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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttatattagtttattatttactgagattatagacatcacttttcaattccattgtttttgttccttatttctatcttatagGTGTTGAGCCCAAATATTTACAATATGCAACTATGGGAAACTTCTGGACACGCCGCAAACTATAAGGAGAACATGTTTGTTTTTGAG

Basic information

species Zea mays
transcript GRMZM2G553314_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G553314_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os08g19850.1 (Oryza sativa), 3'ss of exon 9
----------------------------------gtttatattagtttattatttactgagattatagacatcacttttcaattccattgtttttgttccttatttctat-cttatagGTGTTGAGCCCAAATATTTACAATATGCAACTATGGGAAACTTCTGGACACGCCGCAAACTATAAGGAGAACATGTTTGTTTTTGAG
                                  ||| | ||||  | ||||  |    |||| || | |||   ||| || |    || | | ||||| | || ||| |  ||  |||| ||||||||||||||||||||||||||||| |||||||| |||||||| || |||||||| |||||||| |||||||||||||||
gtgggcattaatttgattggctggtcaatcttttgttcagatta--tgattagattactagatcatgggcatgcatttccactgt--ttctctctgttcatgatgtctgtattttcagGTTTTGAGCCCAAATATTTACAATATGCAACTCTGGGAAACCTCTGGACATGCTGCAAACTACAAGGAGAATATGTTTGTTTTTGAG

upper sequence: GRMZM2G553314_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv01s0026g00340.t01 (Vitis vinifera), 3'ss of exon 9
gtttat--attagtttattatttactgagattatagacatcacttttcaattccattgtttttgttccttatttctatcttatagGTGTTGAGCCCAAATATTTACAATATGCAACTATGGGAAACTTCTGGACACGCCGCAAACTATAAGGAGAACATGTTTGTTTTTGAG
||| ||  | ||  |   || ||  ||  ||   ||| ||   |||  |||   |  |||| |  |  |  || ||   |   |||| ||    |||| ||| || ||||||||||| |||||||| ||||| || || || || || |||||||| |||||||| ||||||
gttaatggactaactctgtagttgttgtaatgccaga-ata--tttataatgaaaaagtttctaatattacttgct--ttggcagGTTTTCTCACCAACTATGTATAATATGCAACTTTGGGAAACATCTGGTCATGCTGCTAATTACAAGGAGAATATGTTTGTATTTGAG
















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|67033102|gb|CO461851.1|CO461851
EST:     AACTGATGGACTTCATGCGACAACAGTACAGAGATAGAGGATACCAAGAG                         GTGTTGAGCCCAAATATTTACAATATGCAACTATGGGAAACTTCTGGACAC
genomic: AACTGATGGACTTCATGCGACAACAGTACAGAGATAGAGGATACCAAGAGgtttatatta ... tatcttatagGTGTTGAGCCCAAATATTTACAATATGCAACTATGGGAAACTTCTGGACAC
EST: gi|26559163|gb|CA831398.1|CA831398
EST:     AACTGATGGACTTCATGCGACAACAGTACAGAGATAGAGGATACCAAGAG                         GTGTTGAGCCCAAATATTTACAATATGCAACTATGGGAAACTT
genomic: AACTGATGGACTTCATGCGACAACAGTACAGAGATAGAGGATACCAAGAGgtttatatta ... tatcttatagGTGTTGAGCCCAAATATTTACAATATGCAACTATGGGAAACTT
EST: gi|87157710|gb|DY402499.1|DY402499
EST:     AACTGATGGACTTCATGCGACAACAGTACAGAGATAGAGGATACCAAGAG                         GTGTTGAGCCCAAATATTTACAATATGCAACTATGGGAAACTTCTGGACAC
genomic: AACTGATGGACTTCATGCGACAACAGTACAGAGATAGAGGATACCAAGAGgtttatatta ... tatcttatagGTGTTGAGCCCAAATATTTACAATATGCAACTATGGGAAACTTCTGGACAC
EST: gi|22542059|gb|BU092497.1|BU092497
EST:     AACTGATGGACTTCATGCGACAACAGTACAGAGATAGAGGATACCAAGAG                         GTGTTGAGCCCAAATATTTACAATATGCAACTATGGGAAACTTCTGGACAC
genomic: AACTGATGGACTTCATGCGACAACAGTACAGAGATAGAGGATACCAAGAGgtttatatta ... tatcttatagGTGTTGAGCCCAAATATTTACAATATGCAACTATGGGAAACTTCTGGACAC
EST: gi|32940354|gb|CF045173.1|CF045173
EST:     ACAGAGATAGAGGATACCAAGAG                         GTGTTGAGCCCAAATATTTACAATATGCAACTATGGGAAACTTCTGGACAC
genomic: ACAGAGATAGAGGATACCAAGAGgtttatatta ... tatcttatagGTGTTGAGCCCAAATATTTACAATATGCAACTATGGGAAACTTCTGGACAC
EST: gi|211165966|gb|FL031946.1|FL031946
EST:     AACTGATGGACTTCATGCGACAACAGTACAGAGATAGAGGATACCAAGAG                         GTGTTGAGCCCAAATATTTACAATATGCAACTATGGGAAAC
genomic: AACTGATGGACTTCATGCGACAACAGTACAGAGATAGAGGATACCAAGAGgtttatatta ... tatcttatagGTGTTGAGCCCAAATATTTACAATATGCAACTATGGGAAAC
EST: gi|9952045|gb|BE638628.1|BE638628
EST:     AACTGATGGACTTCATGCGACAACAGTACAGAGATAGAGGATACCAAGAG                         GTGTTGAGCCCAAATATTTACAATATGCAACTATGGGAAACTTCTGGACAC
genomic: AACTGATGGACTTCATGCGACAACAGTACAGAGATAGAGGATACCAAGAGgtttatatta ... tatcttatagGTGTTGAGCCCAAATATTTACAATATGCAACTATGGGAAACTTCTGGACAC

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), 49 (downstream exon)
Score: 342

CCCTGGAAGCTGCTTCTTCCTTCCACATGGTGCTAGGATATATAACAAACTGATGGACTTCATGCGACAACAGTACAGAGATAGAGGATACCAAGAGgtttatatta ... tatcttatagGTGTTGAGCCCAAATATTTACAATATGCAACTATGGGAAACTTCTGGACACGCCGCAAACTATAAGGAGAACATGTTTGTTTTTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 264

CCCTGGAAGCTGCTTCTTCCTTCCACATGGTGCTAGGATATATAACAAACTGATGGACTTCATGCGACAACAGTACAGAGATAGAGGATACCAAGAGgtttatatta ... tatcttatagGTGTTGAGCCCAAATATTTACAATATGCAACTATGGGAAACTTCTGGACACGCCGCAAACTATAAGGAGAACATGTTTGTTTTTGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 245

CCCTGGAAGCTGCTTCTTCCTTCCACATGGTGCTAGGATATATAACAAACTGATGGACTTCATGCGACAACAGTACAGAGATAGAGGATACCAAGAGgtttatatta ... tatcttatagGTGTTGAGCCCAAATATTTACAATATGCAACTATGGGAAACTTCTGGACACGCCGCAAACTATAAGGAGAACATGTTTGTTTTTGAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 172

CCCTGGAAGCTGCTTCTTCCTTCCACATGGTGCTAGGATATATAACAAACTGATGGACTTCATGCGACAACAGTACAGAGATAGAGGATACCAAGAGgtttatatta ... tatcttatagGTGTTGAGCCCAAATATTTACAATATGCAACTATGGGAAACTTCTGGACACGCCGCAAACTATAAGGAGAACATGTTTGTTTTTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatagacatcacttttcaattccattgtttttgttccttatttctatcttatagGTGTTGAGCCCAAATATTTACAATATGCAACTATGGGAAACTTCTGGACACGCCGCAAACTATAAGGAGAACATGTTTGTTTTTGAG
                            tttttgttccttattt  CT-rich tract
                                      ttatttctatcttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttatattagtttattatttactgagattatagacatcacttttcaattccattgtttttgttccttatttctatcttatagGTGTTGAGCCCAAATATTTACAATATGCAACTATGGGAAACTTCTGGACACGCCGCAAACTATAAGGAGAACATGTTTGTTTTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA