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'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgttatttgttgtttgctgatttgcctgcctcgtcaaaatatggagacatgtcaaaaagcagaacgcttgctcatgtcgcattatgttgatgttctaactcctgaactcgcgtggtgtgtgaccagGCTCTGACGAGATACGTAACTGATGCTATGAGAGAATCAAGGGTTCTTGAGTTTTTGCACGCG

Basic information

species Zea mays
transcript GRMZM2G173928_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G173928_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os06g50030.1 (Oryza sativa), 3'ss of exon 8
gtgcgttatttgttgtttgctgatttgcctgcctcgtcaaaatatggagacatgtcaaa------aagcagaacgc-ttgc-tcatgtcgcattatgttgatgttctaactcctgaactcgcgtggtgtgtgaccagGCTCTGACGAGATACGTAACTGATGCTATGAGAGAATCAAGGGTTCTTGAGTTTTTGCACGCG
||| |||     |   ||  |  | || || |||| |  | |||  |  |||  | | |      |  ||    || || | | |  |   | ||  |    ||| ||||  || || || | |    | |   ||||| || ||| ||||  |||||||||||||||  ||||| ||||||||||| |||||||| |||
gtgagtttaccata--ttatt--tctgactacctcattgagataaaggcacacatgacacttgtcatccaatgtgcattacattacctgtaagtaaatcatagttttaacctcttaattcac-tatcttat--tcagGCACTAACGCGATATTTAACTGATGCTATGAAGGAATCGAGGGTTCTTGAATTTTTGCATGCG
















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|60350012|gb|DN216985.1|DN216985
EST:     AGCTGCTCGAGCCCAGAGACGGGCTCGTATCGCTCGACAACTTTCGGACG                         GCTCTGACGAGATACGTAACTGATGCTATGAGAGAATCAAGGGTTCTTGAG
genomic: AGCTGCTCGAGCCCAGAGACGGGCTCGTATCGCTCGACAACTTTCGGACGgtgcgttatt ... gtgtgaccagGCTCTGACGAGATACGTAACTGATGCTATGAGAGAATCAAGGGTTCTTGAG
EST: gi|37383606|gb|CF628823.1|CF628823
EST:     AGCTGCTCGAGCCCAGAGACGGGCTCGTATCGCTCGACAACTTTCGGACG                         GCTCTGACGAGATACGTAACTGATGCTATGAGAGAATCAAGGGTTCTTGAG
genomic: AGCTGCTCGAGCCCAGAGACGGGCTCGTATCGCTCGACAACTTTCGGACGgtgcgttatt ... gtgtgaccagGCTCTGACGAGATACGTAACTGATGCTATGAGAGAATCAAGGGTTCTTGAG
EST: gi|148929165|gb|EC874655.2|EC874655
EST:     AGTTGCTCGAGCCCAGAGACGGGCTCGTATCGCTCGACAACTTTCGGACG                         GGTCTGACGAGATACGTAACTGATGCTATGAGAGAATCAAGGGTTCTTGAG
genomic: AGCTGCTCGAGCCCAGAGACGGGCTCGTATCGCTCGACAACTTTCGGACGgtgcgttatt ... gtgtgaccagGCTCTGACGAGATACGTAACTGATGCTATGAGAGAATCAAGGGTTCTTGAG

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: 23 (upstream exon), 42 (downstream exon)
Score: 26

ATCTAAGGCTTTAAGGGAGGATGAACTGTTGTATCTTAGATTGCAGTTTAAGCTGCTCGAGCCCAGAGACGGGCTCGTATCGCTCGACAACTTTCGGACGgtgcgttatt ... gtgtgaccagGCTCTGACGAGATACGTAACTGATGCTATGAGAGAATCAAGGGTTCTTGAGTTTTTGCACGCG


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 75

ATCTAAGGCTTTAAGGGAGGATGAACTGTTGTATCTTAGATTGCAGTTTAAGCTGCTCGAGCCCAGAGACGGGCTCGTATCGCTCGACAACTTTCGGACGgtgcgttatt ... gtgtgaccagGCTCTGACGAGATACGTAACTGATGCTATGAGAGAATCAAGGGTTCTTGAGTTTTTGCACGCG


Block sizes: 48 (upstream exon), 42 (downstream exon)
Score: 87

ATCTAAGGCTTTAAGGGAGGATGAACTGTTGTATCTTAGATTGCAGTTTAAGCTGCTCGAGCCCAGAGACGGGCTCGTATCGCTCGACAACTTTCGGACGgtgcgttatt ... gtgtgaccagGCTCTGACGAGATACGTAACTGATGCTATGAGAGAATCAAGGGTTCTTGAGTTTTTGCACGCG


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 34

ATCTAAGGCTTTAAGGGAGGATGAACTGTTGTATCTTAGATTGCAGTTTAAGCTGCTCGAGCCCAGAGACGGGCTCGTATCGCTCGACAACTTTCGGACGgtgcgttatt ... gtgtgaccagGCTCTGACGAGATACGTAACTGATGCTATGAGAGAATCAAGGGTTCTTGAGTTTTTGCACGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatgtcgcattatgttgatgttctaactcctgaactcgcgtggtgtgtgaccagGCTCTGACGAGATACGTAACTGATGCTATGAGAGAATCAAGGGTTCTTGAGTTTTTGCACGCG
                     ttctaac  putative branch site (score: 34)
         attatgtt  TA-rich tract