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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtttattttgttaagttactcacaagatgtttcatattggtctctgacaggaattgttttgtagGTTATGCGGGATTCGAATGGTGTCAGCAGAGGTTCTGGATTTGTTGCTTTCAAATCTGCTGAAGATGCTAACCGAGCT

Basic information

species Zea mays
transcript GRMZM2G102829_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102829_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os09g02700.1 (Oryza sativa), 3'ss of exon 3
gtctgtttattttgttaagttactcacaagat--gtttcatattggtctctg---------acaggaattgttttgtagGTTATGCGGGATTCGAATGGTGTCAGCAGAGGTTCTGGATTTGTTGCTTTCAAATCTGCTGAAGATGCTAACCGAGCT
|| |||||| || ||     ||  ||   | |    | | |||   | ||||         | || || |||    ||||| ||||||||||| |||||||||||||||||||||||||||||||| || ||||||||||||||||||  |||||||
gtttgtttactt-gtctgcctatgcatgtgtttcaatgcttatcaatttctggtgctaataatagaaactgtgccatagGTGATGCGGGATTCAAATGGTGTCAGCAGAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCT
















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|14191311|gb|BG833541.1|BG833541
EST:     AGAAATTGCGTGAACTCTTTGCTGAGTATGGCAATATTACTTCCTGCAAG                         GGTATGCGGGATTCGAATGGTGTCAGCAGAGGTTCTGGATTTGTTGCTTTC
genomic: AGAAATTGCGTGAACTCTTTGCTGAGTATGGCAATATTACTTCCTGCAAGgtctgtttat ... tgttttgtagGTTATGCGGGATTCGAATGGTGTCAGCAGAGGTTCTGGATTTGTTGCTTTC
EST: gi|94478794|gb|EB707752.1|EB707752
EST:     AGAAATTGCGTGAACTCTTTGCGGAGTATGGCAATATTACTTCCTGCAAG                         GTTATGCGGGATTCGAATGGTGTCAGCAGAGGTTCTGGATTTGTTGCTTTC
genomic: AGAAATTGCGTGAACTCTTTGCTGAGTATGGCAATATTACTTCCTGCAAGgtctgtttat ... tgttttgtagGTTATGCGGGATTCGAATGGTGTCAGCAGAGGTTCTGGATTTGTTGCTTTC
EST: gi|67011934|gb|CO440683.1|CO440683
EST:     AGAAATTGCGTGAACTCTTTGCTGAGTATGGCAATATTACTTCCTGCAAG                         GTTATGCGGGATTCGAATGGTGTCAGCAGAGGTTCTGGATTTGTTGCTTTC
genomic: AGAAATTGCGTGAACTCTTTGCTGAGTATGGCAATATTACTTCCTGCAAGgtctgtttat ... tgttttgtagGTTATGCGGGATTCGAATGGTGTCAGCAGAGGTTCTGGATTTGTTGCTTTC
EST: gi|76291690|gb|DV031258.1|DV031258
EST:     AGAAATTGCGTGAACTCTTTGCTGAGTATGGCAATATTACTTCCTGCAAG                         GTTATGCGGGATTCGAATGGTGTCAGCAGAGGTTCTGGATTTGTTGCTTTC
genomic: AGAAATTGCGTGAACTCTTTGCTGAGTATGGCAATATTACTTCCTGCAAGgtctgtttat ... tgttttgtagGTTATGCGGGATTCGAATGGTGTCAGCAGAGGTTCTGGATTTGTTGCTTTC
EST: gi|14191310|gb|BG833540.1|BG833540
EST:     AGAAATTGCGTGAACTCTTTGCTGAGTATGGCAATATTACTTCCTGCAAG                         GGTATGCGGGATTCGAATGGTGTCAGCAGAGGTTCTGGATTTGTTGCTTTC
genomic: AGAAATTGCGTGAACTCTTTGCTGAGTATGGCAATATTACTTCCTGCAAGgtctgtttat ... tgttttgtagGTTATGCGGGATTCGAATGGTGTCAGCAGAGGTTCTGGATTTGTTGCTTTC
EST: gi|23199564|gb|BU582129.1|BU582129
EST:     AGAAATTGCGTGAACTCTTTGCTGAGTATGGCAATATTACTTCCTGCAAG                         GTTATGCGGGATTCGAATGGTGTCAGCAGAGGTTCTGGATTTGTTGCTTTC
genomic: AGAAATTGCGTGAACTCTTTGCTGAGTATGGCAATATTACTTCCTGCAAGgtctgtttat ... tgttttgtagGTTATGCGGGATTCGAATGGTGTCAGCAGAGGTTCTGGATTTGTTGCTTTC

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), 48 (downstream exon)
Score: 947

CCAAAACACAAACTTGTATTTGAAGAACTTAGAGGAGAACATTGATGATGAGAAATTGCGTGAACTCTTTGCTGAGTATGGCAATATTACTTCCTGCAAGgtctgtttat ... tgttttgtagGTTATGCGGGATTCGAATGGTGTCAGCAGAGGTTCTGGATTTGTTGCTTTCAAATCTGCTGAAGATGCTAACCGAGCT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 899

CCAAAACACAAACTTGTATTTGAAGAACTTAGAGGAGAACATTGATGATGAGAAATTGCGTGAACTCTTTGCTGAGTATGGCAATATTACTTCCTGCAAGgtctgtttat ... tgttttgtagGTTATGCGGGATTCGAATGGTGTCAGCAGAGGTTCTGGATTTGTTGCTTTCAAATCTGCTGAAGATGCTAACCGAGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 791

CCAAAACACAAACTTGTATTTGAAGAACTTAGAGGAGAACATTGATGATGAGAAATTGCGTGAACTCTTTGCTGAGTATGGCAATATTACTTCCTGCAAGgtctgtttat ... tgttttgtagGTTATGCGGGATTCGAATGGTGTCAGCAGAGGTTCTGGATTTGTTGCTTTCAAATCTGCTGAAGATGCTAACCGAGCT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 625

CCAAAACACAAACTTGTATTTGAAGAACTTAGAGGAGAACATTGATGATGAGAAATTGCGTGAACTCTTTGCTGAGTATGGCAATATTACTTCCTGCAAGgtctgtttat ... tgttttgtagGTTATGCGGGATTCGAATGGTGTCAGCAGAGGTTCTGGATTTGTTGCTTTCAAATCTGCTGAAGATGCTAACCGAGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttaagttactcacaagatgtttcatattggtctctgacaggaattgttttgtagGTTATGCGGGATTCGAATGGTGTCAGCAGAGGTTCTGGATTTGTTGCTTTCAAATCTGCTGAAGATGCTAACCGAGCT
                                            ttgtttt  CT-rich tract
                    tttcatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtttattttgttaagttactcacaagatgtttcatattggtctctgacaggaattgttttgtagGTTATGCGGGATTCGAATGGTGTCAGCAGAGGTTCTGGATTTGTTGCTTTCAAATCTGCTGAAGATGCTAACCGAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG