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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCTTCCTTCAAAGTACAACAAGTCGATACGACTGGCGCAGGCGATGCGTTTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAAgtaagtcgcctgaaatttgttcattgatctgaaattgttgggtcctacatgccaaggtggtccttcggttttcagttttaccatgtgacattgaaatttggtatctggtgtgaccgcacag

Basic information

species Zea mays
transcript GRMZM2G026969_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G026969_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g66940.1 (Oryza sativa), 5'ss of exon 3
CCCTTCCTTCAAAGTACAACAAGTCGATACGACTGGCGCAGGCGATGCGTTTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAAgtaagtcgcc-tgaaatttgttcattgatctgaaattgttgggtcctacatgccaaggtggtccttcggttttcagttttaccatgtgacattgaaatttggtatctggtgtgaccgcacag
||| |||| ||||||||| ||||| ||||| || || ||||| ||||||||||||||||| ||||| ||||| || ||  | |||||||| ||| | |||||||||  |  | ||     ||  ||| |     ||||||  |  |||||     |||||||  |         ||||  || |            ||||| | | || ||   | |||   
CCCATCCTACAAAGTACAGCAAGTTGATACAACAGGTGCAGGTGATGCGTTTGTTGGTGCTCTGCTGCGAAGAATTGTCCAGGATCCATCATCGTTGCAAgtaagttactgtcaagcacttttgttggt-----attgttatg--ctacagaaataggtggttat---------agttaaacta------------atttgatgtttgctgactctgcag--
















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|37397010|gb|CF635799.1|CF635799
EST:     TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
genomic: TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAAgtaagtcgcc ... gaccgcacagGACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
EST: gi|94474751|gb|EB703709.1|EB703709
EST:     TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
genomic: TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAAgtaagtcgcc ... gaccgcacagGACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
EST: gi|74244918|gb|DT652832.1|DT652832
EST:     TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GACGAGAAGAAGCTTGTAGAGTTTATTAAATTCGTTAATGCGTGTGGAGCA
genomic: TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAAgtaagtcgcc ... gaccgcacagGACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
EST: gi|60394097|gb|DN226967.1|DN226967
EST:     TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
genomic: TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAAgtaagtcgcc ... gaccgcacagGACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
EST: gi|86471494|gb|DY237864.1|DY237864
EST:     TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTCCAA                         GACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
genomic: TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAAgtaagtcgcc ... gaccgcacagGACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
EST: gi|4621429|gb|AI612262.1|AI612262
EST:     TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
genomic: TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAAgtaagtcgcc ... gaccgcacagGACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
EST: gi|9961423|gb|BE644406.1|BE644406
EST:     TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
genomic: TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAAgtaagtcgcc ... gaccgcacagGACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
EST: gi|9743111|gb|BE519259.1|BE519259
EST:     TTG-TGGTGCGCTGCTCCGAAGGATCGCTAAAGATCCATCCTCGCTACAA                         GACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGC
genomic: TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAAgtaagtcgcc ... gaccgcacagGACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGC
EST: gi|148951326|gb|EC897035.2|EC897035
EST:     TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
genomic: TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAAgtaagtcgcc ... gaccgcacagGACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
EST: gi|71772119|gb|DR970056.1|DR970056
EST:     TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
genomic: TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAAgtaagtcgcc ... gaccgcacagGACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
EST: gi|74235494|gb|DT643408.1|DT643408
EST:     TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
genomic: TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAAgtaagtcgcc ... gaccgcacagGACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
EST: gi|211203037|gb|FL442531.1|FL442531
EST:     TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
genomic: TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAAgtaagtcgcc ... gaccgcacagGACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
EST: gi|211362442|gb|FL457502.1|FL457502
EST:     TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
genomic: TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAAgtaagtcgcc ... gaccgcacagGACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
EST: gi|148990818|gb|EE032234.2|EE032234
EST:     TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTCCAA                         GACGAGAAGAAGCTTGTAGAGTTTATTAAATTCGTTAATGCGTGTGGAGCA
genomic: TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAAgtaagtcgcc ... gaccgcacagGACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
EST: gi|211260824|gb|FL469980.1|FL469980
EST:     TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
genomic: TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAAgtaagtcgcc ... gaccgcacagGACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
EST: gi|9733793|gb|BE512545.1|BE512545
EST:     TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
genomic: TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAAgtaagtcgcc ... gaccgcacagGACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
EST: gi|16926239|gb|BM079307.1|BM079307
EST:     TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
genomic: TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAAgtaagtcgcc ... gaccgcacagGACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
EST: gi|71426191|gb|DR807241.1|DR807241
EST:     TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGTTAATGCGTGTGGAGCA
genomic: TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAAgtaagtcgcc ... gaccgcacagGACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
EST: gi|71763640|gb|DR961577.1|DR961577
EST:     TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
genomic: TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAAgtaagtcgcc ... gaccgcacagGACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
EST: gi|50324290|gb|CO519416.1|CO519416
EST:     TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
genomic: TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAAgtaagtcgcc ... gaccgcacagGACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
EST: gi|60344172|gb|DN211145.1|DN211145
EST:     TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
genomic: TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAAgtaagtcgcc ... gaccgcacagGACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
EST: gi|78112339|gb|DV530733.1|DV530733
EST:     TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
genomic: TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAAgtaagtcgcc ... gaccgcacagGACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
EST: gi|40336934|gb|CK371004.1|CK371004
EST:     TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
genomic: TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAAgtaagtcgcc ... gaccgcacagGACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
EST: gi|78092754|gb|DV521128.1|DV521128
EST:     TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAA                         GACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA
genomic: TTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAAgtaagtcgcc ... gaccgcacagGACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCA

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), 49 (downstream exon)
Score: 38

CCCTTCCTTCAAAGTACAACAAGTCGATACGACTGGCGCAGGCGATGCGTTTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAAgtaagtcgcc ... gaccgcacagGACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCAATCACCGCCACGAAGAAGGGTGCGATCCCGTCTTTGCCCACTGAAACTG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 34

CCCTTCCTTCAAAGTACAACAAGTCGATACGACTGGCGCAGGCGATGCGTTTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAAgtaagtcgcc ... gaccgcacagGACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCAATCACCGCCACGAAGAAGGGTGCGATCCCGTCTTTGCCCACTGAAACTG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 36

CCCTTCCTTCAAAGTACAACAAGTCGATACGACTGGCGCAGGCGATGCGTTTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAAgtaagtcgcc ... gaccgcacagGACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCAATCACCGCCACGAAGAAGGGTGCGATCCCGTCTTTGCCCACTGAAACTG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 22

CCCTTCCTTCAAAGTACAACAAGTCGATACGACTGGCGCAGGCGATGCGTTTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAAgtaagtcgcc ... gaccgcacagGACGAGAAGAAGCTTGTAGAGTCTATTAAATTCGCTAATGCGTGTGGAGCAATCACCGCCACGAAGAAGGGTGCGATCCCGTCTTTGCCCACTGAAACTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCTTCCTTCAAAGTACAACAAGTCGATACGACTGGCGCAGGCGATGCGTTTGTTGGTGCGCTGCTCCGAAGGATCGTTAAAGATCCATCCTCGCTACAAgtaagtcgcctgaaatttgttcattgatctgaaattgttgggtcctacatgccaaggtggtccttcggttttcagttttaccatgtgacattgaaatttggtatctggtgtgaccgcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT