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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATTGCTGTTGGCAACCTCTCCAAGTATTTACCATTTATTTTGGATCAGATTGACAATCAACAGAAGAAGCAATATCTGTTGCTCCATTCACTTAAAGAGgtttatttctatttgaattttgatcttaaaatgcattccccatctaactgttgcctaacacatgctcgtactaaaaaactgccag

Basic information

species Zea mays
transcript GRMZM2G168629_T05
intron # 22
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168629_T04 (Zea mays), 5'ss of exon 22
lower sequence: LOC_Os02g07120.1 (Oryza sativa), 5'ss of exon 22
CATTGCTGTTGGCAACCTCTCCAAGTATTTACCATTTATTTTGGATCAGATTGACAATCAACAGAAGAAGCAATATCTGTTGCTCCATTCACTTAAAGAGgtttatttctatttgaattttgatcttaaaatgcattccccatctaactgttgcctaacacatgctcgtactaaaaaactgccag
|||||||||||| ||  | || |||||||| || ||||| ||| ||||||||||||| ||||||||||| || ||||| ||||| |||||||| |||||||||| |  | ||| | |||| |   || |  ||||||| |||| ||  |||||| |||  | |||| |||||  ||| |   |||
CATTGCTGTTGGAAATTTATCGAAGTATTTGCCTTTTATCTTGAATCAGATTGACAACCAACAGAAGAAACAGTATCTATTGCTTCATTCACTGAAAGAGgtttgtccccattaggatttgg--tttgatgtgcattctccatgtatttgttgcttaattcttgcttgtactttaaatcactcag

upper sequence: GRMZM2G168629_T04 (Zea mays), 5'ss of exon 22
lower sequence: GLYMA07G40230.2 (Glycine max), 5'ss of exon 23
CATTGCTGTTGGCAACCTCTCCAAGTATTTACCATTTATTTTGGATCAGATTGACAATCAACAGAAGAAGCAATATCTGTTGCTCCATTCACTTAAAGAGgtttatttctatttgaattttgatcttaa-aatgcattccccatctaactgttgcctaacacatgctcgtactaaaaaactgccag---------------------------------------------
|||||||||||| || ||  | || || || |||||||| |||||||||||||| ||||| |||||||| |||||||| ||||| |||||  | |||||||| | || |  |   ||  |  ||||    |||    |  |  |||||   ||     | | ||||   |  | ||||  ||  |                                              
CATTGCTGTTGGTAATCTTCCAAAATACTTGCCATTTATCTTGGATCAGATTGATAATCAGCAGAAGAAACAATATCTCTTGCTTCATTCTTTGAAAGAGgtgtgttgccttaacaaaatctatctggttaatttgatttctttctaatatttaatatatatatgca-atcatgaaaacttgtgaatatttaatttaatatatatacaattctcttgcccctacctggcag

upper sequence: GRMZM2G168629_T04 (Zea mays), 5'ss of exon 22
lower sequence: GLYMA17G00570.1 (Glycine max), 5'ss of exon 22
CATTGCTGTTGGCAACCTCTCCAAGTATTTACCATTTATTTTGGATCAGATTGACAATCAACAGAAGAAGCAATATCTGTTGCTCCATTCACTTAAAGAGgtttatttctatttgaattttgatcttaaaatgcattccccatctaactgttgcctaacacatgctcgtactaaaaaactgccag-----------------------------------
||||||| |||| || ||  | || || || |||||||| |||||||||||||| ||||| |||||||| |||||||| ||||| |||||  | |||||||| | || |  |   ||     ||| |    |   ||     |||  ||      ||| | ||   |   |   ||||||                                        
CATTGCTATTGGTAATCTTCCAAAATACTTGCCATTTATCTTGGATCAGATTGATAATCAGCAGAAGAAACAATATCTCTTGCTTCATTCTTTGAAAGAGgtgtgttgccttaacaa----aatcatctggttggttttatttctttctaagatttaatatatagacaatcatgaaaactcatttaatatatatgcaattctcttgcccttacctggcag

upper sequence: GRMZM2G168629_T04 (Zea mays), 5'ss of exon 22
lower sequence: AT2G02560.2 (Arabidopsis thaliana), 5'ss of exon 22
CATTGCTGTTGGCAACCTCTCCAAGTATTTACCATTTATTTTGGATCAGATTGACAATCAACAGAAGAAGCAATATCTGTTGCTCCATTCACTTAAAGAGgtttatttctatt--tgaattttgatcttaaaatg-cattccccatctaactgttgcctaacacatgctcgtactaaaaaactgccag
|||||| |||||||| || ||||| ||| |||| ||||| ||||| ||||| || ||||||||||| || |||||| |  | || |||||||| || ||||| | |||   ||    | | |  || ||| |||  ||     |||  ||||| |   |  || || ||  | ||       | ||||
CATTGCCGTTGGCAATCTATCCAATTATCTACCGTTTATATTGGACCAGATCGATAATCAACAGAAAAAACAATATATTCTCCTTCATTCACTCAAGGAGgtatgttttccttaacaagtatccatgttataatatcagattacata-aactgcttgatttcatatcctgttccttgtttttttccag

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|14191175|gb|BG833405.1|BG833405
EST:     TTGACAATCAACAGAAGAAGCAATATCTGTTGCTCCATTCACTTAAAGAG                         GTAATCGTGCGACAATCTGTTGATCATACTGGCCAGAGTGAGCTACAGGAT
genomic: TTGACAATCAACAGAAGAAGCAATATCTGTTGCTCCATTCACTTAAAGAGgtttatttct ... aaactgccagGTAATCGTGCGACAATCTGTTGATCATACTGGCCAGAGTGAGCTACAGGAT
EST: gi|91877710|gb|EB407667.1|EB407667
EST:     TTGACAATCAACAGAAGAAGCAATATCTGTTGCTCCATTCACTTAAAGAG                         GTAATCGTGCGACAATCTGTTGATCATACTGGCCAGAGTGAGCTACAGGAT
genomic: TTGACAATCAACAGAAGAAGCAATATCTGTTGCTCCATTCACTTAAAGAGgtttatttct ... aaactgccagGTAATCGTGCGACAATCTGTTGATCATACTGGCCAGAGTGAGCTACAGGAT
EST: gi|67019143|gb|CO447892.1|CO447892
EST:     TTGACAATCAACAGAAGAAGCAATATCTGTTGCTCCATTCACTTAAAGAG                         GTAATCGTGCGACAATCTGTTGATCATACTGGCCAGAGTGAGCTACAGGAT
genomic: TTGACAATCAACAGAAGAAGCAATATCTGTTGCTCCATTCACTTAAAGAGgtttatttct ... aaactgccagGTAATCGTGCGACAATCTGTTGATCATACTGGCCAGAGTGAGCTACAGGAT
EST: gi|31354241|gb|CD438598.1|CD438598
EST:     TTGACAATCAACAGAAGAAGCAATATCTGTTGCTCCATTCACTTAAAGAG                         GTAATCGTGCGACAATCTGTTGATCATACTGGCCAGAGTGAGCTACAGGAT
genomic: TTGACAATCAACAGAAGAAGCAATATCTGTTGCTCCATTCACTTAAAGAGgtttatttct ... aaactgccagGTAATCGTGCGACAATCTGTTGATCATACTGGCCAGAGTGAGCTACAGGAT
EST: gi|89761370|gb|DY689409.1|DY689409
EST:     TTGACAATCAACAGAAGAAGCAATATCTGTTGCTCCATTCACTTAAAGAG                         GTAATCGTGCGACAATCTGTTGATCATACTGGCCAGAGTGAGCTACAGGAT
genomic: TTGACAATCAACAGAAGAAGCAATATCTGTTGCTCCATTCACTTAAAGAGgtttatttct ... aaactgccagGTAATCGTGCGACAATCTGTTGATCATACTGGCCAGAGTGAGCTACAGGAT
EST: gi|78119497|gb|DV537881.1|DV537881
EST:     TTGACAATCAACAGAAGAAGCAATATCTGTTGCTCCATTCACTTAAAGAG                         GTAATCGTGCGACAATCTGTTGATCATACTGGCCAGAGTGAGCTACAGGAT
genomic: TTGACAATCAACAGAAGAAGCAATATCTGTTGCTCCATTCACTTAAAGAGgtttatttct ... aaactgccagGTAATCGTGCGACAATCTGTTGATCATACTGGCCAGAGTGAGCTACAGGAT
EST: gi|71448044|gb|DR829094.1|DR829094
EST:     TTGACAATCAACAGAAGAAGCAATATCTGTTGCTCCATTCACTTAAAGAG                         GTAATCGTGCGACAATCTGTTGATCATACTGGCCAGAGTGAGCTACA
genomic: TTGACAATCAACAGAAGAAGCAATATCTGTTGCTCCATTCACTTAAAGAGgtttatttct ... aaactgccagGTAATCGTGCGACAATCTGTTGATCATACTGGCCAGAGTGAGCTACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATTGCTGTTGGCAACCTCTCCAAGTATTTACCATTTATTTTGGATCAGATTGACAATCAACAGAAGAAGCAATATCTGTTGCTCCATTCACTTAAAGAGgtttatttctatttgaattttgatcttaaaatgcattccccatctaactgttgcctaacacatgctcgtactaaaaaactgccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA