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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTCCCTTGCATCTGATTTCATGTACAATCAAATGACAAAGGATGTAACAGCAAGCTTTGGTTATGATTATATGCTGAGACAGgtatccttgtttgtttgacccatctgctatttttcccatgcttccatttgttattgtaatgcaaatgttagataaaatgcttgagggcaatcgatctttc...

Basic information

species Zea mays
transcript GRMZM2G120876_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120876_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os01g16910.1 (Oryza sativa), 5'ss of exon 9
GTTTCCCTTGCATCTGATTTCATGTACAATCAAATGACAAAGGATGTAACAGCAAGCTTTGGTTATGATTATATGCTGAGACAGgtat-ccttgtttgtttg-acccatctgctatttttcccatgcttccatttgttattgtaatgcaaatgttagataaaatgcttgagggcaatcgatctttc
|||||||||||||||||||| ||||||||||| ||| | ||||||||||||||||| || || |||||||||||| ||||||||||||  |||| ||||||  |||  |  | | |||||    ||| |   | |   || |||      |||| | |     |||   |     | | || ||| 
GTTTCCCTTGCATCTGATTTTATGTACAATCATATGGCGAAGGATGTAACAGCAAGTTTCGGCTATGATTATATGTTGAGACAGgtatatcttgattgtttccaccttttcggttttttttttgtgcgttggtctagcatggtatgtgggatgtaaaagttgctgcaacaacttgagc-atattt-

upper sequence: GRMZM2G120876_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv03s0097g00590.t01 (Vitis vinifera), 5'ss of exon 9
GTTTCCCTTGCATCTGATTTCATGTACAATCAAATGACAAAGGATGTAACAGCAAGCTTTGGTTATGATTATATGCTGAGACAGgtatccttgtttgtttgacccatctgctatttttcccatgcttccatttgttattgtaatgcaaatgttagataaaatgcttgagg---gcaatcgatctttc-
|||||  | ||||| ||||||||||||||| | ||| |||  ||||| || ||||| |||||||||||||| || ||  ||||||||   |    | ||     ||    || | ||  | |    |    ||  |    |     | || |||  | || || ||  |    |||||   | || | 
GTTTCTTTAGCATCAGATTTCATGTACAATTATATGTCAAGAGATGTCACTGCAAGTTTTGGTTATGATTACATCCTTCGACAGgtaatttctagtatt----gcaaaaactttcttatctagatattatgtttgtgcctttgcatatatattacttcaattgtttttgtcacgcaataattgttcct
















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|84977313|gb|DW475735.1|DW475735
EST:     TGACAAAGGATGTAACAGCAAGCTTTGGTTATGATTATATGCTGAGACAG                         TGTCGATTGAGAGGGAAACTGGATACCAATGGCGTAATTTCTTCTCTTTTG
genomic: TGACAAAGGATGTAACAGCAAGCTTTGGTTATGATTATATGCTGAGACAGgtatccttgt ... atatttgcagTGTCGATTGAGAGGGAAACTGGATACCAATGGCGTAATTTCTTCTCTTTTG
EST: gi|149101278|gb|EE187391.2|EE187391
EST:     TGACAAAGGATGTAACAGCAAGCTTTGGTTATGATTATATGCTGAGACAG                         TGTCGATTGAGAGGGAAACTGGATACCAATGGCGTAATTTCTTCTCTTTTG
genomic: TGACAAAGGATGTAACAGCAAGCTTTGGTTATGATTATATGCTGAGACAGgtatccttgt ... atatttgcagTGTCGATTGAGAGGGAAACTGGATACCAATGGCGTAATTTCTTCTCTTTTG
EST: gi|18660880|gb|BM501096.1|BM501096
EST:     TGACAAAGGATGTAACAGCAAGCTTTGGTTATGATTATATGCTGAGACAG                         TGTCGATTGAGAGGGAAACTGGATACCAATGGCGTAATTTCTTCTCTTTTG
genomic: TGACAAAGGATGTAACAGCAAGCTTTGGTTATGATTATATGCTGAGACAGgtatccttgt ... atatttgcagTGTCGATTGAGAGGGAAACTGGATACCAATGGCGTAATTTCTTCTCTTTTG
EST: gi|211134090|gb|FL422145.1|FL422145
EST:     TGACAAAGGATGTAACAGCAAGCTTTGGTTATGATTATATGCTGAGACAG                         TGTCGATTGAGAGGGAAACTGGATACCAATGGCGTAATTTCTTCTCT
genomic: TGACAAAGGATGTAACAGCAAGCTTTGGTTATGATTATATGCTGAGACAGgtatccttgt ... atatttgcagTGTCGATTGAGAGGGAAACTGGATACCAATGGCGTAATTTCTTCTCT
EST: gi|116828230|gb|EC855796.1|EC855796
EST:     TGACAAAGGATGTAACAGC-AGCTTTGGTTATGATTATATGCTGAGACAG                         TGTCGATTGAGAGGGAAACTGGATACCAATGGCGTAATTTCTTCTCTTTTG
genomic: TGACAAAGGATGTAACAGCAAGCTTTGGTTATGATTATATGCTGAGACAGgtatccttgt ... atatttgcagTGTCGATTGAGAGGGAAACTGGATACCAATGGCGTAATTTCTTCTCTTTTG
EST: gi|211538850|gb|FL377090.1|FL377090
EST:     TGACAAAGGATGTAACAGCAAGCTTTGGTTATGATTATATGCTGAGACAG                         TGTCGATTGAGAGGGAAACTGGATACCAATGGCGTAATTTCTTCTCTTTT
genomic: TGACAAAGGATGTAACAGCAAGCTTTGGTTATGATTATATGCTGAGACAGgtatccttgt ... atatttgcagTGTCGATTGAGAGGGAAACTGGATACCAATGGCGTAATTTCTTCTCTTTT
EST: gi|211045137|gb|FL385512.1|FL385512
EST:     TGACAAAGGATGTAACAGCAAGCTTTGGTTATGATTATATGCTGAGACAG                         TGTCGATTGAGAGG
genomic: TGACAAAGGATGTAACAGCAAGCTTTGGTTATGATTATATGCTGAGACAGgtatccttgt ... atatttgcagTGTCGATTGAGAGG

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), 44 (downstream exon)
Score: 233

GTTTCCCTTGCATCTGATTTCATGTACAATCAAATGACAAAGGATGTAACAGCAAGCTTTGGTTATGATTATATGCTGAGACAGgtatccttgt ... atatttgcagTGTCGATTGAGAGGGAAACTGGATACCAATGGCGTAATTTCTTCTCTTTTGGAGGAGCGATTGACTCCAGGTGTCACTTTCCAGTTGTCTGCAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 163

GTTTCCCTTGCATCTGATTTCATGTACAATCAAATGACAAAGGATGTAACAGCAAGCTTTGGTTATGATTATATGCTGAGACAGgtatccttgt ... atatttgcagTGTCGATTGAGAGGGAAACTGGATACCAATGGCGTAATTTCTTCTCTTTTGGAGGAGCGATTGACTCCAGGTGTCACTTTCCAGTTGTCTGCAGAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 165

GTTTCCCTTGCATCTGATTTCATGTACAATCAAATGACAAAGGATGTAACAGCAAGCTTTGGTTATGATTATATGCTGAGACAGgtatccttgt ... atatttgcagTGTCGATTGAGAGGGAAACTGGATACCAATGGCGTAATTTCTTCTCTTTTGGAGGAGCGATTGACTCCAGGTGTCACTTTCCAGTTGTCTGCAGAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 144

GTTTCCCTTGCATCTGATTTCATGTACAATCAAATGACAAAGGATGTAACAGCAAGCTTTGGTTATGATTATATGCTGAGACAGgtatccttgt ... atatttgcagTGTCGATTGAGAGGGAAACTGGATACCAATGGCGTAATTTCTTCTCTTTTGGAGGAGCGATTGACTCCAGGTGTCACTTTCCAGTTGTCTGCAGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTCCCTTGCATCTGATTTCATGTACAATCAAATGACAAAGGATGTAACAGCAAGCTTTGGTTATGATTATATGCTGAGACAGgtatccttgtttgtttgacccatctgctatttttcccatgcttccatttgttattgtaatgcaaatgttagataaaatgcttgagggcaatcgatctttc

- - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agataaaa