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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgcaagcttatgcttttattgaggatatgaacagaactttcttctcttctccatcctatacccatacttgaatgtcttcactcatcatctttccttttagGCCTCACGGAAACTTGTGCTGGATCTTTCGTCTCGCTACCAAATCAAATGTCCATGATAGGAACTGTTGGCCCCCCAGTGCCAAACATCGATGTTCGTCT

Basic information

species Zea mays
transcript GRMZM5G861300_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G861300_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os01g46750.1 (Oryza sativa), 3'ss of exon 14
-cgcaagcttatgcttttattgaggatatgaacagaactttcttctcttctccatcctatacccatacttgaatgtcttcactcatcatctttccttttagGCCTCACGGAAACTTGTGCTGGATCTTTCGTCTCGCTACCAAATCAAATGTCCATGATAGGAACTGTTGGCCCCCCAGTGCCAAACATCGATGTTCGTCT
   |||   | | ||    |  |||  || | ||    |   |           |  | | || | |      ||| || | ||||  |  |  |||||||| |||||||| ||||||||||||||||||||||| ||||||||||| |||| ||||||||| |||||||| || ||||||||||| || |||||  | ||
aaacaaaagtttcctaaattgtaggtcattatcattgatccatgtaacctgaattttttttccaacagaactttgttttgaatcatt-tggtctcttttagGTCTCACGGAGACTTGTGCTGGATCTTTCGTCTCCCTACCAAATCAGATGTGCATGATAGGGACTGTTGGTCCTCCAGTGCCAAATATTGATGTCTGCCT
















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|9733729|gb|BE512481.1|BE512481
EST:     TGAAGAATACTTGCGTGTGGTCACATGTGCACATGTCGTACAAGGATATG                         GCCTCACGGAAACTTGTGCTGGATCTTTCGTCTCGCTACCAAATCAAATGT
genomic: TGAAGAATACTTGCGTGTGGTCACATGTGCACATGTCGTACAAGGATATGgtacatttct ... ttccttttagGCCTCACGGAAACTTGTGCTGGATCTTTCGTCTCGCTACCAAATCAAATGT
EST: gi|32930132|gb|CF034944.1|CF034944
EST:     TACAAGGATATG                         GTCTCACGGAAACTTGTGCTGGATCTTTCGTCTCGCTACCAAATCAAATGT
genomic: TACAAGGATATGgtacatttct ... ttccttttagGCCTCACGGAAACTTGTGCTGGATCTTTCGTCTCGCTACCAAATCAAATGT
EST: gi|60354962|gb|DN221935.1|DN221935
EST:     TGAAGAATACTTGCGTGTGGTCACATGTGCACATGTCGTACAAGGATATG                         GTCTCACGGAAACTTGTGCTGGATCTTTCGTCTCGCTACCAAATCAAATGT
genomic: TGAAGAATACTTGCGTGTGGTCACATGTGCACATGTCGTACAAGGATATGgtacatttct ... ttccttttagGCCTCACGGAAACTTGTGCTGGATCTTTCGTCTCGCTACCAAATCAAATGT
EST: gi|32919588|gb|CF024400.1|CF024400
EST:     TGAAGAATACTTGCGTGTGGTCACATGTGCACATGTCGTACAAGGATATG                         GTCTCACGGAAACTTGTGCTGGATCTTTCGTCTCGCTACCAAATCAAATGT
genomic: TGAAGAATACTTGCGTGTGGTCACATGTGCACATGTCGTACAAGGATATGgtacatttct ... ttccttttagGCCTCACGGAAACTTGTGCTGGATCTTTCGTCTCGCTACCAAATCAAATGT
EST: gi|32933924|gb|CF038736.1|CF038736
EST:     GTACAAAGGATATG                         GTCTCACGGAAACTTGTGCTGGATCTTTCGTCTCGCTACCAAATCAAATG
genomic: GTAC-AAGGATATGgtacatttct ... ttccttttagGCCTCACGGAAACTTGTGCTGGATCTTTCGTCTCGCTACCAAATCAAATG
EST: gi|5901236|gb|AW042336.1|AW042336
EST:     TGAAGAATACTTGCGTGTGGTCACATGTGCACATGTCGTACAAGGATATG                         GTCTCACGGAAACTTGTGCTGGATCTTTCGTCTCGCTACCAAATCAAATGT
genomic: TGAAGAATACTTGCGTGTGGTCACATGTGCACATGTCGTACAAGGATATGgtacatttct ... ttccttttagGCCTCACGGAAACTTGTGCTGGATCTTTCGTCTCGCTACCAAATCAAATGT
EST: gi|60348658|gb|DN215631.1|DN215631
EST:     TGAAGAATACTTGCGTGTGGTCACATGTGCACATGTCGTACAAGGATATG                         GCCTCACGGAAACTTGTGCTGGATCTTTCGTCTCGCTACCAAATCAAATGT
genomic: TGAAGAATACTTGCGTGTGGTCACATGTGCACATGTCGTACAAGGATATGgtacatttct ... ttccttttagGCCTCACGGAAACTTGTGCTGGATCTTTCGTCTCGCTACCAAATCAAATGT
EST: gi|60348666|gb|DN215639.1|DN215639
EST:     TGAAGAATACTTGCGTGTGGTCACATGTGCACATGTCGTACAAGGATATG                         GCCTCACGGAAACTTGTGCTGGATCTTTCGTCTCGCTACCAAATCAAATGT
genomic: TGAAGAATACTTGCGTGTGGTCACATGTGCACATGTCGTACAAGGATATGgtacatttct ... ttccttttagGCCTCACGGAAACTTGTGCTGGATCTTTCGTCTCGCTACCAAATCAAATGT
EST: gi|6095468|gb|AW120135.1|AW120135
EST:     CACATGTCGTACAAGGATATG                         GTCTCACGGAAACTTGTGCTGGATCTTTCGTCTCGCTACCAAATCAAATGT
genomic: CACATGTCGTACAAGGATATGgtacatttct ... ttccttttagGCCTCACGGAAACTTGTGCTGGATCTTTCGTCTCGCTACCAAATCAAATGT
EST: gi|32919644|gb|CF024456.1|CF024456
EST:     TGAAGAATACTTGCGTGTGGTCACATGTGCACATGTCGTACAAGGATATG                         GTCTCACGGAAACTTGTGCTGGATCTTTCGTCTCGCTACCAAATCAAATGT
genomic: TGAAGAATACTTGCGTGTGGTCACATGTGCACATGTCGTACAAGGATATGgtacatttct ... ttccttttagGCCTCACGGAAACTTGTGCTGGATCTTTCGTCTCGCTACCAAATCAAATGT

