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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgagttttacaaactagatgttgacatgcatattcatgtgaagagtttagttttatgcagccgtatctcatcataatctgtagcttgaactgaaatgtagATTGTCCAAGATATCCCAAATCCCTTGCCGGAAAATTTACCAATGGTTCTTATAAAGCCACCTGAAGCATGCTCAACTGCTGAAGTTTACAAG

Basic information

species Zea mays
transcript GRMZM5G859195_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G859195_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g58790.2 (Oryza sativa), 3'ss of exon 6
tgagttttacaaactagatgttgacatgcatattcatgtgaagagtttagtttta-tgcagccgtatctcatcataatctgtagct-tgaactgaaatgta----gATTGTCCAAGATATCCCAAATCCCTTGCCGGAAAATTTACCAATGGTTCTTATAAAGCCACCTGAAGCATGCTCAACTGCTGAAGTTTACAAG
    ||| ||||  | | | | || ||| ||||   | |||  | | | |  ||  | ||    | ||| ||||||||||  | || || ||| |||||||    ||||||  ||||||| |  ||||| ||||| | |||||| || ||||| ||  ||||||||||||||||||||||||| |||||||||||||||
----tttgacaacattggtatggagatgtatatc--tttgatcaatattgccttgctccaaaaatgtctgatcataatctccaactctggacttaaatgtatgaagATTGTTGAAGATATTCGGAATCCATTGCCAGCAAATTTGCCGATGGTACTAGTAAAGCCACCTGAAGCATGCTCAACAGCTGAAGTTTACAAG

upper sequence: GRMZM5G859195_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA20G08930.1 (Glycine max), 3'ss of exon 6
----tgagttttacaaactagatgttgacatgcatattcatgtgaagagtttagttttatgcagccgtatctcatcataatctgtagcttgaactgaaatgtagATTGTCCAAGATATCCCAAATCCCTTGCCGGAAAATTTACCAATGGTTCTTATAAAGCCACCTGAAGCATGCTCAACTGCTGAAGTTTACAAG
      |    |   |||    ||  | ||   | | | || |      |    |   |  ||    ||| | |||  |   | |   || |  |   ||| || |||| ||  |||| ||    ||  |  |     || | ||||||||||| |||||||| || |||||||| |||||||||||||| ||||||
ctaaatatcccttttaaccttttgcagccagctaaacttatattccatatgatttcccaatcaat-atattttatccaagatttttctttcactt---atgcagGTTGTTCAGAATATTCCTCCACCAGTATCTCTGGATGTTCCAATGGTTCTCATAAAGCCCCCAGAAGCATGTTCAACTGCTGAAGTCTACAAG

upper sequence: GRMZM5G859195_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA13G04120.1 (Glycine max), 3'ss of exon 6
---tgagttttacaaactagatgttgacatgcatattcatgtgaagagtttagttttatgcagccgtatctcatcataatctgtagcttgaactgaaatgtagATTGTCCAAGATATCCCAAATCCCTTGCCGGAAAATTTACCAATGGTTCTTATAAAGCCACCTGAAGCATGCTCAACTGCTGAAGTTTACAAG
     |    |   |||    ||  | ||   | | | || |  |   |    |   |  ||    ||| | ||   ||    |  |||  ||| |  || || |||| ||  |||| ||    ||  |  |   | || | ||||||||||| |||||||| || |||||||| |||||||| ||||| ||||||
taaatatcccttttaaccttttgcaggcagctaaacttatattcaatatgatttcccaatcaat-atattttattcaaaaaaatttctttcactta--tgcagGTTGTTCAGAATATTCCTCCACCAGTATCTCTAGATGTTCCAATGGTTCTCATAAAGCCCCCAGAAGCATGTTCAACTGCCGAAGTCTACAAG

upper sequence: GRMZM5G859195_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv06s0009g02320.t01 (Vitis vinifera), 3'ss of exon 6
tgagttttacaaactagatgttgacatgcatattc---atgtgaagagtttagttttatgcagccgtatctcatcataatctgtagcttgaactgaaatgt--agATTGTCCAAGATATCCCAAATCCCTTGCCGGAAAATTTACCAATGGTTCTTATAAAGCCACCTGAAGCATGCTCAACTGCTGAAGTTTACAAG
       | | || |  ||    | |||||  |||   || |    |  |  | |||     |   ||     |   ||   | || |||  |||   ||   || ||||  |||||||  |    ||  | ||     |  | |||||||||||| ||||||||||  | |||||||| || |||||||||||||||
----gcatgctaaatgaattcatatatgcaatttctaaatatttttaaatgggattt-catggtgataagaagttcgaactagaagtttgctctggcttgctcagGTTGTTGAAGATATTTCCCTGCCAATACCTTTGGACATTCCAATGGTTCTTGTAAAGCCACCGCAGGCATGCTCCACCGCTGAAGTTTACAAG

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|148969055|gb|EE019774.2|EE019774
EST:     TCCCCTTTTTCTTTTCACGAGGAGCAGCATATTGTACAGGTAGAGGAGAG                         ATTGTCCAAGATATCCCAAATCCCTTGCCCGAAAATTTACCAATGGTTCTT
genomic: TCCCCTTTTTCTTTTCACGAGGAGCAGCATATTGTACAGGTAGAGGAGAGgtacgttttc ... tgaaatgtagATTGTCCAAGATATCCCAAATCCCTTGCCGGAAAATTTACCAATGGTTCTT
EST: gi|32934305|gb|CF039117.1|CF039117
EST:     ACAGGTAGAGGAGAG                         ATTGTCCAAGATATCCCAAATCCCTTGCCGGAAAATTTACCAATGGTTCTT
genomic: ACAGGTAGAGGAGAGgtacgttttc ... tgaaatgtagATTGTCCAAGATATCCCAAATCCCTTGCCGGAAAATTTACCAATGGTTCTT
EST: gi|76021627|gb|DT948797.1|DT948797
EST:     TCCCCTTTTTCTTTTCACGAGGAGCAGCATATTGTACAGGTAGAGGAGAG                         ATTGTCCAAGATATCCCAAATCCCTTGCCGGGAAATTTACCAATGGTTCTT
genomic: TCCCCTTTTTCTTTTCACGAGGAGCAGCATATTGTACAGGTAGAGGAGAGgtacgttttc ... tgaaatgtagATTGTCCAAGATATCCCAAATCCCTTGCCGGAAAATTTACCAATGGTTCTT
EST: gi|91870954|gb|EB401166.1|EB401166
EST:     TCCCCTTTTTCTTTTCACGAGGAGCAGCATATTGTACAGGTAGAGGAGAG                         ATTGTCCAAGATATCCCCAATCCCTTGCCGGAAAATTTACCAATGGGTCTT
genomic: TCCCCTTTTTCTTTTCACGAGGAGCAGCATATTGTACAGGTAGAGGAGAGgtacgttttc ... tgaaatgtagATTGTCCAAGATATCCCAAATCCCTTGCCGGAAAATTTACCAATGGTTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagttttatgcagccgtatctcatcataatctgtagcttgaactgaaatgtagATTGTCCAAGATATCCCAAATCCCTTGCCGGAAAATTTACCAATGGTTCTTATAAAGCCACCTGAAGCATGCTCAACTGCTGAAGTTTACAAG
                        atcataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgagttttacaaactagatgttgacatgcatattcatgtgaagagtttagttttatgcagccgtatctcatcataatctgtagcttgaactgaaatgtagATTGTCCAAGATATCCCAAATCCCTTGCCGGAAAATTTACCAATGGTTCTTATAAAGCCACCTGAAGCATGCTCAACTGCTGAAGTTTACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - gatgttg
- - - - - - - - - - - -acatgca
- - - - - - - - - - - - - - - -attcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcagcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgtagc