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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgctgttctatctatcctttaagtcatgataagggtttgctgagatcaccagatgaatttatccgagcttatgtttctcagGTAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGTTTTAAGGAAACTACTGAGCCAGCCGTTTGCTTGAGTGAAG

Basic information

species Zea mays
transcript GRMZM2G389362_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G389362_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os11g02464.1 (Oryza sativa), 3'ss of exon 4
gtatgtgctgttctatctatc----ctttaagtcatgataagggtttgctgagatcaccagatgaatttatccgagcttatgtttctcagGTAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGTTTTAAGGAAACTACTGAGCCAGCCGTTTGCTTGAGTGAAG
|| |||||| | ||||| |||    ||  |||   |   | |   ||  |||| |  |  | ||   |||||| |   | ||||| ||||| || ||||| |||||||| |||||||| ||| ||||||||||||||   ||||| ||||| ||||| ||||||||||||||||
gtttgtgctctgctatccatcataactacaagaagtagaacgcaatt-ttgaggttccttg-tgtgcttatccaaatctttgtttgtcagGGAAACTTGATAAAGGAGCGGTTCTTAAGGCAATTTGTGCTGGTTTTCGAGAAACCACTGAACCAGCTGTTTGCTTGAGTGAAG

upper sequence: GRMZM2G389362_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os12g02390.1 (Oryza sativa), 3'ss of exon 4
gtatgtgctgttctatctatc----ctttaagtcatgataagggtttgctgagatcaccagatgaatttatccgagcttatgtttctcagGTAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGTTTTAAGGAAACTACTGAGCCAGCCGTTTGCTTGAGTGAAG
|| |||||| | ||||| |||    ||  |||   |   | |   ||  |||| |  || | ||   |||||| |   | ||||| ||||| || ||||| |||||||| |||||||| ||| ||||||||||||||   ||||| ||||| ||||| ||||||||||||||||
gtttgtgctctgctatccatcataactacaagaagtagaatgcaatt-ttgaggtt-cctggtgtgcttatccaaatctttgtttgtcagGGAAACTTGATAAAGGAGCGGTTCTTAAGGCAATTTGTGCTGGTTTTCGAGAAACCACTGAACCAGCTGTTTGCTTGAGTGAAG

upper sequence: GRMZM2G389362_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv08s0058g01360.t01 (Vitis vinifera), 3'ss of exon 4
gtatgtg-ctgt-tctatctatcctttaagtcatgataagggtttgctgagatcaccagatgaatttatccgagcttatgtttctcagGTAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGTTTTAAGGAAACTACTGAGCCAGCCGTTTGCTTGAGTGAAG
|| |||| | || | |||  |   ||| |||  || ||      | ||  |           ||  | | |  |||  |   | ||||||||||| ||||||||||||||||| || ||  ||||||| |||||  | || || ||||| ||| || ||||  | ||||| |
gtttgtggcagtatttatagagaatttcagt--tgctagccaactccttgggctgtttccgtaacctttact-gctgcttggtttcagGTAAGCTGGACAAAGGAGCAGTTCTCAAGGCCATTTGTGCCGGTTTCCAAGAGACCACTGAACCAACCATTTGTCTTAGTGACG

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|67022369|gb|CO451118.1|CO451118
EST:     TGATGTTACCATCTTACCAACTCTGGTAATTAACAATAGACAATACAGAG                         GTAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTTGTTTTAAGG
genomic: TGATGTTACCATCTTACCAACTCTGGTAATTAACAATAGACAATACAGAGgtatgtgctg ... tgtttctcagGTAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGTTTTAAGG
EST: gi|211315830|gb|FK969313.1|FK969313
EST:     TGATGTTACCATCTTACCAACTCTGGTAATTAACAATAGACAATACAGAG                         GTAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGTTTTAAGG
genomic: TGATGTTACCATCTTACCAACTCTGGTAATTAACAATAGACAATACAGAGgtatgtgctg ... tgtttctcagGTAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGTTTTAAGG
EST: gi|211313814|gb|FK969304.1|FK969304
EST:     TGATGTTACCATCTTACCAACTCTGGTAATTAACAATAGACAATACAGAG                         GTAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTS-TGGTTTTAAGG
genomic: TGATGTTACCATCTTACCAACTCTGGTAATTAACAATAGACAATACAGAGgtatgtgctg ... tgtttctcagGTAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGTTTTAAGG
EST: gi|211313816|gb|FK969306.1|FK969306
EST:     TGATGTTACCATCTTACCAACTCTGGTAATTAACAATAGACAATACAGAG                         GTAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGNTTTAAGG
genomic: TGATGTTACCATCTTACCAACTCTGGTAATTAACAATAGACAATACAGAGgtatgtgctg ... tgtttctcagGTAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGTTTTAAGG
EST: gi|211313815|gb|FK969305.1|FK969305
EST:     TGATGTTACCATCTTACCAACTCTGGTAATTAACAATAGACAATACAGAG                         GTAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGTTTTAAGG
genomic: TGATGTTACCATCTTACCAACTCTGGTAATTAACAATAGACAATACAGAGgtatgtgctg ... tgtttctcagGTAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGTTTTAAGG
EST: gi|32937726|gb|CF042545.1|CF042545
EST:     TGATGTTACCATCTTACCAACTCTGGTAATTAACAATAGACAATACAGAG                         GTAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGTTTTAAGG
genomic: TGATGTTACCATCTTACCAACTCTGGTAATTAACAATAGACAATACAGAGgtatgtgctg ... tgtttctcagGTAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGTTTTAAGG
EST: gi|211313813|gb|FK969303.1|FK969303
EST:     TGATGTTACCATCTTACCAACTCTGGTAATTAACAATAGACAATACAGAG                         GTAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGTTTTAAGG
genomic: TGATGTTACCATCTTACCAACTCTGGTAATTAACAATAGACAATACAGAGgtatgtgctg ... tgtttctcagGTAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGTTTTAAGG
EST: gi|211313817|gb|FK969307.1|FK969307
EST:     TGATGTTACCATCTTACCAACTCTGGTAATTAACAATAGACAATACAGAG                         GTAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGTTTTAAGG
genomic: TGATGTTACCATCTTACCAACTCTGGTAATTAACAATAGACAATACAGAGgtatgtgctg ... tgtttctcagGTAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGTTTTAAGG
EST: gi|67026759|gb|CO455508.1|CO455508
EST:     TGATGTTACCATCTTACCAACTCTGGTAATTAACAATAGACAATACAGAG                         GTAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGTTTTAAGG
genomic: TGATGTTACCATCTTACCAACTCTGGTAATTAACAATAGACAATACAGAGgtatgtgctg ... tgtttctcagGTAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGTTTTAAGG
EST: gi|32937931|gb|CF042750.1|CF042750
EST:     TGATGTTACCATCTTACCAACTCTGGTAATTAACAATAGACAATACAGAG                         GTAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGTTTTAAGG
genomic: TGATGTTACCATCTTACCAACTCTGGTAATTAACAATAGACAATACAGAGgtatgtgctg ... tgtttctcagGTAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGTTTTAAGG

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), 46 (downstream exon)
Score: 194

ATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATTAACAATAGACAATACAGAGgtatgtgctg ... tgtttctcagGTAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGTTTTAAGGAAACTACTGAGCCAGCCGTTTGCTTGAGTGAAG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 141

ATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATTAACAATAGACAATACAGAGgtatgtgctg ... tgtttctcagGTAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGTTTTAAGGAAACTACTGAGCCAGCCGTTTGCTTGAGTGAAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 131

ATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATTAACAATAGACAATACAGAGgtatgtgctg ... tgtttctcagGTAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGTTTTAAGGAAACTACTGAGCCAGCCGTTTGCTTGAGTGAAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 195

ATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATTAACAATAGACAATACAGAGgtatgtgctg ... tgtttctcagGTAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGTTTTAAGGAAACTACTGAGCCAGCCGTTTGCTTGAGTGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgataagggtttgctgagatcaccagatgaatttatccgagcttatgtttctcagGTAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGTTTTAAGGAAACTACTGAGCCAGCCGTTTGCTTGAGTGAAG
                                             tgtttctc  CT-rich tract
                          atgaatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgctgttctatctatcctttaagtcatgataagggtttgctgagatcaccagatgaatttatccgagcttatgtttctcagGTAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGTTTTAAGGAAACTACTGAGCCAGCCGTTTGCTTGAGTGAAG

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