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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataaaatctaatttgaaggttttcctatatgttaaagtgcattttacgatcatcattgtctgttacttcttggtccatgatattgggcattcttgtatagGAGCATGGATCTTACTGAAGCACTGCGCCTTCAGATGGAAGTCCAGAAACGGCTTCATGAACAGCTTGAG

Basic information

species Zea mays
transcript GRMZM2G006477_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006477_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g21240.1 (Oryza sativa), 3'ss of exon 6
ataaaatctaatttgaaggttttcctatatgttaaagtgcattttacgatcatcattgtctgttact---tcttggtccatgatattgggcattcttgtatagGAGCATGGATCTTACTGAAGCACTGCGCCTTCAGATGGAAGTCCAGAAACGGCTTCATGAACAGCTTGAG
    | |  |  || |   || |  |  ||    |||||||   |    |   || |  |   ||||   |     | ||| || |||    | ||| | ||||||||||||||||||||||||||||||||||||||||||||| ||||| || ||||||||||| || |||
--gtatttcatgttcatttttctgttggatcagtaagtgcaccatgttcttcccagtcaccagtactagatacccttgcattatgttgttt-tgcttatgtagGAGCATGGATCTTACTGAAGCACTGCGCCTTCAGATGGAAGTTCAGAAGCGCCTTCATGAACAACTCGAG
















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|211437679|gb|FL100403.1|FL100403
EST:     AGCCACTGAAGAGCTGGTCCTGGACCTGAAAAC                         GAGCATGGATCTTACTGAAGCACTGCGCCTTCAGATGGAAATCCAGAAACG
genomic: AGCCACTGAAGAGCTGGTCCTGGACCTGAAAACgtgagtgaga ... tcttgtatagGAGCATGGATCTTACTGAAGCACTGCGCCTTCAGATGGAAGTCCAGAAACG
EST: gi|6056536|gb|AW090926.1|AW090926
EST:     ACATCGGAAAAAAGGACAGCCACTGAAGAGCTGGTCCTGGACCTGAAAAC                         GAGCATGGATCTTACTGAAGCGCTGCGCCTTCAGATGGAAGTCCAGAAACG
genomic: ACATCGGAAAAAAGGACAGCCACTGAAGAGCTGGTCCTGGACCTGAAAACgtgagtgaga ... tcttgtatagGAGCATGGATCTTACTGAAGCACTGCGCCTTCAGATGGAAGTCCAGAAACG
EST: gi|89251548|gb|DY623334.1|DY623334
EST:     ACATCGGAAAAAAGGACAGCCACTGAAGAGGTGGTCCTGGACCTGAAAAC                         GAGCATGGATCTTACTGAAGCACTGCGCCTTCAGATGGAAGTCCAGAAACG
genomic: ACATCGGAAAAAAGGACAGCCACTGAAGAGCTGGTCCTGGACCTGAAAACgtgagtgaga ... tcttgtatagGAGCATGGATCTTACTGAAGCACTGCGCCTTCAGATGGAAGTCCAGAAACG

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: 102

GTACATCGGAAAAAAGGACAGCCACTGAAGAGCTGGTCCTGGACCTGAAAACgtgagtgaga ... tcttgtatagGAGCATGGATCTTACTGAAGCACTGCGCCTTCAGATGGAAGTCCAGAAACGGCTTCATGAACAGCTTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 143

GTACATCGGAAAAAAGGACAGCCACTGAAGAGCTGGTCCTGGACCTGAAAACgtgagtgaga ... tcttgtatagGAGCATGGATCTTACTGAAGCACTGCGCCTTCAGATGGAAGTCCAGAAACGGCTTCATGAACAGCTTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 168

GTACATCGGAAAAAAGGACAGCCACTGAAGAGCTGGTCCTGGACCTGAAAACgtgagtgaga ... tcttgtatagGAGCATGGATCTTACTGAAGCACTGCGCCTTCAGATGGAAGTCCAGAAACGGCTTCATGAACAGCTTGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 119

GTACATCGGAAAAAAGGACAGCCACTGAAGAGCTGGTCCTGGACCTGAAAACgtgagtgaga ... tcttgtatagGAGCATGGATCTTACTGAAGCACTGCGCCTTCAGATGGAAGTCCAGAAACGGCTTCATGAACAGCTTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgatcatcattgtctgttacttcttggtccatgatattgggcattcttgtatagGAGCATGGATCTTACTGAAGCACTGCGCCTTCAGATGGAAGTCCAGAAACGGCTTCATGAACAGCTTGAG
                                          cattctt  CT-rich tract
                               atgatatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataaaatctaatttgaaggttttcctatatgttaaagtgcattttacgatcatcattgtctgttacttcttggtccatgatattgggcattcttgtatagGAGCATGGATCTTACTGAAGCACTGCGCCTTCAGATGGAAGTCCAGAAACGGCTTCATGAACAGCTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG