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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATAGGGCTCCAGAGCTCATATTTGGTGCCACTGAGTATACCACAGCGATTGACATTTGGTCTGCTGGATGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtaaggtgtctcaaatttttattgccattttaaaaaaggttttcaagccaacaaggtcctttcagttcacactgtcttacaagaactatttggacag

Basic information

species Zea mays
transcript GRMZM2G024151_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G024151_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os01g14860.3 (Oryza sativa), 5'ss of exon 7
CTATAGGGCTCCAGAGCTCATATTTGGTGCCACTGAGTATACCACAGCGATTGACATTTGGTCTGCTGGATGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtaaggtgtctcaaatttttattgccattttaaaaaaggttttcaa--gccaacaaggtcctttcagttcacac-----tgtcttacaagaactatttg---gacag
|||||||||||| |||||||||||||||||||| || || || ||||| |||||||| |||||||||||||||||||||||||| |||||| |||||||||||||  | ||  | ||| | |   ||||||    ||| || |      ||| |  || |  |   ||  |        || |||||||    | | ||   |||||
CTATAGGGCTCCGGAGCTCATATTTGGTGCCACCGAATACACTACAGCTATTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaag-cggctggattttctttgcacattttggggaagtttgttgtttaccaccctggactctattgtcgaagtcggtatgccttacaattgttttctgttcgacag
















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|32837926|gb|CD977604.1|CD977604
EST:     TTGACATTTGGTCTGCTGGATGTGTTCTTGCTGAGCTTATGCTAGGGCAG                         CCTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAG
genomic: TTGACATTTGGTCTGCTGGATGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtaaggtgtc ... atttggacagCCTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAG
EST: gi|211165156|gb|FL324133.1|FL324133
EST:     TTGACATTTGGTCTGCTGGATGTGTTCTTGCTGAGCTTATGCTAGGGCAG                         CCTTTGTTTCCGGGTGAAAGTGGTGTGGAC-AACTT
genomic: TTGACATTTGGTCTGCTGGATGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtaaggtgtc ... atttggacagCCTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTT
EST: gi|211161694|gb|FL418712.1|FL418712
EST:     TTGACATTTGGTCTGCTGGATGTGTTCTTGCTGAGCTTATGCTAGGGCAG                         CCTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTCGAAATCATCAAG
genomic: TTGACATTTGGTCTGCTGGATGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtaaggtgtc ... atttggacagCCTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAG
EST: gi|61117965|gb|DN558926.1|DN558926
EST:     TTGACATTTGGTCTGCTGGATGTGTTCTTGCTGAGCTTATGCTAGGGCAG                         CCTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTCGAAATCATCAAG
genomic: TTGACATTTGGTCTGCTGGATGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtaaggtgtc ... atttggacagCCTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAG
EST: gi|32838828|gb|CD978509.1|CD978509
EST:     TTGACATTTGGTCTGCTGGATGTGTTCTTGCTGAGCTTATGCTAGGGCAG                         CCTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAG
genomic: TTGACATTTGGTCTGCTGGATGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtaaggtgtc ... atttggacagCCTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAG
EST: gi|61117966|gb|DN558927.1|DN558927
EST:     TTGACATTTGGTCTGCTGGATGTGTTCTTGCTGAGCTTATGCTAGGGCAG                         CCTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTCGAAATCATCAAG
genomic: TTGACATTTGGTCTGCTGGATGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtaaggtgtc ... atttggacagCCTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAG
EST: gi|33097248|gb|CF057208.1|CF057208
EST:     TTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAG                         CCTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAG
genomic: TTGACATTTGGTCTGCTGGATGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtaaggtgtc ... atttggacagCCTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAG
EST: gi|60349962|gb|DN216935.1|DN216935
EST:     TTGACATTTGGTCTGCTGGATGTGTTCTTGCTGAGCTTATGCTAGGGCAG                         CCTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAA
genomic: TTGACATTTGGTCTGCTGGATGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtaaggtgtc ... atttggacagCCTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAG

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: 555

CTATAGGGCTCCAGAGCTCATATTTGGTGCCACTGAGTATACCACAGCGATTGACATTTGGTCTGCTGGATGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtaaggtgtc ... atttggacagCCTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 125

CTATAGGGCTCCAGAGCTCATATTTGGTGCCACTGAGTATACCACAGCGATTGACATTTGGTCTGCTGGATGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtaaggtgtc ... atttggacagCCTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 152

CTATAGGGCTCCAGAGCTCATATTTGGTGCCACTGAGTATACCACAGCGATTGACATTTGGTCTGCTGGATGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtaaggtgtc ... atttggacagCCTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 159

CTATAGGGCTCCAGAGCTCATATTTGGTGCCACTGAGTATACCACAGCGATTGACATTTGGTCTGCTGGATGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtaaggtgtc ... atttggacagCCTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTATAGGGCTCCAGAGCTCATATTTGGTGCCACTGAGTATACCACAGCGATTGACATTTGGTCTGCTGGATGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtaaggtgtctcaaatttttattgccattttaaaaaaggttttcaagccaacaaggtcctttcagttcacactgtcttacaagaactatttggacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT