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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAGAGAGCACTTGCTCACCTGCTCCCCGCCCCCCTCTGCTGGCGCTGGACTTGCTCGGAGTGGAGATCCATCCGGACCTGGTTCGATTTCTTCATTTCGgtaagtaaccctagcttgctgggttgattcttttgactcttaagagttttttttgtttgctgaacggaaggattccgagtgtttagtttgttgcggatttgctgtctgagagcgttgtaatctatccatgcag

Basic information

species Zea mays
transcript GRMZM2G174284_T01
intron # 1
splice site 5'
intron type U2

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|74243508|gb|DT651422.1|DT651422
EST:     CTTGCTCGGAGTGGAGATCCATCCGGACCTGGTTCGATTTCTTCATTTCG                         GGTTCGATTCGGTTTTTCTATCCCAGAGCGAAAGATCAATATCACCTGACA
genomic: CTTGCTCGGAGTGGAGATCCATCCGGACCTGGTTCGATTTCTTCATTTCGgtaagtaacc ... atccatgcagGGTTCGATTCGGTTTTTCTATCCCAGAGCGAAAGATCAATATCACCTGACA
EST: gi|50325948|gb|CO521074.1|CO521074
EST:     CTTGCTCGGAGTGGAGATCCATCCGGACCTGGTTCGATTTCTTCATTTCG                         GGTTCGATTCGGTTTTTCTATCCCAGAGCGAAAGATCAATATCACCTGACA
genomic: CTTGCTCGGAGTGGAGATCCATCCGGACCTGGTTCGATTTCTTCATTTCGgtaagtaacc ... atccatgcagGGTTCGATTCGGTTTTTCTATCCCAGAGCGAAAGATCAATATCACCTGACA
EST: gi|71449116|gb|DR830166.1|DR830166
EST:     TCGGAGTGGAGATCCATCCGGACCTCACCTGGTTCGATTTCTTCATTTCG                         GGTTCGATTCGGTTTTTCTATCCCAGAGCGAAAGATCAATATCACCTGACA
genomic: TCGGAGTGGAGATCCATCCGGACCT-----GGTTCGATTTCTTCATTTCGgtaagtaacc ... atccatgcagGGTTCGATTCGGTTTTTCTATCCCAGAGCGAAAGATCAATATCACCTGACA
EST: gi|211445699|gb|FL163996.1|FL163996
EST:     CTTGCTCGGAGTGGAGATCCATCCGGACCTGGTTCGATTTCTTCATTTCG                         GGTTCGATTCGGTTTTTCTATCCCAGAGCGAAAGATCAATATCACCTGACA
genomic: CTTGCTCGGAGTGGAGATCCATCCGGACCTGGTTCGATTTCTTCATTTCGgtaagtaacc ... atccatgcagGGTTCGATTCGGTTTTTCTATCCCAGAGCGAAAGATCAATATCACCTGACA
EST: gi|60397433|gb|DN230249.1|DN230249
EST:     CTTGCTCGGAGTGGAGATCCATCCGGACCTGGTTCGATTTCTTCATTTCG                         GGTTCGATTCGGTTTTTCTATCCCAGAGCGAAAGATCAATATCACCTGACA
genomic: CTTGCTCGGAGTGGAGATCCATCCGGACCTGGTTCGATTTCTTCATTTCGgtaagtaacc ... atccatgcagGGTTCGATTCGGTTTTTCTATCCCAGAGCGAAAGATCAATATCACCTGACA

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: 47 (upstream exon), 48 (downstream exon)
Score: 51

GTAGAGAGCACTTGCTCACCTGCTCCCCGCCCCCCTCTGCTGGCGCTGGACTTGCTCGGAGTGGAGATCCATCCGGACCTGGTTCGATTTCTTCATTTCGgtaagtaacc ... atccatgcagGGTTCGATTCGGTTTTTCTATCCCAGAGCGAAAGATCAATATCACCTGACACAACATAACGATTTCGTGGAAGCCGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 188

GTAGAGAGCACTTGCTCACCTGCTCCCCGCCCCCCTCTGCTGGCGCTGGACTTGCTCGGAGTGGAGATCCATCCGGACCTGGTTCGATTTCTTCATTTCGgtaagtaacc ... atccatgcagGGTTCGATTCGGTTTTTCTATCCCAGAGCGAAAGATCAATATCACCTGACACAACATAACGATTTCGTGGAAGCCGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 238

GTAGAGAGCACTTGCTCACCTGCTCCCCGCCCCCCTCTGCTGGCGCTGGACTTGCTCGGAGTGGAGATCCATCCGGACCTGGTTCGATTTCTTCATTTCGgtaagtaacc ... atccatgcagGGTTCGATTCGGTTTTTCTATCCCAGAGCGAAAGATCAATATCACCTGACACAACATAACGATTTCGTGGAAGCCGAG


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 48

GTAGAGAGCACTTGCTCACCTGCTCCCCGCCCCCCTCTGCTGGCGCTGGACTTGCTCGGAGTGGAGATCCATCCGGACCTGGTTCGATTTCTTCATTTCGgtaagtaacc ... atccatgcagGGTTCGATTCGGTTTTTCTATCCCAGAGCGAAAGATCAATATCACCTGACACAACATAACGATTTCGTGGAAGCCGAG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAGAGAGCACTTGCTCACCTGCTCCCCGCCCCCCTCTGCTGGCGCTGGACTTGCTCGGAGTGGAGATCCATCCGGACCTGGTTCGATTTCTTCATTTCGgtaagtaaccctagcttgctgggttgattcttttgactcttaagagttttttttgtttgctgaacggaaggattccgagtgtttagtttgttgcggatttgctgtctgagagcgttgtaatctatccatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC