGACTATGCCAGGCAGAAATTGTCAGCACCAAACT------
|||||  || || ||||    |||| ||   ||||||  || | || |||  ||  ||||||  ||  | || || |     ||||||   |||||||||| |||||||||||| |||||||||||||||||||| ||||| || || ||||||||||||||||||||| | ||| | |||||||      
gtgtgctttgtggtttcgtgcttgttttcgtttgtacaccacaagttccagattcactaatattgagatgctgtttgc---acaggatcagCATGACCCAAACCGTAACCGTGGCTTCCTCTTTGTTGAGTATTACAACCATGCCTGCGCAGACTATGCCAGGCAGAAACTTTCATCTCCAAACTTCAAGG

upper sequence: LOC_Os11g14430.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G103430_T05 (Zea mays), 3'ss of exon 3
gtgtgtcttttgatttcacagttgtatt---ttgtacgacaaaggtcccaagtttgctaatagagatgttctcttggtcctgcagGATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTATAACCACGCTTGTGCAGACTATGCCAGGCAGAAATTGTCAGCACCAAACT
|||||  || || ||||    |||| ||   ||||||  || | || |||  ||  ||||||  ||  | || || |     ||||||   |||||||||| |||||||||||| |||||||||||||||||||| ||||| || || ||||||||||||||||||||| | ||| | |||||||
gtgtgctttgtggtttcgtgcttgttttcgtttgtacaccacaagttccagattcactaatattgagatgctgtttgc---acagGATCAGCATGACCCAAACCGTAACCGTGGCTTCCTCTTTGTTGAGTATTACAACCATGCCTGCGCAGACTATGCCAGGCAGAAACTTTCATCTCCAAACT

upper sequence: LOC_Os11g14430.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv15s0048g02700.t01 (Vitis vinifera), 3'ss of exon 4
gtgtgtcttttgatt-----tcacagttgtattttgtacgacaaaggtcccaagtttgctaatagagatgtt------ctcttggtc--ctgcagGATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTATAACCACGCTTGTGCAGACTATGCCAGGCAGAAATTGTCAGCACCAAACT
|||    |||  |||     | ||  |     ||  |   | || |     | |  |||| ||      ||       || ||| |    | ||||||   ||  | ||||||||||| ||||| ||    |||||||||||||| ||| | ||||||||||| ||||  ||||||||| ||||     |||| |
gtgcagttttgaattgaaattgactatccaccttattttaagaatgaatagacgaatgcttatgtgagagtctaatgccttttgtttaattacagGATCCTCAAAATCCAAGCCGTAATCGTGGTTTTGCTTTTGTTGAGTATTACAACAATGCTTGTGCAGATTATGGGAGGCAGAAAATGTCTAGTTCAAATT

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|29639969|gb|CB644978.1|CB644978
EST:     AGATAATCCAAGGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAG                         GATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
genomic: AGATAATCCAAGGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAGgtgtgtcttt ... ggtcctgcagGATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
EST: gi|218479912|gb|FG956819.1|FG956819
EST:     GTGTTGTCAACATTGAGA-G-TCAAG                         GGTTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
genomic: GTGTTGTCAACATTGAGATGTTCAAGgtgtgtcttt ... ggtcctgcagGATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
EST: gi|29664577|gb|CB660852.1|CB660852
EST:     AGATAATCCAAGGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAG                         GATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
genomic: AGATAATCCAAGGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAGgtgtgtcttt ... ggtcctgcagGATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
EST: gi|58609361|gb|CK037394.1|CK037394
EST:     AGATAATCCAGGGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAG                         GATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
genomic: AGATAATCCAAGGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAGgtgtgtcttt ... ggtcctgcagGATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
EST: gi|58693279|gb|CK081966.1|CK081966
EST:     AGATAATCCAAGGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAG                         GATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
genomic: AGATAATCCAAGGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAGgtgtgtcttt ... ggtcctgcagGATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
EST: gi|29640012|gb|CB645021.1|CB645021
EST:     AGATAATCCAAGGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAG                         GATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
genomic: AGATAATCCAAGGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAGgtgtgtcttt ... ggtcctgcagGATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
EST: gi|38473107|gb|CF957239.1|CF957239
EST:     GGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAG                         GATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
genomic: GGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAGgtgtgtcttt ... ggtcctgcagGATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtacgacaaaggtcccaagtttgctaatagagatgttctcttggtcctgcagGATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTATAACCACGCTTGTGCAGACTATGCCAGGCAGAAATTGTCAGCACCAAACT
                        tgctaat  putative branch site (score: 2)
                                      ttctcttg  putative PPT
                           taataga  TA-rich tract