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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtttcctgaagttccgctcatttggcatttctcatccgtagtcaaagctctcggcttttggctgttgatagagcggttcacattgttcatgattcatgtcaacgtttgcaaaaaaccaattttcatcatttgtggtaatccagGCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGACGTGGCCTAGTCAGGACGGGAGAGAGCAAAGGCAAAATTGGAGGCGGTGA

Basic information

species Zea mays
transcript GRMZM2G047219_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047219_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g01970.5 (Oryza sativa), 3'ss of exon 1
gtaggtttcctgaagttccgctcatttggcatttctcatccgtagtcaaagctctcggcttttggctgttgatagagcggttcacattgttcatgattcatgtcaacgtttgcaaaaaaccaattttcatcatttgtggtaatccagGCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGACGTGGCCTAGTCAGGACGGGAGAGAGCAAAGGCAAAATTGGAGGCGGTGA
                                         | | || |   ||  |    |   || |||  |||    || ||   |||     | | | |       |||||    ||  | |       |  || |  | ||||||| ||||||||||||||| | |||||||||| ||  || ||||||||  | || ||||||||||| | ||||||||||| ||| ||||| |||| || 
-----------------------------------------gaaatctagtttcgtgcacatctactcttgcaagaat--ttgactcggttt----tcccttttgcacgctgcaattggcctctctgtgatgatgatgatctttcagGCCAGATTGTGTACAAGAAGCTCAAGGAGAGGGCAGACCAATTTGTGGGGAGAGGGCTAGTCAGGACTGAAGAGAGCAAAGCCAAGATTGGGGGCGCTGC
















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|50331999|gb|CO527125.1|CO527125
EST:     CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAG                         GCCAAATTGTGTACAAGAAGTTGAAGGACAGGGAAGGACAGTTTGTGGGAC
genomic: CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAGgtaggtttcc ... ggtaatccagGCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
EST: gi|211142589|gb|FL359509.1|FL359509
EST:     CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAG                         GCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
genomic: CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAGgtaggtttcc ... ggtaatccagGCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
EST: gi|211395952|gb|FL307387.1|FL307387
EST:     CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAG                         GCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
genomic: CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAGgtaggtttcc ... ggtaatccagGCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
EST: gi|211529297|gb|FL356731.1|FL356731
EST:     CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAG                         GCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
genomic: CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAGgtaggtttcc ... ggtaatccagGCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
EST: gi|149015400|gb|EE045246.2|EE045246
EST:     CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAG                         GCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
genomic: CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAGgtaggtttcc ... ggtaatccagGCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
EST: gi|13490392|gb|BG517156.1|BG517156
EST:     CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAG                         GCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACA
genomic: CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAGgtaggtttcc ... ggtaatccagGCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACA
EST: gi|74243388|gb|DT651302.1|DT651302
EST:     CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAG                         GCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
genomic: CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAGgtaggtttcc ... ggtaatccagGCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
EST: gi|148966374|gb|EE017368.2|EE017368
EST:     CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAG                         GCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
genomic: CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAGgtaggtttcc ... ggtaatccagGCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
EST: gi|13198604|gb|BG354406.1|BG354406
EST:     CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAG                         GCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
genomic: CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAGgtaggtttcc ... ggtaatccagGCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
EST: gi|148996959|gb|EE035773.2|EE035773
EST:     CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAG                         GCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
genomic: CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAGgtaggtttcc ... ggtaatccagGCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
EST: gi|211026165|gb|FL334138.1|FL334138
EST:     CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAG                         GCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
genomic: CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAGgtaggtttcc ... ggtaatccagGCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
EST: gi|148935909|gb|EC879959.2|EC879959
EST:     CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAG                         GCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
genomic: CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAGgtaggtttcc ... ggtaatccagGCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
EST: gi|76293497|gb|DV033065.1|DV033065
EST:     CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAG                         GCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
genomic: CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAGgtaggtttcc ... ggtaatccagGCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
EST: gi|211254886|gb|FL311677.1|FL311677
EST:     CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAG                         GCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
genomic: CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAGgtaggtttcc ... ggtaatccagGCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
EST: gi|211394348|gb|FL351051.1|FL351051
EST:     CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAG                         GCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
genomic: CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAGgtaggtttcc ... ggtaatccagGCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
EST: gi|89251955|gb|DY623741.1|DY623741
EST:     CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAG                         GCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
genomic: CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAGgtaggtttcc ... ggtaatccagGCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
EST: gi|211200628|gb|FL339642.1|FL339642
EST:     CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAG                         GCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
genomic: CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAGgtaggtttcc ... ggtaatccagGCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
EST: gi|89762676|gb|DY690164.1|DY690164
EST:     CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAG                         GCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
genomic: CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAGgtaggtttcc ... ggtaatccagGCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
EST: gi|71774203|gb|DR972081.1|DR972081
EST:     CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAG                         GCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
genomic: CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAGgtaggtttcc ... ggtaatccagGCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
EST: gi|211267296|gb|FL319984.1|FL319984
EST:     CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAG                         GCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
genomic: CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAGgtaggtttcc ... ggtaatccagGCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
EST: gi|91055640|gb|EB166058.1|EB166058
EST:     CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAG                         GCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC
genomic: CGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAGgtaggtttcc ... ggtaatccagGCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGAC

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 2 RNA-Seq libraries.


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 19

AGGCGGGGACCCAGGAGGGCCGGGCTGGCCGTCACGGCGGCGGCTGCCGCCGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAGgtaggtttcc ... ggtaatccagGCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGACGTGGCCTAGTCAGGACGGGAGAGAGCAAAGGCAAAATTGGAGGCGGTGA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 16

AGGCGGGGACCCAGGAGGGCCGGGCTGGCCGTCACGGCGGCGGCTGCCGCCGGTGGATCGCCGCGCACTGTGCTCGTCACCGGCGCGGGCGGCCGAACAGgtaggtttcc ... ggtaatccagGCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGACGTGGCCTAGTCAGGACGGGAGAGAGCAAAGGCAAAATTGGAGGCGGTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgattcatgtcaacgtttgcaaaaaaccaattttcatcatttgtggtaatccagGCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGACGTGGCCTAGTCAGGACGGGAGAGAGCAAAGGCAAAATTGGAGGCGGTGA
                     aaaaaaccaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtttcctgaagttccgctcatttggcatttctcatccgtagtcaaagctctcggcttttggctgttgatagagcggttcacattgttcatgattcatgtcaacgtttgcaaaaaaccaattttcatcatttgtggtaatccagGCCAAATTGTGTACAAGAAGTTGAAGGAGAGGGAAGGACAGTTTGTGGGACGTGGCCTAGTCAGGACGGGAGAGAGCAAAGGCAAAATTGGAGGCGGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG