Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacaatgctgacttataggagtagatcagtggcagtaggttcatgccggtcgtatttctttgactgatgcatatgcatacctgctgctgtactgcacatatatgatgcagGCGCCGGCCTGCAGCTCCCGGCTCACTTCTCCCCGATCTACTTCCCCGTCGGAAACGCGGCGACCGGGTTCTTCGTCATCTTCGCCGTGATCGCCGGGGT

Basic information

species Zea mays
transcript GRMZM2G057283_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057283_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g50440.1 (Oryza sativa), 3'ss of exon 1
-----------------------------------------------------------------gtaacaatgctgacttataggagtagatcagtggc--agtaggttcat-----gccggt-cgtatttctttgactgatgcatatgcatacctgctgctgtactgcacatatatgatgcagGCGCCGGCCTGCAGCTCCCGGCTCACTTCTCCCCGATCTACTTCCCCGTCGGAAACGCGGCGACCGGGTTCTTCGTCATCTTCGCCGTGATCGCCGGGGT
                                                                 | | |||  ||  ||  ||     ||||  ||| |  | || |||  |     |   || | ||| | ||  |   |    | ||  |   ||    | |      ||| || | || |||  ||||  ||  ||| |||||  ||||||||||||||||||||||  | || |||||||||||||||||||||||||||||||| ||||||||||| ||
gtaaaactagctcacattttgatttaccgtgtcgatctcgatggtgtcttgttatcgggcacaacgaaccaaaacttgctc-taaattgagattggtgcctaattatgtttgtcaatagaaagtgcatatattttgaagctagatttgtgactgtttgagcgtatgtactgcatgtacg-tgtagGTTCCGGGATGGCGCTGCCGGCGAACTTCTCCCCGATCTACTTCCCGATGGGGAACGCGGCGACCGGGTTCTTCGTCATCTTCGCGGTGATCGCCGGAGT
















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|91871799|gb|EB401756.1|EB401756
EST:     GGTGGGCGGCTGGGCCATCAACCACGCCATCAACTACGGCTTCTTCATCG                         GCGCCGGCCTGCAGCTCCCGGCTCACTTCTCCCCGATCTACTTCCCCGTCG
genomic: GGTGGGCGGCTGGGCCATCAACCACGCCATCAACTACGGCTTCTTCATCGgtaacaatgc ... tatgatgcagGCGCCGGCCTGCAGCTCCCGGCTCACTTCTCCCCGATCTACTTCCCCGTCG
EST: gi|78089270|gb|DV517644.1|DV517644
EST:     GGTGGGCGGCTGGGCCATCAACCACGCCATCAACTACGGCTTCTTCATCG                         GCGCCGGCCTGCAGCTCCCGGCTCACTTCTCCCCGATCTACTTCCCCGTCG
genomic: GGTGGGCGGCTGGGCCATCAACCACGCCATCAACTACGGCTTCTTCATCGgtaacaatgc ... tatgatgcagGCGCCGGCCTGCAGCTCCCGGCTCACTTCTCCCCGATCTACTTCCCCGTCG
EST: gi|211368356|gb|FL375187.1|FL375187
EST:     GGTGGGCGGCTGGGCCATCAACCACGCCATCAACTACGGCTTCTTCATCG                         GCGCCGGCCTGCAGCTCCCGGCTCACTTCTCCCCGATCTACTTCCCCGTCG
genomic: GGTGGGCGGCTGGGCCATCAACCACGCCATCAACTACGGCTTCTTCATCGgtaacaatgc ... tatgatgcagGCGCCGGCCTGCAGCTCCCGGCTCACTTCTCCCCGATCTACTTCCCCGTCG
EST: gi|91871798|gb|EB401755.1|EB401755
EST:     GGTGGGCGGGTGGGCCATCAACCACGCCATCAACTACGGCTTCTTCATCG                         GCGCCGGCCTGCAGCTCCCGGCTCACTTCTCCCCGATCTACTTCCCCGTCG
genomic: GGTGGGCGGCTGGGCCATCAACCACGCCATCAACTACGGCTTCTTCATCGgtaacaatgc ... tatgatgcagGCGCCGGCCTGCAGCTCCCGGCTCACTTCTCCCCGATCTACTTCCCCGTCG
EST: gi|78089269|gb|DV517643.1|DV517643
EST:     GGTGGGCGGCTGGGCCATCAACCACGCCATCAACTACGGCTTCTTCATCG                         GCGCCGGCCTGCAGCTCCCGGCTCACTTCTCCCCGATCTACTTCCCCGTCG
genomic: GGTGGGCGGCTGGGCCATCAACCACGCCATCAACTACGGCTTCTTCATCGgtaacaatgc ... tatgatgcagGCGCCGGCCTGCAGCTCCCGGCTCACTTCTCCCCGATCTACTTCCCCGTCG
EST: gi|211304856|gb|FL374670.1|FL374670
EST:     GGTGGGCGGCTGGGCCATCAACCACGCCATCAACTACGGCTTCTTCATCG                         GCGCCGGCCTGCAGCTCCCGGCTCACTTCTCCCCGATCTACTTCCCCGTCG
genomic: GGTGGGCGGCTGGGCCATCAACCACGCCATCAACTACGGCTTCTTCATCGgtaacaatgc ... tatgatgcagGCGCCGGCCTGCAGCTCCCGGCTCACTTCTCCCCGATCTACTTCCCCGTCG
EST: gi|16925336|gb|BM078404.1|BM078404
EST:     GGGCCATCAACCACGCCATCAACTACGGATTCTTCATCG                         GCGCCGGCCTGCAGCTCCCGGCTCACTTCTCCCCGATCTACTTCCCCGTCG
genomic: GGGCCATCAACCACGCCATCAACTACGGCTTCTTCATCGgtaacaatgc ... tatgatgcagGCGCCGGCCTGCAGCTCCCGGCTCACTTCTCCCCGATCTACTTCCCCGTCG
EST: gi|14244256|gb|BG842235.2|BG842235
EST:     GGTGGGCGGCTGGGCCATCAACCACGCCATCAACTACGGCTTCTTCATCG                         GCGCCGGCCTGCAGCTCCCGGCTCACTTCTCCCCGATCTACTTCCCCGTCG
genomic: GGTGGGCGGCTGGGCCATCAACCACGCCATCAACTACGGCTTCTTCATCGgtaacaatgc ... tatgatgcagGCGCCGGCCTGCAGCTCCCGGCTCACTTCTCCCCGATCTACTTCCCCGTCG

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 3 RNA-Seq libraries.


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 13

GCCGGCCTCCTCCTGGTGCTCAACTTCTGCATGTACATCATCGTGGCGGCGGTGGGCGGCTGGGCCATCAACCACGCCATCAACTACGGCTTCTTCATCGgtaacaatgc ... tatgatgcagGCGCCGGCCTGCAGCTCCCGGCTCACTTCTCCCCGATCTACTTCCCCGTCGGAAACGCGGCGACCGGGTTCTTCGTCATCTTCGCCGTGATCGCCGGGGT


Block sizes: 47 (upstream exon), 35 (downstream exon)
Score: 21

GCCGGCCTCCTCCTGGTGCTCAACTTCTGCATGTACATCATCGTGGCGGCGGTGGGCGGCTGGGCCATCAACCACGCCATCAACTACGGCTTCTTCATCGgtaacaatgc ... tatgatgcagGCGCCGGCCTGCAGCTCCCGGCTCACTTCTCCCCGATCTACTTCCCCGTCGGAAACGCGGCGACCGGGTTCTTCGTCATCTTCGCCGTGATCGCCGGGGT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 55

GCCGGCCTCCTCCTGGTGCTCAACTTCTGCATGTACATCATCGTGGCGGCGGTGGGCGGCTGGGCCATCAACCACGCCATCAACTACGGCTTCTTCATCGgtaacaatgc ... tatgatgcagGCGCCGGCCTGCAGCTCCCGGCTCACTTCTCCCCGATCTACTTCCCCGTCGGAAACGCGGCGACCGGGTTCTTCGTCATCTTCGCCGTGATCGCCGGGGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttgactgatgcatatgcatacctgctgctgtactgcacatatatgatgcagGCGCCGGCCTGCAGCTCCCGGCTCACTTCTCCCCGATCTACTTCCCCGTCGGAAACGCGGCGACCGGGTTCTTCGTCATCTTCGCCGTGATCGCCGGGGT
      gactgat  putative branch site (score: 55)
                                          atatatgat  TA-rich tract