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'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgctgttaattgtcttttgattctccacttccgataacacaacttaaactattagttgatttggttttgcatccaaattggcagGAGACTGGCGGCTATTATGCTTTCGTGGAATTCGAGGAACTCAGCGGTGTACACAATGCGTTAAAG

Basic information

species Zea mays
transcript GRMZM2G167932_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G167932_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g03890.2 (Oryza sativa), 3'ss of exon 6
gtttgctgttaattgtcttttgattctccacttccgataacacaacttaaactattagttgatttggt-tttgcatccaaattggcagGAGACTGGCGGCTATTATGCTTTCGTGGAATTCGAGGAACTCAGCGGTGTACACAATGCGTTAAAG
    |  |||  || | | |  ||| |  | | |   | | |  | |  || | |   |||| || || |||| ||  | ||||||||||||| || ||||| ||||| |||||||||||||| ||||| || ||||| |||||||| || |||
----gtggttccttatatgt--attttttattac--gtgatatga-tagaattttcttttgacttagtgtttgtatg-acattggcagGAGACCGGAGGCTACTATGCGTTCGTGGAATTCGAAGAACTTAGTGGTGTTCACAATGCATTGAAG
















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|31351085|gb|CD435442.1|CD435442
EST:     AGAAATTTGGCCGGCTTATTCCTGACGGTGTTGCTATCAGAAGCCGAAAG                         GAGACTGGCGGCTATTATGCTTTCGTGGAATTCGAGGAACTCAGCGGTGTA
genomic: AGAAATTTGGCCGGCTTATTCCTGACGGTGTTGCTATCAGAAGCCGAAAGgtttgctgtt ... aaattggcagGAGACTGGCGGCTATTATGCTTTCGTGGAATTCGAGGAACTCAGCGGTGTA
EST: gi|31354051|gb|CD438408.1|CD438408
EST:     AGAAATTTGGCCGGCTTATTCCTGACGGTGTTGCTATCAGAAGCCGAAAG                         GAGACTGGCGGCTATTATGCTTTCGTGGAATTCGAGGAACTCAGCGGTGTA
genomic: AGAAATTTGGCCGGCTTATTCCTGACGGTGTTGCTATCAGAAGCCGAAAGgtttgctgtt ... aaattggcagGAGACTGGCGGCTATTATGCTTTCGTGGAATTCGAGGAACTCAGCGGTGTA
EST: gi|22542391|gb|BU092829.1|BU092829
EST:     AGAAATTTGGCCGGCTTATTCCTGACGGTGTTGCTATCAGAAGCCGAAAG                         GAGACTGGCGGCTATTATGCTTTCGTGGAATTCGAGGAACTCAGCGGTGTA
genomic: AGAAATTTGGCCGGCTTATTCCTGACGGTGTTGCTATCAGAAGCCGAAAGgtttgctgtt ... aaattggcagGAGACTGGCGGCTATTATGCTTTCGTGGAATTCGAGGAACTCAGCGGTGTA
EST: gi|8367891|gb|BE050836.1|BE050836
EST:     AGAAATTTGGCCGGCTTATTCCTGACGGTGTTGCTATCAGAAGCCGAAAG                         GAGACTGGCGGCTATTATGCTTTCG-GGAATTCGAGGAACTCAGCGGTGTA
genomic: AGAAATTTGGCCGGCTTATTCCTGACGGTGTTGCTATCAGAAGCCGAAAGgtttgctgtt ... aaattggcagGAGACTGGCGGCTATTATGCTTTCGTGGAATTCGAGGAACTCAGCGGTGTA
EST: gi|32847652|gb|CD987333.1|CD987333
EST:     AGAAATTTGGCCGGCTTATTCCTGACGGTGTTGCTATCAGAAGCCGAAAG                         GAGACTGGCGGCTATTATGCTTTCGTGGAATTCGAGGAACTCAGCGGTGTA
genomic: AGAAATTTGGCCGGCTTATTCCTGACGGTGTTGCTATCAGAAGCCGAAAGgtttgctgtt ... aaattggcagGAGACTGGCGGCTATTATGCTTTCGTGGAATTCGAGGAACTCAGCGGTGTA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 294

CGGCAACGTGCCATCATCTGTAAGTGAGGCTGATCTTGAAAACGAGTTCAAGAAATTTGGCCGGCTTATTCCTGACGGTGTTGCTATCAGAAGCCGAAAGgtttgctgtt ... aaattggcagGAGACTGGCGGCTATTATGCTTTCGTGGAATTCGAGGAACTCAGCGGTGTACACAATGCGTTAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 213

CGGCAACGTGCCATCATCTGTAAGTGAGGCTGATCTTGAAAACGAGTTCAAGAAATTTGGCCGGCTTATTCCTGACGGTGTTGCTATCAGAAGCCGAAAGgtttgctgtt ... aaattggcagGAGACTGGCGGCTATTATGCTTTCGTGGAATTCGAGGAACTCAGCGGTGTACACAATGCGTTAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 228

CGGCAACGTGCCATCATCTGTAAGTGAGGCTGATCTTGAAAACGAGTTCAAGAAATTTGGCCGGCTTATTCCTGACGGTGTTGCTATCAGAAGCCGAAAGgtttgctgtt ... aaattggcagGAGACTGGCGGCTATTATGCTTTCGTGGAATTCGAGGAACTCAGCGGTGTACACAATGCGTTAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 163

CGGCAACGTGCCATCATCTGTAAGTGAGGCTGATCTTGAAAACGAGTTCAAGAAATTTGGCCGGCTTATTCCTGACGGTGTTGCTATCAGAAGCCGAAAGgtttgctgtt ... aaattggcagGAGACTGGCGGCTATTATGCTTTCGTGGAATTCGAGGAACTCAGCGGTGTACACAATGCGTTAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccgataacacaacttaaactattagttgatttggttttgcatccaaattggcagGAGACTGGCGGCTATTATGCTTTCGTGGAATTCGAGGAACTCAGCGGTGTACACAATGCGTTAAAG
           aacttaaactatta  TA-rich tract