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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgagtgcgccttgcgcccatttttttttttcttcatgtgcgctaactttaacttggcaactgattttcgatttctgtttcctgtatgtatggctccagAGGGACGACATGGAGGTGCTTGACGAGCCTCTCTACGCAAATTTCCTGCGTGCCACAGGCGTCGACAGGCCCTACCGGCAGGAGCTCCTGTCCAAAATG

Basic information

species Zea mays
transcript GRMZM2G108416_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108416_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g24460.2 (Oryza sativa), 3'ss of exon 1
---------------------------------------------------------------------------------------tctgagtgcgcc-ttgcgcccattt----ttttttttcttcatgtgcgctaactttaacttggcaactgatt-ttcgatttctgtttcctgtatgtatggctccagAGGGACGACATGGAGGTGCTTGACGAGCCTCTCTACGCAAATTTCCTGCGTGCCACAGGCGTCGACAGGCCCTACCGGCAGGAGCTCCTGTCCAAAATG
                                                                                        | | |  | ||   ||  |||  |    |   |   |  |  |  ||||  |      | |    |||||  ||   ||| |  ||| ||| | |  |     ||||||| |||||||||||||| |||||||| |||||||| ||||||||||| | ||| |||||||||||||| || ||  ||||||| ||||| || |||
gtccgcgcctcctccttcgcctcgcctcggcctcgcccaccccgctgcgcacgggggatccccctgggccggcggcgagtcggcgaaccgggggccaccgccgcaaccagctgcattacctgcacggccggctcgcttcccccgtttcgctttctgatgattttttttttaattcttgtgtttgggat---agAGGGATGACATGGAGGTGCTCGACGAGCCGCTCTACGCTAATTTCCTGCGCGTCACCGGCGTCGACAGGCCGTATCGCGAGGAGCTTCTGTCTAACATG

upper sequence: GRMZM2G108416_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA19G42530.1 (Glycine max), 3'ss of exon 1
tctgagtgcgccttgcgcccatttttttttttcttcat-gtgcgctaactttaact-tggcaactgattttcgatttctgt-ttcctgtatgtatggctc-cagAGGGACGACATGGAGGTGCTTGACGAGCCTCTCTACGCAAATTTCCTGCGTGCCACAGGCGTCGACAGGCCCTACCGGCAGGAGCTCCTGTCCAAAATG
  | | |     |    |  |  ||| || ||    ||     |  ||   |   | ||   |  |  |||| |||||  |  |  | |  || || | | |||||||| ||||| || |||||||| ||||| ||||| |||||||||||  | |  || ||  | || || |||||| || ||||||| || |||||||||
--taattaa--ttgaaactgagctttgttattgacgattacctgaaaatcctgtttctgatcatggtgtttccatttccatgcttatatccgtgtgccacgcagAGGGATGACATAGAAGTGCTTGATGAGCCCCTCTATGCAAATTTCCTTAGAGTAACTGGTCTTGATAGACCCTACAGGGAGGAGCTACTCTCCAAAATG

upper sequence: GRMZM2G108416_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA03G40000.2 (Glycine max), 3'ss of exon 1
tctgagtgcgccttgcgcccatttttttttttcttcatgtgcgctaactttaacttggcaactgattttcgatttctgt-ttcctgtatgtatggctc-cagAGGGACGACATGGAGGTGCTTGACGAGCCTCTCTACGCAAATTTCCTGCGTGCCACAGGCGTCGACAGGCCCTACCGGCAGGAGCTCCTGTCCAAAATG
  | | |     | | ||    || ||       | |  ||    | | |     ||  ||  |  |||| |||||  |  |  | |  || ||   | |||||||| ||||| || |||||||| ||||| ||||| |||||||||||  | |  || ||  | || || |||||| || ||||||| || |||||||||
-attaattgaaatcgagctttgttattgacgcgattacctg-aaaatcctgtttctgataatggtgtttccatttccatgcttatatccgtgtgctacacagAGGGATGACATAGAAGTGCTTGATGAGCCCCTCTATGCAAATTTCCTTAGAGTAACTGGTCTTGATAGACCCTACAGGGAGGAGCTACTCTCCAAAATG

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|148969665|gb|EE020530.2|EE020530
EST:     GGTCGGCGCCGCGCTCCCTCAGCACCAGCCTCATGTACTCCTTCGCCCAG                         AGGGACGACATGGAGGTGCTTGACGAGCCTCTCTACGCAAATTTCCTGCGT
genomic: GGTCGGCGCCGCGCTCCCTCAGCACCAGCCTCATGTACTCCTTCGCCCAGgtctgctcct ... atggctccagAGGGACGACATGGAGGTGCTTGACGAGCCTCTCTACGCAAATTTCCTGCGT
EST: gi|211222333|gb|FL205469.1|FL205469
EST:     GGTCGGCGCCGCGCTCCCTCAGCACCAGCCTCATGTACTCCTTCGCCCAG                         AGGGACGACATGGAGGTGCTTGACGAGCCTCTCTACGCAAATTTCCTGCGT
genomic: GGTCGGCGCCGCGCTCCCTCAGCACCAGCCTCATGTACTCCTTCGCCCAGgtctgctcct ... atggctccagAGGGACGACATGGAGGTGCTTGACGAGCCTCTCTACGCAAATTTCCTGCGT
EST: gi|71430886|gb|DR811936.1|DR811936
EST:     GGTCGGCGCCGCGCTCCCTCAGCACCAGCCTCATGTACTCCTTCGCCCAG                         AGGGACGACATGGAGGTGCTTGACGAGCCTCTCTACGCAAATTTCCTGCGT
genomic: GGTCGGCGCCGCGCTCCCTCAGCACCAGCCTCATGTACTCCTTCGCCCAGgtctgctcct ... atggctccagAGGGACGACATGGAGGTGCTTGACGAGCCTCTCTACGCAAATTTCCTGCGT
EST: gi|71332464|gb|DR803192.1|DR803192
EST:     GGTCGGCGCCGCGCTCCCTCAGCACCAGCCTCATGTACTCCTTCGCCCAG                         AGGGACGACATGGAGGTGCTTGACGAGCCTCTCTACGCAAATTTCCTGCGT
genomic: GGTCGGCGCCGCGCTCCCTCAGCACCAGCCTCATGTACTCCTTCGCCCAGgtctgctcct ... atggctccagAGGGACGACATGGAGGTGCTTGACGAGCCTCTCTACGCAAATTTCCTGCGT
EST: gi|211222335|gb|FL205471.1|FL205471
EST:     GGTCGGCGCCGCGCTCCCTCAGCACCAGCCTCATGTACTCCTTCGCCCAG                         AGGGACGACATGGAGGTGCTTGACGAGCCTCTCTACGCAAATTTCCTGCGT
genomic: GGTCGGCGCCGCGCTCCCTCAGCACCAGCCTCATGTACTCCTTCGCCCAGgtctgctcct ... atggctccagAGGGACGACATGGAGGTGCTTGACGAGCCTCTCTACGCAAATTTCCTGCGT
EST: gi|149084135|gb|EE173538.2|EE173538
EST:     GGTCGGCGCCGCGCTCCCTCAGCACCAGCCTCATGTACTCCTTCGCCCAG                         AGGGACGACATGGAGGTGCTTGACGAGCCTCTCTACGCAAATTTCCTGCGT
genomic: GGTCGGCGCCGCGCTCCCTCAGCACCAGCCTCATGTACTCCTTCGCCCAGgtctgctcct ... atggctccagAGGGACGACATGGAGGTGCTTGACGAGCCTCTCTACGCAAATTTCCTGCGT
EST: gi|211222334|gb|FL205470.1|FL205470
EST:     GGTCGGCGCCGCGCTCCCTCAGCACCAGCCTCATGTACTCCTTCGCCCAG                         AGGGACGACATGGAGGTGCTTGACGAGCCTCTCTACGCAAATTTCCTGCGT
genomic: GGTCGGCGCCGCGCTCCCTCAGCACCAGCCTCATGTACTCCTTCGCCCAGgtctgctcct ... atggctccagAGGGACGACATGGAGGTGCTTGACGAGCCTCTCTACGCAAATTTCCTGCGT
EST: gi|211222331|gb|FL205467.1|FL205467
EST:     GGTCGGCGCCGCGCTCCCTCAGCACCAGCCTCATGTACTCCTTCGCCCAG                         AGGGACGACATGGAGGTGCTTGACGAGCCTCTCTACGCAAATTTCCTGCGT
genomic: GGTCGGCGCCGCGCTCCCTCAGCACCAGCCTCATGTACTCCTTCGCCCAGgtctgctcct ... atggctccagAGGGACGACATGGAGGTGCTTGACGAGCCTCTCTACGCAAATTTCCTGCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactttaacttggcaactgattttcgatttctgtttcctgtatgtatggctccagAGGGACGACATGGAGGTGCTTGACGAGCCTCTCTACGCAAATTTCCTGCGTGCCACAGGCGTCGACAGGCCCTACCGGCAGGAGCTCCTGTCCAAAATG
                 tgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgagtgcgccttgcgcccatttttttttttcttcatgtgcgctaactttaacttggcaactgattttcgatttctgtttcctgtatgtatggctccagAGGGACGACATGGAGGTGCTTGACGAGCCTCTCTACGCAAATTTCCTGCGTGCCACAGGCGTCGACAGGCCCTACCGGCAGGAGCTCCTGTCCAAAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - -gccttgc
- - - - - - - - - - - - - - - - cttcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcaactg