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 5'  3'   		2  
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgttctctcacgctgcagtgttcttttaatctcagagttttcttttttttgagcggtcgcgtggttatgtggggggtgtttcttgtttgcagGCCGAGAAGATCGCCACCATCGTGAAGGCGGCCAACATCAAGGTCGAGTCCTACTGGCCGGCGCTCTTCGCTAAGCTCCTGGAGAAGCGCAGCGTTGAGG

Basic information

species Zea mays
transcript GRMZM2G157443_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157443_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g02340.2 (Oryza sativa), 3'ss of exon 1
----------gtgcgttctctcacgctgcagtgttcttttaatc--tcagagttttcttttttttgagcggtcgcgtggttatgtggggggtgtttc--ttgtttgcagGCCGAGAAGATCGCCACCATCGTGAAGGCGGCCAACATCAAGGTCGAGTCCTACTGGCCGGCGCTCTTCGCTAAGCTCCTGGAGAAGCGCAGCGTTGAGG
             | ||| | |         | ||  |||  |      | | |   |||  | || | | | |  |  |||| | |  |||| ||   |     |||| | ||||||||||||||| | ||||||||||||||||||||||||||| |||||||||| |  |||||||| |||||||| ||| | |||||||| || |
gtgcgttactacaccttcacccctatcttgattttgcttttcttggcttggggtggatttggtgtgtgagattgattatttattttgttggtgatttggtgacgagcagTCTGAGAAGATCGCCACCCTGGTGAAGGCGGCCAACATCAAGGTCGAGGCCTACTGGCCCGGTCTCTTCGCCAAGCTCCTCGAGCACCGCAGCGTCGATG
















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|211042138|gb|FL385016.1|FL385016
EST:     CCTGCACCTACGCCGCCCTCATCCTCAGCGACGACGGCATCNCCATCACC                         GCCGAGAAGATCGCCACCATCGTGAAGGCGGNCAACATCAAGGTCGAGTCC
genomic: CCTGCACCTACGCCGCCCTCATCCTCAGCGACGACGGCATCGCCATCACCgtgcgttctc ... ttgtttgcagGCCGAGAAGATCGCCACCATCGTGAAGGCGGCCAACATCAAGGTCGAGTCC
EST: gi|211529784|gb|FL373525.1|FL373525
EST:     CCTGCACCTACGCCGCCCTCATCCTCAGCGACGACGGCATCGCCATCACC                         GCCGAGAAGATCGCCACCATCGTGAAGGCGGCCAACATCAAGGTCGAGTCC
genomic: CCTGCACCTACGCCGCCCTCATCCTCAGCGACGACGGCATCGCCATCACCgtgcgttctc ... ttgtttgcagGCCGAGAAGATCGCCACCATCGTGAAGGCGGCCAACATCAAGGTCGAGTCC
EST: gi|211507235|gb|FL422061.1|FL422061
EST:     CCTGCACCTACGCCGCCCTCATCCTCAGCGACGACGGCATCGCCATCACC                         GCCGAGAAGATCGCCACCATCGTGAAGGCGGCCAACATCAAGGTCGAGTCC
genomic: CCTGCACCTACGCCGCCCTCATCCTCAGCGACGACGGCATCGCCATCACCgtgcgttctc ... ttgtttgcagGCCGAGAAGATCGCCACCATCGTGAAGGCGGCCAACATCAAGGTCGAGTCC
EST: gi|211014153|gb|FL393610.1|FL393610
EST:     CCTGCACCTACGCCGCCCTCATCCTCAGCGACGACGGCNTCGCCATCACC                         GCCGAGAAGATCGCCACCATCGTGAAGGCGGCCAACATCAAGGTCGAGTCC
genomic: CCTGCACCTACGCCGCCCTCATCCTCAGCGACGACGGCATCGCCATCACCgtgcgttctc ... ttgtttgcagGCCGAGAAGATCGCCACCATCGTGAAGGCGGCCAACATCAAGGTCGAGTCC
EST: gi|211151701|gb|FL395047.1|FL395047
EST:     CCTGCACCTACGCCGCCCTCATCCTCAGCGACGACGGGATCGCCATCACC                         GCCGAGAAGATCGCCACCATCGTGAAGGCGGCCAACATCAAGGTCGAGTCC
genomic: CCTGCACCTACGCCGCCCTCATCCTCAGCGACGACGGCATCGCCATCACCgtgcgttctc ... ttgtttgcagGCCGAGAAGATCGCCACCATCGTGAAGGCGGCCAACATCAAGGTCGAGTCC
EST: gi|9794508|gb|BE552816.1|BE552816
EST:     CCTGCACCTACGCCGCCCTCATCCTCAGCGACGACGGCATCGCCATCACC                         GCCGAGAAGATCGCCACCATCGTGAAGGCGGTCAACATCAAGGTCGAGTCC
genomic: CCTGCACCTACGCCGCCCTCATCCTCAGCGACGACGGCATCGCCATCACCgtgcgttctc ... ttgtttgcagGCCGAGAAGATCGCCACCATCGTGAAGGCGGCCAACATCAAGGTCGAGTCC
EST: gi|211038599|gb|FL345810.1|FL345810
EST:     CCTGCACCTACGCCGCCCTCATCCTCAGCGACGACGGCATCGCCATCACC                         GCCGAGAAGATCGCCACCATCGTGAAGGCGGCCAACATCAAGGTCGAGTCC
genomic: CCTGCACCTACGCCGCCCTCATCCTCAGCGACGACGGCATCGCCATCACCgtgcgttctc ... ttgtttgcagGCCGAGAAGATCGCCACCATCGTGAAGGCGGCCAACATCAAGGTCGAGTCC
EST: gi|211376384|gb|FL377804.1|FL377804
EST:     CCTGCACCTACGCCGCCCTCATCCTCAGCGACGACGGCATCGCCATCACC                         GCCGAGAAGATCGCCACCATCGTGAAGGCGGCCAACATCAAGGTCGAGTCC
genomic: CCTGCACCTACGCCGCCCTCATCCTCAGCGACGACGGCATCGCCATCACCgtgcgttctc ... ttgtttgcagGCCGAGAAGATCGCCACCATCGTGAAGGCGGCCAACATCAAGGTCGAGTCC
EST: gi|211298275|gb|FL361776.1|FL361776
EST:     CCTGCACCTACGCCGCCCTCATCCTCAGCGACGACGGCATCGCCATCACC                         GCCGAGAAGATCGCCACCATCGTGAAGGCGGNCAACATCAAGGTCGAGTCC
genomic: CCTGCACCTACGCCGCCCTCATCCTCAGCGACGACGGCATCGCCATCACCgtgcgttctc ... ttgtttgcagGCCGAGAAGATCGCCACCATCGTGAAGGCGGCCAACATCAAGGTCGAGTCC
EST: gi|211102283|gb|FL386869.1|FL386869
EST:     CCTGCACCTACGCCGCCCTCATCCTCAGCGACGACGGCATCGCCATCACC                         GCCGAGAAGATCGCCACCATCGTGAAGGCGGCCAACATCAAGGTCGAGTCC
genomic: CCTGCACCTACGCCGCCCTCATCCTCAGCGACGACGGCATCGCCATCACCgtgcgttctc ... ttgtttgcagGCCGAGAAGATCGCCACCATCGTGAAGGCGGCCAACATCAAGGTCGAGTCC
EST: gi|211235863|gb|FL372783.1|FL372783
EST:     CCTGCACCTACGCCGCCCTCATCCTCAGCGACGACGGCATCGCCATCACC                         GCCGAGAAGATCGCCACCATCGTGAAGGCGGCCAACATCAAGGTCGAGTCC
genomic: CCTGCACCTACGCCGCCCTCATCCTCAGCGACGACGGCATCGCCATCACCgtgcgttctc ... ttgtttgcagGCCGAGAAGATCGCCACCATCGTGAAGGCGGCCAACATCAAGGTCGAGTCC
EST: gi|211406019|gb|FL414976.1|FL414976
EST:     CCTGCACCTACGCCGCCCTCATCCTCAGCGACGACGGCATCGCCATCACC                         GCCGAGAAGATCGCCACCATCGTGAAGGCGGCCAACATCAAGGTCGAGTCC
genomic: CCTGCACCTACGCCGCCCTCATCCTCAGCGACGACGGCATCGCCATCACCgtgcgttctc ... ttgtttgcagGCCGAGAAGATCGCCACCATCGTGAAGGCGGCCAACATCAAGGTCGAGTCC
EST: gi|211307145|gb|FL392851.1|FL392851
EST:     CCTGCACCTACGCCGCCCTCATCCTCAGCGACGACGGCATCGCCATCACC                         GCCGAGAAGATCGCCACCATCGTGAAGGCGGCCA
genomic: CCTGCACCTACGCCGCCCTCATCCTCAGCGACGACGGCATCGCCATCACCgtgcgttctc ... ttgtttgcagGCCGAGAAGATCGCCACCATCGTGAAGGCGGCCA

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: 859

TCCGTCCGGTTAGACGAAGCCGCCCGCACCCATGGCCTCCGGTGAGCTCGCCTGCACCTACGCCGCCCTCATCCTCAGCGACGACGGCATCGCCATCACCgtgcgttctc ... ttgtttgcagGCCGAGAAGATCGCCACCATCGTGAAGGCGGCCAACATCAAGGTCGAGTCCTACTGGCCGGCGCTCTTCGCTAAGCTCCTGGAGAAGCGCAGCGTTGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 215

TCCGTCCGGTTAGACGAAGCCGCCCGCACCCATGGCCTCCGGTGAGCTCGCCTGCACCTACGCCGCCCTCATCCTCAGCGACGACGGCATCGCCATCACCgtgcgttctc ... ttgtttgcagGCCGAGAAGATCGCCACCATCGTGAAGGCGGCCAACATCAAGGTCGAGTCCTACTGGCCGGCGCTCTTCGCTAAGCTCCTGGAGAAGCGCAGCGTTGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 182

TCCGTCCGGTTAGACGAAGCCGCCCGCACCCATGGCCTCCGGTGAGCTCGCCTGCACCTACGCCGCCCTCATCCTCAGCGACGACGGCATCGCCATCACCgtgcgttctc ... ttgtttgcagGCCGAGAAGATCGCCACCATCGTGAAGGCGGCCAACATCAAGGTCGAGTCCTACTGGCCGGCGCTCTTCGCTAAGCTCCTGGAGAAGCGCAGCGTTGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 274

TCCGTCCGGTTAGACGAAGCCGCCCGCACCCATGGCCTCCGGTGAGCTCGCCTGCACCTACGCCGCCCTCATCCTCAGCGACGACGGCATCGCCATCACCgtgcgttctc ... ttgtttgcagGCCGAGAAGATCGCCACCATCGTGAAGGCGGCCAACATCAAGGTCGAGTCCTACTGGCCGGCGCTCTTCGCTAAGCTCCTGGAGAAGCGCAGCGTTGAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcttttttttgagcggtcgcgtggttatgtggggggtgtttcttgtttgcagGCCGAGAAGATCGCCACCATCGTGAAGGCGGCCAACATCAAGGTCGAGTCCTACTGGCCGGCGCTCTTCGCTAAGCTCCTGGAGAAGCGCAGCGTTGAGG
                                         tttcttgttt  CT-rich tract
     ttttttttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgttctctcacgctgcagtgttcttttaatctcagagttttcttttttttgagcggtcgcgtggttatgtggggggtgtttcttgtttgcagGCCGAGAAGATCGCCACCATCGTGAAGGCGGCCAACATCAAGGTCGAGTCCTACTGGCCGGCGCTCTTCGCTAAGCTCCTGGAGAAGCGCAGCGTTGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC