Skip to another splice site:
1  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGCAGATGCCGGTGGAGATGCATCAGGGGTGACAGATGAGTTGCACACTGTACCAGAGGACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAGgttcgcttcttttctttttgtagcgtttactacaagcctgatagcttggtgtgtttcatattactactgccctcatgcttatttaaagacccacgtatct...

Basic information

species Zea mays
transcript GRMZM2G106690_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G106690_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g57450.1 (Oryza sativa), 5'ss of exon 1
GCTGCAGATGCCGGTGGAGATGCATCAGGGGTGACAGATGAGTTGCACACTGTACCAGAGGACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAGgttcgcttcttttctttttgtag--cgtttactacaagcctgatagcttggtgtgtttcatattactactgccctcatgcttatttaaa-gacccacgtatct-
||||||| |||||  || || ||| |||||   ||||||||| |||||||||| || ||||| |||||||| ||||| ||||||||||| ||||||||||||| ||   ||| | ||    |   |  |  |||  | |   ||    || | | |  |   ||| |||        || | ||| ||| ||   || |||   
GCTGCAGGTGCCGACGGGGAGGCAGCAGGGCCAACAGATGAGCTGCACACTGTGCCTGAGGATGAACCTGTGTATCATGATGCACCTGATGTGCAGAAAGgtttgcccttttacattgctcaattcaatcgctattaactgtatttgctgatttat--cggtttattaccatgagt-tgttcattgaaatgatttac-tataga
















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|211139822|gb|FL090202.1|FL090202
EST:     TGTACCAGAGGACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAG                         AAAACTGAGGCAACGGCCACATGCGGCTGAAGAACGAAGGAAAACATGAGG
genomic: TGTACCAGAGGACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAGgttcgcttct ... tggactgcagAAAACTGAGGCAACGGCCACATGCGGCTGAAGAACGAAGGAAAACATGAGG
EST: gi|60398987|gb|DN231803.1|DN231803
EST:     TGTACCAGAGGACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAG                         AAAACTGAGGCAACGGCCACATGCGGCTGAAGAACGAAGGAAAACATGAGG
genomic: TGTACCAGAGGACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAGgttcgcttct ... tggactgcagAAAACTGAGGCAACGGCCACATGCGGCTGAAGAACGAAGGAAAACATGAGG
EST: gi|166526932|gb|EG059974.1|EG059974
EST:     TGTACCAGAGGACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAG                         AAAACTGAGGCAACGGCCACATGCGG
genomic: TGTACCAGAGGACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAGgttcgcttct ... tggactgcagAAAACTGAGGCAACGGCCACATGCGG
EST: gi|113679892|gb|DW837713.1|DW837713
EST:     ACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAG                         AAAACTGAGGCAACGGCCACATGCGGCTGAAGAACGAAGGAAAACATGAGG
genomic: ACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAGgttcgcttct ... tggactgcagAAAACTGAGGCAACGGCCACATGCGGCTGAAGAACGAAGGAAAACATGAGG
EST: gi|5080977|gb|AI738239.1|AI738239
EST:     TGTACCAGAGGACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAG                         AAAACTGAGGCAACGGCCACATGCAGCTGAAGAACGAAGGAAAACACGAGG
genomic: TGTACCAGAGGACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAGgttcgcttct ... tggactgcagAAAACTGAGGCAACGGCCACATGCGGCTGAAGAACGAAGGAAAACATGAGG
EST: gi|60401193|gb|DN234000.1|DN234000
EST:     TGTACCAGAGGACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAG                         AAAACTGAGGCAACGGCCACATGCGGCTGAAGAACGAAGGAAAACATGAGG
genomic: TGTACCAGAGGACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAGgttcgcttct ... tggactgcagAAAACTGAGGCAACGGCCACATGCGGCTGAAGAACGAAGGAAAACATGAGG
EST: gi|29945855|gb|CB815854.1|CB815854
EST:     TGTACCAGAGGACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAG                         AAAACTGAGGCAACGGCCACATGCGGCTGAAGAACGAAGGAAAACATGAGG
genomic: TGTACCAGAGGACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAGgttcgcttct ... tggactgcagAAAACTGAGGCAACGGCCACATGCGGCTGAAGAACGAAGGAAAACATGAGG
EST: gi|87157259|gb|DY402048.1|DY402048
EST:     TGTACCAGAGGACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAG                         AAAACTGAGGCAACGGCCACATGCAGCTGAAGAACGAAGGAAAACACGAGG
genomic: TGTACCAGAGGACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAGgttcgcttct ... tggactgcagAAAACTGAGGCAACGGCCACATGCGGCTGAAGAACGAAGGAAAACATGAGG
EST: gi|211327261|gb|FL468831.1|FL468831
EST:     TGTACCAGAGGACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAG                         AAAACTGAGGCAACGGCCACATGCAGCTGAAGAACGAAGGAAAACACGAGG
genomic: TGTACCAGAGGACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAGgttcgcttct ... tggactgcagAAAACTGAGGCAACGGCCACATGCGGCTGAAGAACGAAGGAAAACATGAGG
EST: gi|24768159|gb|CA403288.1|CA403288
EST:     TGTACCAGAGGACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAG                         AAAACTGAGGCAACGGCCACATGCAGCTGAAGAACGAAGGAAAACACGAGG
genomic: TGTACCAGAGGACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAGgttcgcttct ... tggactgcagAAAACTGAGGCAACGGCCACATGCGGCTGAAGAACGAAGGAAAACATGAGG
EST: gi|211167568|gb|FL481154.1|FL481154
EST:     TGTACCAGAGGACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAG                         AAAACTGAGGCAACGGCCACATGCAGCTGAAGAACGAAGGAAAACACGAGG
genomic: TGTACCAGAGGACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAGgttcgcttct ... tggactgcagAAAACTGAGGCAACGGCCACATGCGGCTGAAGAACGAAGGAAAACATGAGG
EST: gi|113781770|gb|DW902748.1|DW902748
EST:     TGTACCAGAGGACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAG                         AAAACTGAGGCAACGGCCACATGCGG
genomic: TGTACCAGAGGACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAGgttcgcttct ... tggactgcagAAAACTGAGGCAACGGCCACATGCGG
EST: gi|78023715|gb|DV492102.1|DV492102
EST:     TGTACCAGAGGACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAG                         AAAACTGAGGCAACGGCCACATGCAGCTGAAGAACGAAGGAAAACACGAGG
genomic: TGTACCAGAGGACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAGgttcgcttct ... tggactgcagAAAACTGAGGCAACGGCCACATGCGGCTGAAGAACGAAGGAAAACATGAGG
EST: gi|60353329|gb|DN220302.1|DN220302
EST:     TGTACCAGAGGACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAG                         AAAACTGAGGCAACGGCCACATGCGGCTGAAGAACGAAGGAAAACATGAGG
genomic: TGTACCAGAGGACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAGgttcgcttct ... tggactgcagAAAACTGAGGCAACGGCCACATGCGGCTGAAGAACGAAGGAAAACATGAGG
EST: gi|60338104|gb|DN205077.1|DN205077
EST:     TGTACCAGAGGACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAG                         AAAACTGAGGCAACGGCCACATGCGGCTGAAGAACGAAGGAAAACATGAGG
genomic: TGTACCAGAGGACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAGgttcgcttct ... tggactgcagAAAACTGAGGCAACGGCCACATGCGGCTGAAGAACGAAGGAAAACATGAGG

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: 232

GCTGCAGATGCCGGTGGAGATGCATCAGGGGTGACAGATGAGTTGCACACTGTACCAGAGGACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAGgttcgcttct ... tggactgcagAAAACTGAGGCAACGGCCACATGCGGCTGAAGAACGAAGGAAAACATGAGGCTTGTAGTGAGGCAATCCTGTGTATCTGGAAGATGGGACCGGCTGTTTA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 114

GCTGCAGATGCCGGTGGAGATGCATCAGGGGTGACAGATGAGTTGCACACTGTACCAGAGGACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAGgttcgcttct ... tggactgcagAAAACTGAGGCAACGGCCACATGCGGCTGAAGAACGAAGGAAAACATGAGGCTTGTAGTGAGGCAATCCTGTGTATCTGGAAGATGGGACCGGCTGTTTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 202

GCTGCAGATGCCGGTGGAGATGCATCAGGGGTGACAGATGAGTTGCACACTGTACCAGAGGACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAGgttcgcttct ... tggactgcagAAAACTGAGGCAACGGCCACATGCGGCTGAAGAACGAAGGAAAACATGAGGCTTGTAGTGAGGCAATCCTGTGTATCTGGAAGATGGGACCGGCTGTTTA


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

GCTGCAGATGCCGGTGGAGATGCATCAGGGGTGACAGATGAGTTGCACACTGTACCAGAGGACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAGgttcgcttct ... tggactgcagAAAACTGAGGCAACGGCCACATGCGGCTGAAGAACGAAGGAAAACATGAGGCTTGTAGTGAGGCAATCCTGTGTATCTGGAAGATGGGACCGGCTGTTTA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGCAGATGCCGGTGGAGATGCATCAGGGGTGACAGATGAGTTGCACACTGTACCAGAGGACGAACCTGTTTATCACGATGCACCTGAGGTGCAGAAAGgttcgcttcttttctttttgtagcgtttactacaagcctgatagcttggtgtgtttcatattactactgccctcatgcttatttaaagacccacgtatct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA