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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgatcacctccttccccgtcgtcttccaccgtcaccgttgggcttgtttgcatctgaacttgtttggttgcggattgcagGGAAGAAGAAGGAGGTGAAGAAGGAGACGAAGCTCGGGATGGCCTATAAGAAGGACGACAACTTCGGGGAGTGGTACTCCGAG

Basic information

species Zea mays
transcript GRMZM2G094123_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094123_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os12g25710.3 (Oryza sativa), 3'ss of exon 1
----------gttcgatcacctccttccccgtcgtc--ttccaccgtcaccgttgggcttgtt-tgcatctgaactt-----gtttggttgcgg----attgcagGGAAGAAGAAGGAGGTGAAGAAGGAGACGAAGCTCGGGATGGCCTATAAGAAGGACGACAACTTCGGGGAGTGGTACTCCGAG
          ||| | |    |        || |    ||     |      |  |  ||||| | || ||||   |     ||||||| ||||     ||||||||||||||||||||||||||||||||||||||||||||||||| || |||||||| |||||||||||||||||||||||||||
gtgcggcgtggttgggttgggttgggttgggttggagatttgggtgggtttttgcgttttgttcttcaactgatgatggggggtttggtggcggttgagttgcagGGAAGAAGAAGGAGGTGAAGAAGGAGACGAAGCTCGGGATGGCGTACAAGAAGGATGACAACTTCGGGGAGTGGTACTCCGAG

upper sequence: GRMZM2G094123_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA03G38340.1 (Glycine max), 3'ss of exon 2
---gttcgatcacctccttccccgtcgtcttccaccg----tcaccgttgggcttgtttg--catctgaacttgtttggttgcgga-ttgcagG---GAAGAAGAAGGAGGTGAAGAAGGAGACGAAGCTCGGGATGGCCTATAAGAAGGACGACAACTTCGGGGAGTGGTACTCCGAG
    ||||     ||| ||  |   | | |||    |    ||    ||| || |||| |  | ||| |    |   |   |  |  |||||||   |||||||||||||||||||||||||||     | ||  |  |  ||  |||||  || |||||||| |||||||| ||||||
gtaattcgcattactcgttttcgtgcatgttcgtttgcgtttcgtgtttgtgcatgttcgttcttctaacggcgaccgaacgaagccttgcagGTGGGAAGAAGAAGGAGGTGAAGAAGGAGACTGGCTTAGGTCTCACGCATCGGAAGGCGGAGAACTTCGGAGAGTGGTATTCCGAG
















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|22542882|gb|BU093320.1|BU093320
EST:     TCTGTGAGCCATGTCGACCAACAAGGGCAGCGCGGCCAAGGGCGGCGGAG                         GGAAGAAGAAGGAGGTGAAGAAGGAGACGAAGCTCGGGATGGCCTATAAGA
genomic: TCTGTGAGCCATGTCGACCAACAAGGGCAGCGCGGCCAAGGGCGGCGGAGgttcgatcac ... cggattgcagGGAAGAAGAAGGAGGTGAAGAAGGAGACGAAGCTCGGGATGGCCTATAAGA
EST: gi|71332073|gb|DR802941.1|DR802941
EST:     TCTGTGAGCCATGTCGACCAACAAGGGCAGCGCGGCCAAGGGCGGCGGAG                         GGAAGAAGAAGGAGGTGAAGAAGGAGACGAAGCTCGGGATGGCCTATAAGA
genomic: TCTGTGAGCCATGTCGACCAACAAGGGCAGCGCGGCCAAGGGCGGCGGAGgttcgatcac ... cggattgcagGGAAGAAGAAGGAGGTGAAGAAGGAGACGAAGCTCGGGATGGCCTATAAGA
EST: gi|15312974|gb|BI478491.1|BI478491
EST:     AGGGCAGCGCGGCCAAGGGCGGCGGAG                         GGAAGAAGAAGGAGGTGAAGAAGGAGACGAAGCTCGGGATGGCCTATAAGA
genomic: AGGGCAGCGCGGCCAAGGGCGGCGGAGgttcgatcac ... cggattgcagGGAAGAAGAAGGAGGTGAAGAAGGAGACGAAGCTCGGGATGGCCTATAAGA
EST: gi|211280528|gb|FL042846.1|FL042846
EST:     TCTGTGAGCCATGTCGACCAACAAGGGCAGCGCGGCCAAGGGCGGCGGAG                         GGAAGAAGAAGGAGGTGAAGAAGGAGACGAAGCTCGGGATGGCCTATAAGA
genomic: TCTGTGAGCCATGTCGACCAACAAGGGCAGCGCGGCCAAGGGCGGCGGAGgttcgatcac ... cggattgcagGGAAGAAGAAGGAGGTGAAGAAGGAGACGAAGCTCGGGATGGCCTATAAGA
EST: gi|67027739|gb|CO456488.1|CO456488
EST:     TCTGTGAGCCATGTCGACCAACAAGGGCAGCGCGGCCAAGGGCGGCGGAG                         GGAAGAAGAAGGAGGTGAAGAAGGAGACGAAGCTCGGGATGGCCTATAAGA
genomic: TCTGTGAGCCATGTCGACCAACAAGGGCAGCGCGGCCAAGGGCGGCGGAGgttcgatcac ... cggattgcagGGAAGAAGAAGGAGGTGAAGAAGGAGACGAAGCTCGGGATGGCCTATAAGA
EST: gi|211280526|gb|FL042844.1|FL042844
EST:     TCTGTGAGCCATGTCGACCAACAAGGGCAGCGCGGCCAAGGGCGGCGGAG                         GGAAGAAGAAGGAGGTGAAGAAGGAGACGAAGCTCGGGATGGCCTATAAGA
genomic: TCTGTGAGCCATGTCGACCAACAAGGGCAGCGCGGCCAAGGGCGGCGGAGgttcgatcac ... cggattgcagGGAAGAAGAAGGAGGTGAAGAAGGAGACGAAGCTCGGGATGGCCTATAAGA
EST: gi|211280529|gb|FL042847.1|FL042847
EST:     TCTGTGAGCCATGTCGACCAACAAGGGCAGCGCGGCCAAGGGCGGCGGAG                         GGAAGAAGAAGGAGGTGAAGAAGGAGACGAAGCTCGGGATGGCCTATAAGA
genomic: TCTGTGAGCCATGTCGACCAACAAGGGCAGCGCGGCCAAGGGCGGCGGAGgttcgatcac ... cggattgcagGGAAGAAGAAGGAGGTGAAGAAGGAGACGAAGCTCGGGATGGCCTATAAGA
EST: gi|148961334|gb|EE012063.2|EE012063
EST:     TCTGTGAGCCATGTCGACCAACAAGGGCAGCGCGGCCAAGGGCGGCGGAG                         GGAAGAAGAAGGAGGTGAAGAAGGAGACGAAGCTCGGGATGGCCTATAAGA
genomic: TCTGTGAGCCATGTCGACCAACAAGGGCAGCGCGGCCAAGGGCGGCGGAGgttcgatcac ... cggattgcagGGAAGAAGAAGGAGGTGAAGAAGGAGACGAAGCTCGGGATGGCCTATAAGA
EST: gi|211280527|gb|FL042845.1|FL042845
EST:     TCTGTGAGCCATGTCGACCAACAAGGGCAGCGCGGCCAAGGGCGGCGGAG                         GGAAGAAGAAGGAGGTGAAGAAGGAGACGAAGCTCGGGATGGCCTATAAGA
genomic: TCTGTGAGCCATGTCGACCAACAAGGGCAGCGCGGCCAAGGGCGGCGGAGgttcgatcac ... cggattgcagGGAAGAAGAAGGAGGTGAAGAAGGAGACGAAGCTCGGGATGGCCTATAAGA

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: 620

CCTCTCGGACCCCCGGTGGCCGGTGCAGAGCTGCGCGACCGAGAACCGAATCTGTGAGCCATGTCGACCAACAAGGGCAGCGCGGCCAAGGGCGGCGGAGgttcgatcac ... cggattgcagGGAAGAAGAAGGAGGTGAAGAAGGAGACGAAGCTCGGGATGGCCTATAAGAAGGACGACAACTTCGGGGAGTGGTACTCCGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 399

CCTCTCGGACCCCCGGTGGCCGGTGCAGAGCTGCGCGACCGAGAACCGAATCTGTGAGCCATGTCGACCAACAAGGGCAGCGCGGCCAAGGGCGGCGGAGgttcgatcac ... cggattgcagGGAAGAAGAAGGAGGTGAAGAAGGAGACGAAGCTCGGGATGGCCTATAAGAAGGACGACAACTTCGGGGAGTGGTACTCCGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 213

CCTCTCGGACCCCCGGTGGCCGGTGCAGAGCTGCGCGACCGAGAACCGAATCTGTGAGCCATGTCGACCAACAAGGGCAGCGCGGCCAAGGGCGGCGGAGgttcgatcac ... cggattgcagGGAAGAAGAAGGAGGTGAAGAAGGAGACGAAGCTCGGGATGGCCTATAAGAAGGACGACAACTTCGGGGAGTGGTACTCCGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 400

CCTCTCGGACCCCCGGTGGCCGGTGCAGAGCTGCGCGACCGAGAACCGAATCTGTGAGCCATGTCGACCAACAAGGGCAGCGCGGCCAAGGGCGGCGGAGgttcgatcac ... cggattgcagGGAAGAAGAAGGAGGTGAAGAAGGAGACGAAGCTCGGGATGGCCTATAAGAAGGACGACAACTTCGGGGAGTGGTACTCCGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgatcacctccttccccgtcgtcttccaccgtcaccgttgggcttgtttgcatctgaacttgtttggttgcggattgcagGGAAGAAGAAGGAGGTGAAGAAGGAGACGAAGCTCGGGATGGCCTATAAGAAGGACGACAACTTCGGGGAGTGGTACTCCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG