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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgttcatggcagcttgtggcaaattaatggggcaagtttgttcaactgtgctgatcgttgatgttaagcatcaactgtcttctgctcgacaattttgcagGGAGGTTGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCTGCAAG

Basic information

species Zea mays
transcript GRMZM5G836588_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G836588_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os10g30750.1 (Oryza sativa), 3'ss of exon 2
gtactgttcatggcagcttgtggcaaattaatggggcaagtttgttcaactgtgctgatcgttgatgttaagcatcaactgtc-ttctgctcgacaattttgcagGGAGGTTGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCTGCAAG
             | |||||     || |  |||||  | || |||||| | ||| | |  |||  |  |||  |||  |||  ||||| |  |   |||| |||||||| ||||||||||||||||| |||||||||||||| || ||||||||||||||
----------gtacggcttg----gaaattgtgggg--atttggttcaattctgc-ggtgattgggg--aagtgtcatttgttgttctgtttcaatttttttcagGGAGGATGCCGAACTGGGATGGCGAAGATGACCAATGCTTATGATCTGCCTGCAAG
















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|211381535|gb|FL250722.1|FL250722
EST:     GGTTGCATGCTGCTGCCGGGTCAGGGCTCGCCGAGGAGTGCGCCACCTTG                         GGAGGTTGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCT
genomic: GGTTGCATGCTGCTGCCGGGTCAGGGCTCGCCGAGGAGTGCGCCACCTTGgtactgttca ... aattttgcagGGAGGTTGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCT
EST: gi|76286118|gb|DV025686.1|DV025686
EST:     GGTTGCATGCTGCTGCCGGGTCAGGGCTCGCCGAGGAGTGCGCCACCTTG                         GGAGGTTGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCT
genomic: GGTTGCATGCTGCTGCCGGGTCAGGGCTCGCCGAGGAGTGCGCCACCTTGgtactgttca ... aattttgcagGGAGGTTGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCT
EST: gi|211381543|gb|FL250730.1|FL250730
EST:     GGTTGCATGCTGCTGCCGGGTCAGGGCTCGCCGAGGAGTGCGCCACCTTG                         GGAGGTTGCCGAACTGGGA
genomic: GGTTGCATGCTGCTGCCGGGTCAGGGCTCGCCGAGGAGTGCGCCACCTTGgtactgttca ... aattttgcagGGAGGTTGCCGAACTGGGA
EST: gi|211381540|gb|FL250727.1|FL250727
EST:     GGTTGCATGCTGCTGCCGGGTCAGGGCTCGCCGAGGAGTGCGCCACCTTG                         GGAGGTTGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCT
genomic: GGTTGCATGCTGCTGCCGGGTCAGGGCTCGCCGAGGAGTGCGCCACCTTGgtactgttca ... aattttgcagGGAGGTTGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCT
EST: gi|211381538|gb|FL250725.1|FL250725
EST:     TTGCATGCTGCTGCCGGGTCAGGCCTCGCCGAGGAAGTGCGCCACCCTTG                         GGAGGTTGCCAAACTG
genomic: TTGCATGCTGCTGCCGGGTCAGGGCTCGCCGAGGA-GTGCGCCACC-TTGgtactgttca ... aattttgcagGGAGGTTGCCGAACTG
EST: gi|211378900|gb|FL250717.1|FL250717
EST:     GGTTGCATGCTGCTGCCGGGTCAGGGCTCGCCGAGGAGTGCGCCACCTTG                         GGAGGTTGCCGAACTGGGATGGCCAAGATGACCCATGCCTACGATCTGCCT
genomic: GGTTGCATGCTGCTGCCGGGTCAGGGCTCGCCGAGGAGTGCGCCACCTTGgtactgttca ... aattttgcagGGAGGTTGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCT
EST: gi|91051901|gb|EB162319.1|EB162319
EST:     GGTTGCATGCTGCTGCCGGGTCAGGGCTCGCCGAGGAGTGCGCCACCTTG                         GGAGGTTGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCT
genomic: GGTTGCATGCTGCTGCCGGGTCAGGGCTCGCCGAGGAGTGCGCCACCTTGgtactgttca ... aattttgcagGGAGGTTGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCT
EST: gi|211381541|gb|FL250728.1|FL250728
EST:     GTTGCATGCTGCTGCCGGGTCAGGGCTCGCCGAGGAGTGCGCCACCCTTG                         GGAGGTTGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCC
genomic: GTTGCATGCTGCTGCCGGGTCAGGGCTCGCCGAGGAGTGCGCCACC-TTGgtactgttca ... aattttgcagGGAGGTTGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCC
EST: gi|148931777|gb|EC875053.2|EC875053
EST:     GGTTGCATGCTGCTGCCGGGTCAGGGCTCGCCGAGGAGTGCGCCACCTTG                         GGAGGTTGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCT
genomic: GGTTGCATGCTGCTGCCGGGTCAGGGCTCGCCGAGGAGTGCGCCACCTTGgtactgttca ... aattttgcagGGAGGTTGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCT
EST: gi|94478487|gb|EB707445.1|EB707445
EST:     GGTTGCATGCTGCTGCCGGGTCAGGGCTCGCCGAGGAGTGCGCCACCTTG                         GGAGGTTGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCT
genomic: GGTTGCATGCTGCTGCCGGGTCAGGGCTCGCCGAGGAGTGCGCCACCTTGgtactgttca ... aattttgcagGGAGGTTGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCT

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: 45 (upstream exon), 47 (downstream exon)
Score: 37

AGCTTGGACGAGGCGCACAGTAGCCCGGGGTTGCATGCTGCTGCCGGGTCAGGGCTCGCCGAGGAGTGCGCCACCTTGgtactgttca ... aattttgcagGGAGGTTGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCTGCAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 68

AGCTTGGACGAGGCGCACAGTAGCCCGGGGTTGCATGCTGCTGCCGGGTCAGGGCTCGCCGAGGAGTGCGCCACCTTGgtactgttca ... aattttgcagGGAGGTTGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCTGCAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 31

AGCTTGGACGAGGCGCACAGTAGCCCGGGGTTGCATGCTGCTGCCGGGTCAGGGCTCGCCGAGGAGTGCGCCACCTTGgtactgttca ... aattttgcagGGAGGTTGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCTGCAAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 37

AGCTTGGACGAGGCGCACAGTAGCCCGGGGTTGCATGCTGCTGCCGGGTCAGGGCTCGCCGAGGAGTGCGCCACCTTGgtactgttca ... aattttgcagGGAGGTTGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCTGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtgctgatcgttgatgttaagcatcaactgtcttctgctcgacaattttgcagGGAGGTTGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCTGCAAG
                                           acaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgttcatggcagcttgtggcaaattaatggggcaagtttgttcaactgtgctgatcgttgatgttaagcatcaactgtcttctgctcgacaattttgcagGGAGGTTGCCGAACTGGGATGGCCAAGATGACCAATGCCTACGATCTGCCTGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG