Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtagttactttttttttgtatgtattttttgaaatattttgcatctaattcagcttaaatttttcctcttagACAAACGTCTTGTCAGCCAAGTATGTGATGAAAACAGATGATGATGCTTTTGTCCGTGTGGATGAGATACTTTTATCTTTAGATCGCGTGAACATCAGTC

Basic information

species Oryza sativa
transcript LOC_Os06g12390.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g12390.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G164072_T01 (Zea mays), 3'ss of exon 4
-----------gtatgtagttacttttt-ttttgtatgtattttttgaaatattttgcatctaattcagcttaaatttttcctcttagACAAACGTCTTGTCAGCCAAGTATGTGATGAAAACAGATGATGATGCTTTTGTCCGTGTGGATGAGATACTTTTATCTTTAGATCGCGTGAACATCAGTC
            |||    ||| ||||| ||||   || ||        ||||| ||  |  | ||       || | ||| |   ||||||| ||| ||||||||||||||||||||||||| ||||||||||||||||| || || ||||| |||||||  ||  | || ||    || |||||||
gtatatatgatttattgcattattttttattttacttggatgacacttgatattatgtttgcattttctaagcaagtgttctttgcagACAAATGTCCTGTCAGCCAAGTATGTGATGAAAACTGATGATGATGCTTTTGTTCGAGTAGATGAAATACTTTCTTCCCTCGACCGAACCAATATCAGTC

upper sequence: LOC_Os06g12390.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G042607_T01 (Zea mays), 3'ss of exon 4
-----------gtatgtagttacttttt-ttttgtatgtattttttgaaatattttgcatctaattcagcttaaatttttcctcttagACAAACGTCTTGTCAGCCAAGTATGTGATGAAAACAGATGATGATGCTTTTGTCCGTGTGGATGAGATACTTTTATCTTTAGATCGCGTGAACATCAGTC
            |||    ||| ||||| |||| | |  |        |||||| ||  |  | ||       || | ||| |   ||||||| ||| |||||||||| |||||||||||||| ||||| ||||||||||| || || |||||  ||||||  ||  | || ||    ||  |||  |
gtatatctgatttattgcattattttttattttatttagacgacacttaatattatgtttgcattttctaaacaagtgttctttacagACAAATGTCCTGTCAGCCAACTATGTGATGAAAACTGATGACGATGCTTTTGTTCGAGTAGATGAAGTACTTTCTTCCCTTGACCGAACTAATGTCAACC

upper sequence: LOC_Os06g12390.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv01s0026g02530.t01 (Vitis vinifera), 3'ss of exon 4
gtatgtagttactttttttttgtatgtattttttgaaatattttgcatctaattcagcttaaatttttcctcttagACAAACGTCTTGTCAGCCAAGTATGTGATGAAAACAGATGATGATGCTTTTGTCCGTGTGGATGAGATACTTTTATCTTTAGATCGCGTGAACATCAGTC
    |||    ||| | | |||  |  ||     | | |||  | | | |   |||         | || |   ||||  | ||  | || || |||| ||| ||||| |||||||||||||| ||||| |||||||||||  |  |    |||||| |  |  | ||  |    |
----gtaaagtcttgtctcttgcttaaatg---aggactatccttcctttgcctcattgacctcatctcttaacagACGGAGGTTGTTTCGGCAAAGTTTGTCATGAAGACAGATGATGATGCATTTGTTCGTGTGGATGAAGTGTTAGCTTCTTTAAACAGGATAAATGTGTCAC

upper sequence: LOC_Os06g12390.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv14s0108g00890.t01 (Vitis vinifera), 3'ss of exon 4
gtatgtagttactttttttttgtatgtattttttgaaatattttgcatctaattcagcttaaatttttcctcttagACAAACGTCTTGTCAGCCAAGTATGTGATGAAAACAGATGATGATGCTTTTGTCCGTGTGGATGAGATACTTTTATCTTTAGATCGCGTGAACATCAGTC
    ||| ||       |  |    ||        || | | |   || |   |||  |     | ||  |  |||||  | |   | || |||||||||||||||||||||||||||||| | ||||| |||||||||||  | |||   |||||| |       ||  | | ||
----gtaattttccacctccttctggtgacaaagaaagtttatcatatgtg-ctcatttc---ctctttttaatagACTGAAGCTGTTTCGGCCAAGTATGTGATGAAAACAGATGATGATTCATTTGTTCGTGTGGATGAAGTGCTTGCTTCTTTAAAGAAGACCAAAGTGACTC

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|27577040|gb|CA999734.1|CA999734
EST:     ATTATTATAGCCTGATTCTATGGAAGACTATAGCCATCTGCATCTATGGG                         ACAAACGTCTTGTCAGCCAAGTATGTGATGAAAACAGATGATGATGCTTTT
genomic: ATTATTATAGCCTGATTCTATGGAAGACTATAGCCATCTGCATCTATGGGgtatgtagtt ... ttcctcttagACAAACGTCTTGTCAGCCAAGTATGTGATGAAAACAGATGATGATGCTTTT
EST: gi|58682889|gb|CK071576.1|CK071576
EST:     ATTATTATAGCCTGATTCTATGGAAGACTATAGCCATCTGCATCTATGGG                         ACAAACGTCTTGTCAGCCAAGTATGTGATGAAAACAGATGATGATGCTTTT
genomic: ATTATTATAGCCTGATTCTATGGAAGACTATAGCCATCTGCATCTATGGGgtatgtagtt ... ttcctcttagACAAACGTCTTGTCAGCCAAGTATGTGATGAAAACAGATGATGATGCTTTT
EST: gi|218485432|gb|FG946449.1|FG946449
EST:     ATTATTATAGCCTGATTCTATGGAAGACTATAGCCATCTGCATCTATGGG                         ACAAACGTCTTGTCAGCCAAGTATGTGATGAAAACAGATGATGATGCTTTT
genomic: ATTATTATAGCCTGATTCTATGGAAGACTATAGCCATCTGCATCTATGGGgtatgtagtt ... ttcctcttagACAAACGTCTTGTCAGCCAAGTATGTGATGAAAACAGATGATGATGCTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatgtattttttgaaatattttgcatctaattcagcttaaatttttcctcttagACAAACGTCTTGTCAGCCAAGTATGTGATGAAAACAGATGATGATGCTTTTGTCCGTGTGGATGAGATACTTTTATCTTTAGATCGCGTGAACATCAGTC
                         atctaat  putative branch site (score: 3)
                                          tttttcctctt  putative PPT
     tattttttgaaatatt  TA-rich tract