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: 48 (upstream exon), 49 (downstream exon)
Score: 176

GGAAATGTTAGAGTTATTTTATCTGGAGCTGCTCCACTTGCTACCCATGTTGAAGAATACTTGCGTGTGGTCACATGTGCACATGTCGTACAAGGATATGgtacatttct ... ttccttttagGCCTCACGGAAACTTGTGCTGGATCTTTCGTCTCGCTACCAAATCAAATGTCCATGATAGGAACTGTTGGCCCCCCAGTGCCAAACATCGATGTTCGTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 274

GGAAATGTTAGAGTTATTTTATCTGGAGCTGCTCCACTTGCTACCCATGTTGAAGAATACTTGCGTGTGGTCACATGTGCACATGTCGTACAAGGATATGgtacatttct ... ttccttttagGCCTCACGGAAACTTGTGCTGGATCTTTCGTCTCGCTACCAAATCAAATGTCCATGATAGGAACTGTTGGCCCCCCAGTGCCAAACATCGATGTTCGTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 212

GGAAATGTTAGAGTTATTTTATCTGGAGCTGCTCCACTTGCTACCCATGTTGAAGAATACTTGCGTGTGGTCACATGTGCACATGTCGTACAAGGATATGgtacatttct ... ttccttttagGCCTCACGGAAACTTGTGCTGGATCTTTCGTCTCGCTACCAAATCAAATGTCCATGATAGGAACTGTTGGCCCCCCAGTGCCAAACATCGATGTTCGTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 122

GGAAATGTTAGAGTTATTTTATCTGGAGCTGCTCCACTTGCTACCCATGTTGAAGAATACTTGCGTGTGGTCACATGTGCACATGTCGTACAAGGATATGgtacatttct ... ttccttttagGCCTCACGGAAACTTGTGCTGGATCTTTCGTCTCGCTACCAAATCAAATGTCCATGATAGGAACTGTTGGCCCCCCAGTGCCAAACATCGATGTTCGTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctccatcctatacccatacttgaatgtcttcactcatcatctttccttttagGCCTCACGGAAACTTGTGCTGGATCTTTCGTCTCGCTACCAAATCAAATGTCCATGATAGGAACTGTTGGCCCCCCAGTGCCAAACATCGATGTTCGTCT
                             tcttcactcatcatct  CT-rich tract
                                                 tttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgcaagcttatgcttttattgaggatatgaacagaactttcttctcttctccatcctatacccatacttgaatgtcttcactcatcatctttccttttagGCCTCACGGAAACTTGTGCTGGATCTTTCGTCTCGCTACCAAATCAAATGTCCATGATAGGAACTGTTGGCCCCCCAGTGCCAAACATCGATGTTCGTCT

- - -gcttatg
- - - - - - - - - - - - - - -aacagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgaatg