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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatttatataaccagctactttatctgccttttggccaagtaactggcttatccaaaacattttgttgctgcaaccagGATACTATGGAGAGTGTGGTAAAAGAGGAGGGTACATGGAGATTACTGGCTTCAGTGCTCCAGTAAGAGAGCAGATCTACAAGATAGCTTCAGTGAACCT

Basic information

species Zea mays
transcript GRMZM2G088064_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088064_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os10g25130.1 (Oryza sativa), 3'ss of exon 11
gtaaatttatataaccagctactttatctgccttttggccaagtaactggcttatccaaaacattttgttgctgcaaccagGATACTATGGAGAGTGTGGTAAAAGAGGAGGGTACATGGAGATTACTGGCTTCAGTGCTCCAGTAAGAGAGCAGATCTACAAGATAGCTTCAGTGAACCT
||||||    || | | | |   |||| |  || |||||      ||||| || || |||  ||||| ||||||  | ||||||| ||||| || ||||| ||||||||||| |||||||||||||||||||||||||||||||| |||||||||||||||||  | || ||||||||| |
gtaaatacg-atgatctgttttcttattt-tctattggc------actggattctcaaaaggattttcttgctgacaacagGATATTATGGTGAATGTGGCAAAAGAGGAGGCTACATGGAGATTACTGGCTTCAGTGCTCCAGTTAGAGAGCAGATCTACAAAGTGGCGTCAGTGAACTT

upper sequence: GRMZM2G088064_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT1G72330.3 (Arabidopsis thaliana), 3'ss of exon 10
gtaaatttatataaccagctactttatctgccttttggccaagtaactggcttatccaaaacattttgttgctgcaaccagGATACTATGGAGAGTGTGGTAAAAGAGGAGGGTACATGGAGATTACTGGCTTCAGTGCTCCAGTAAGAGAGCAGATCTACAAGATAGCTTCAGTGAACCT
|||||   | |       ||     ||  || | |   | ||  ||  || || |       | | |  | |||     |||||| |||||||| ||||| ||||||||||| ||||||||| ||||||| |||| | ||   |||||||| ||||| ||||| || ||||| ||||| ||
gtaaaagaacaacttttactgtccaat--gcttgtcatctaaaaaatggggtttttgtttttaatattcttctgttgatagGATATTATGGAGAATGTGGAAAAAGAGGAGGTTACATGGAGGTTACTGGATTCACTTCTGATGTAAGAGAACAGATATACAAAATGGCTTCTGTGAATCT

upper sequence: GRMZM2G088064_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT1G17290.1 (Arabidopsis thaliana), 3'ss of exon 10
-------------gtaaatttatataaccagctactttatctgccttttg-gccaagtaactggcttatccaaaacattttgttgctgcaaccagGATACTATGGAGAGTGTGGTAAAAGAGGAGGGTACATGGAGATTACTGGCTTCAGTGCTCCAGTAAGAGAGCAGATCTACAAGATAGCTTCAGTGAACCT
               |||| | | ||  ||  |  |   ||||    ||| |    | |||| | | |   ||   | ||  ||  | |   |||| ||||||||||||||||| |||||||| || ||||||||| ||||||| |||| | ||   |||||||||||||| ||||| || ||||| ||||| ||
gtttgatacaaaaacaaatctct-tagtcaattgataattctgatcattgcgatgggaaactag-tcagaaaactgaattcattatttctgacagGGTACTATGGAGAGTGTGGGAAAAGAGGTGGTTACATGGAGGTTACTGGATTCACTTCTGATGTAAGAGAGCAGATATACAAAATGGCTTCTGTGAATCT

upper sequence: GRMZM2G088064_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv09s0002g00340.t01 (Vitis vinifera), 3'ss of exon 11
------------------gtaaatttat-ataaccagctactttat--ctgccttttggccaagtaact--ggcttatccaaaacattttgttgctgcaaccagGATACTATGGAGAGTGTGGTAAAAGAGGAGGGTACATGGAGATTACTGGCTTCAGTGCTCCAGTAAGAGAGCAGATCTACAAGATAGCTTCAGTGAACCT
                    ||||| || | ||| || ||    ||  |||||    |   |   |  |  |  |||  ||  |  | |  ||||||    |||| |||||||| |||||||| ||||||||||| ||||||||| | ||||| ||  | |||   ||  | || ||||| |||||  | || || ||||| ||
gtatgttgatcttatcagccaaattgatcaaaacaagataggaaataactgccagaagaatattgagtttggatttaatcagcatgtgtctttgctggcttcagGGTACTATGGGGAGTGTGGAAAAAGAGGAGGTTACATGGAGGTAACTGGGTTTGGCGCTGATGTGCGGGAACAGATATACAAAGTGGCATCTGTGAATCT

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|116816986|gb|EC859784.1|EC859784
EST:     GTATGGCGAGGATGATCTCCCTCTAGTATCGTTACAGTCTGTTTCCAAAG                         GATACTATGGAGACGTGTGGTAAAAGAGGAGGGTACATGGAGATTACTGGC
genomic: GTATGGCGAGGATGATCTCCCTCTAGTATCGTTACAGTCTGTTTCCAAAGgtaaatttat ... ctgcaaccagGATACTATGGAGA-GTGTGGTAAAAGAGGAGGGTACATGGAGATTACTGGC
EST: gi|47962226|gb|CN844935.1|CN844935
EST:     GTATGGCGAGGATGATCTCCCTCTAGTATCGTTACAGTCTGTTTCCAAAG                         GATACTATGGAGAGTGTGGTAAAAGAGGAGGGTACATGGAGATTACTGGCT
genomic: GTATGGCGAGGATGATCTCCCTCTAGTATCGTTACAGTCTGTTTCCAAAGgtaaatttat ... ctgcaaccagGATACTATGGAGAGTGTGGTAAAAGAGGAGGGTACATGGAGATTACTGGCT
EST: gi|44681923|gb|CK786971.1|CK786971
EST:     GTATGGCGAGGATGATCTCCCTCTAGTATCGTTACAGTCTGTTTCCAAAG                         GATACTATGGAGAGTGTGGTAAAAGAGGAGGGTACATGGAGATTACTGGCT
genomic: GTATGGCGAGGATGATCTCCCTCTAGTATCGTTACAGTCTGTTTCCAAAGgtaaatttat ... ctgcaaccagGATACTATGGAGAGTGTGGTAAAAGAGGAGGGTACATGGAGATTACTGGCT
EST: gi|31355085|gb|CD439442.1|CD439442
EST:     TTACAGTCTGTTTCCAAAG                         GATACTATGGAGAGTGTCGTAAAAGAGGAGGGTACATGGAGATTACTGGCT
genomic: TTACAGTCTGTTTCCAAAGgtaaatttat ... ctgcaaccagGATACTATGGAGAGTGTGGTAAAAGAGGAGGGTACATGGAGATTACTGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgccttttggccaagtaactggcttatccaaaacattttgttgctgcaaccagGATACTATGGAGAGTGTGGTAAAAGAGGAGGGTACATGGAGATTACTGGCTTCAGTGCTCCAGTAAGAGAGCAGATCTACAAGATAGCTTCAGTGAACCT
              aagtaac  putative branch site (score: 2)
                               aaaacatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatttatataaccagctactttatctgccttttggccaagtaactggcttatccaaaacattttgttgctgcaaccagGATACTATGGAGAGTGTGGTAAAAGAGGAGGGTACATGGAGATTACTGGCTTCAGTGCTCCAGTAAGAGAGCAGATCTACAAGATAGCTTCAGTGAACCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT