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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGGGTTCAACTGTCTTCTGGGTTGGAGAATGGTTTATAAAAAAAATGCCATTTGTAAGGCACATATACTCTGCATCAAAGCAAGTTAGTACTGCTGTTt

Basic information

species Zea mays
transcript GRMZM2G073415_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G073415_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g36110.4 (Oryza sativa), 5'ss of exon 4
GGTGGGTTCAACTGTCTTCTGGGTTGGAGAATGGTTTATAAAAAAAATGCCATTTGTAAGGCACATATACTCTGCATCAAAGCAAGTTAGTACTGCTGTTt----------------------------------------------------------------------------------------------------------
       ||||||||||| ||| |||||||||||||||| || |||||||| ||||||||||||||||| |||||||| ||||||||||| ||||||||||                                                                                                          
-------TCAACTGTCTTTTGGATTGGAGAATGGTTTATTAAGAAAATGCCTTTTGTAAGGCACATATATTCTGCATCGAAGCAAGTTAGCACTGCTGTTTCACCAGgtgattcatacgtatatacaaatctatgtgctttgaaatagtctacccatgatatttctttttaactcattcatgtttttcacttggagtgacacattga

upper sequence: GRMZM2G073415_T03 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA06G15360.2 (Glycine max), 5'ss of exon 4
GGTGGGTTCAACTGTCTTCTGGGTTGGAGAATGGTTTATAAAAAAAATGCCATTTGTAAGGCACATATACTCTGCATCAAAGCAAGTTAGTACTGCTGTTt----------------------------------------------------------------------------------------------------------
        | ||||| |||||| ||||||| ||||| |||||   ||||||  |||| ||||| |||||||||||||| |||||  ||||| ||||  | |                                                                                                          
-------GCCACTGTTTTCTGGATTGGAGAGTGGTTCATAAAGCGAATGCCCCTTGTTAGGCATATATACTCTGCATCCAAGCAGATTAGTGCTGCAATATCTCCAGgtattctctacataactgcgtagtccaattaggatttagccagaaaagagtttgatggtgggtccgaattcacatggatgagcagtaagccacatatagg

upper sequence: GRMZM2G073415_T03 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA04G39490.1 (Glycine max), 5'ss of exon 4
GGTGGGTTCAACTGTCTTCTGGGTTGGAGAATGGTTTATAAAAAAAATGCCATTTGTAAGGCACATATACTCTGCATCAAAGCAAGTTAGTACTGCTGTTt----------------------------------------------------------------------------------------------------------
        | ||||| |||||| ||||||||||||| |||||   ||||||  |||| ||||| |||||||||||||| |||||  | ||| ||||  | |                                                                                                          
-------GCCACTGTTTTCTGGATTGGAGAATGGTTCATAAAGCGAATGCCCCTTGTTAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATATCTCCAGgtatgctctacataactgcatagtccaattagaatttagccataaaagagtttgatggtgggttctgaattcatatggatgagcagtaagccacatgtag

upper sequence: GRMZM2G073415_T03 (Zea mays), 5'ss of exon 4
lower sequence: Vv07s0031g02010.t01 (Vitis vinifera), 5'ss of exon 4
GGTGGGTTCAACTGTCTTCTGGGTTGGAGAATGGTTTATAAAAAAAATGCCATTTGTAAGGCACATATACTCTGCATCAAAGCAAGTTAGTACTGCTGTTt----------------------------------------------------------------------------------------------------------
        | ||||| |||||| ||||||||||||||||||| | |||||| ||||| | ||| |||||||| || || |||||| ||||| | ||  |||                                                                                                          
-------GCCACTGTTTTCTGGCTTGGAGAATGGTTTATAAAGAGAATGCCCTTTGTTAAGCATATATACTCGGCCTCCAAGCAAATTAGTGCCGCAATTTCTCCAGgtaactcctgaagtttttttacatttttgcttaccgactttcaacgcctagttgtttggtgcaaaaatacttgcattatgaacataaattgaaatttctg

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|149096886|gb|EE182683.2|EE182683
EST:     CATTTGTAAGGCACATATACTCTGCATCAAAGCAAGTTAGTACTGCTGTT                         TCACCAG
genomic: CATTTGTAAGGCACATATACTCTGCATCAAAGCAAGTTAGTACTGCTGTTt ... tTCACCAGgtaatgtaat ... ctt
EST: gi|76291081|gb|DV030649.1|DV030649
EST:     CATTTGTAAGGCACATATACTCTGCATCAAAGCAAGTTAGTACTGCTGTT                         TCACCAG
genomic: CATTTGTAAGGCACATATACTCTGCATCAAAGCAAGTTAGTACTGCTGTTt ... tTCACCAGgtaatgtaat ... ctt
EST: gi|67012407|gb|CO441156.1|CO441156
EST:     CATTTGTAAGGCACATATACTCTGCATCAAAGCAAGTTAGTACTGCTGTT                         TCACCAG
genomic: CATTTGTAAGGCACATATACTCTGCATCAAAGCAAGTTAGTACTGCTGTTt ... tTCACCAGgtaatgtaat ... ctt
EST: gi|60341304|gb|DN208277.1|DN208277
EST:     TTGTAAGGCACATATACTCTGCATCAAAGCAAGTTAGTACTGCTGTT                         TCACCAG
genomic: TTGTAAGGCACATATACTCTGCATCAAAGCAAGTTAGTACTGCTGTTt ... tTCACCAGgtaatgtaat ... ctt
EST: gi|76291080|gb|DV030648.1|DV030648
EST:     CATTTGTAAGGCACATATACTCTGCATCAAAGCAAGTTAGTACTGCTGTT                         TCACCAG
genomic: CATTTGTAAGGCACATATACTCTGCATCAAAGCAAGTTAGTACTGCTGTTt ... tTCACCAGgtaatgtaat ... ctt
EST: gi|91055827|gb|EB166245.1|EB166245
EST:     CATTTGTAAGGCACATATACTCTGCATCAAAGCAAGTTAGTACTGCTGTT                         TCACCAG
genomic: CATTTGTAAGGCACATATACTCTGCATCAAAGCAAGTTAGTACTGCTGTTt ... tTCACCAGgtaatgtaat ... ctt
EST: gi|149104749|gb|EE290203.2|EE290203
EST:     CATTTGTAAGGCACATATACTCTGCATCAAAGCAAGTTAGTATTGCTGTT                         TCACCAG
genomic: CATTTGTAAGGCACATATACTCTGCATCAAAGCAAGTTAGTACTGCTGTTt ... tTCACCAGgtaatgtaat ... ctt
EST: gi|148971483|gb|EE022178.2|EE022178
EST:     CATTTGTAAGGCACATATACTCTGCATCAAAGCAAGTTAGTACTGCTGTT                         TCACCAG
genomic: CATTTGTAAGGCACATATACTCTGCATCAAAGCAAGTTAGTACTGCTGTTt ... tTCACCAGgtaatgtaat ... ctt
EST: gi|60347004|gb|DN213977.1|DN213977
EST:     CATTTGTAAGGCACATATACTCTGCATCAAAGCAAGTTAGTACTGCTGTT                         TCACCAG
genomic: CATTTGTAAGGCACATATACTCTGCATCAAAGCAAGTTAGTACTGCTGTTt ... tTCACCAGgtaatgtaat ... ctt
EST: gi|211119697|gb|FL001617.1|FL001617
EST:     CATTTGTAAGGCACATATACTCTGCATCAAAGCAAGTTAGTACTGCTGTT                         TCACCAG
genomic: CATTTGTAAGGCACATATACTCTGCATCAAAGCAAGTTAGTACTGCTGTTt ... tTCACCAGgtaatgtaat ... ctt

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGGGTTCAACTGTCTTCTGGGTTGGAGAATGGTTTATAAAAAAAATGCCATTTGTAAGGCACATATACTCTGCATCAAAGCAAGTTAGTACTGCTGTTt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT