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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAATAGAAGAGAAGATTAACAAGATCAAGTGGTGCCAAACAACCAACAATGCACTCTTTCTCTTGTCTACAAATGACAAAACAATCAAGTATTGGAAGgtatgtataaaagaggttgctcgttggtttactttcatatgtttacaacttcataggtcatcctttgtttaactagactagacctgttatgccttggtgt...

Basic information

species Zea mays
transcript GRMZM2G069631_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069631_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 5'ss of exon 4
GGAAATAGAAGAGAAGATTAACAAGATCAAGTGGTGCCAAACAACCAACAATGCACTCTTTCTCTTGTCTACAAATGACAAAACAATCAAGTATTGGAAGgta----tgtataaaagaggttgctcgttggtttactttcatatgtttacaacttcataggtcatcctttgtttaactagactagacctgttatgccttggtgt
||||||||| ||||||||||||||||||||||||||||||||| ||||||| || ||||||||||| ||||||||||| ||||||||||||||||||||||||    ||| | |   || || |  |||  |||  |||| ||||  ||  |  |||   | |  | |  ||   |  ||  |  | | | |||   || || |
GGAAATAGAGGAGAAGATTAACAAGATCAAGTGGTGCCAAACAGCCAACAACGCCCTCTTTCTCTTATCTACAAATGATAAAACAATCAAGTATTGGAAGgtacagttgtgtcacgaagcttccatgttcatttcgtttcttatgggtatga--tcaattgcctacatcggtactagaagtttgcatccgatat--tttagttt

upper sequence: GRMZM2G069631_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA07G01440.1 (Glycine max), 5'ss of exon 4
GGAAATAGAAGAGAAGATTAACAAGATCAAGTGGTGCCAAACAACCAACAATGCACTCTTTCTCTTGTCTACAAATGACAAAACAATCAAGTATTGGAAGgtatgtataaaagaggttgctcgttggtttactttcatatgtttacaacttcataggtcatcctttgtttaactagactagacctgttatgccttggtgt---------
||||||||||||||| |||||||| ||||| |||||||||||| | ||   |||  | || ||  | || |||||||| ||||| ||||| | ||||||||||||     ||  |  |||||  | ||    |     ||| |   |  ||  |   |||   | | | | | | |||       ||||    |  ||           
GGAAATAGAAGAGAAAATTAACAAAATCAAATGGTGCCAAACAGCTAATGGTGCTTTGTTCCTTCTATCCACAAATGATAAAACCATCAAATTTTGGAAGgtatg-----aaatgaatgctcacttgtgggatgctgaatgct---attttttttattcaatttatatatgaat-gacacacatggttacatttctgtcaaaataagtt

upper sequence: GRMZM2G069631_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA13G42800.1 (Glycine max), 5'ss of exon 4
GGAAATAGAAGAGAAGATTAACAAGATCAAGTGGTGCCAAACAACCAACAATGCACTCTTTCTCTTGTCTACAAATGACAAAACAATCAAGTATTGGAAGgtatgtataaaagaggttgctcgttggtttactttcatatgtttacaacttcataggtcatcctttgttta---actagactagacctgttatgc-cttggtgt
|||||| |||||||| || ||||| ||||  |||||||||| | | ||   ||| ||||| ||  | ||||||||||| ||||||||||| | |||||||||||| | |  |  | |  | | || |  | |||| |  || |  ||  ||   |  ||||   |   ||    || ||  |  || | | | |  ||  || |
GGAAATTGAAGAGAAAATCAACAAAATCAGATGGTGCCAAATAGCTAATGGTGCCCTCTTCCTTCTTTCTACAAATGATAAAACAATCAAATTTTGGAAGgtatg-aaatgaatgatcac-ctttagcatgctttta-gtgctgtca-tttatcaattcattgataaattgtgcacaaggttgcacttctgaggaactaagttt

upper sequence: GRMZM2G069631_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA08G20830.1 (Glycine max), 5'ss of exon 4
GGAAATAGAAGAGAAGATTAACAAGATCAAGTGGTGCCAAACAACCAACAATGCACTCTTTCTCTTGTCTACAAATGACAAAACAATCAAGTATTGGAAGgtatgtataaaagaggttgctcgttgg---tttactttcatatgtttaca-acttcataggtca-tcctttgtttaactagactagacctgttatgccttggtgt
||||||||||||||| |||||||| ||||| |||||||||||| ||||   |||  | || ||  | || |||||||| ||||| ||||| | |||||||||||| | |  |    |  || || ||    | | |   || | ||||   | || |||  | | |        |   || | |    ||||     ||  || |
GGAAATAGAAGAGAAAATTAACAAAATCAAATGGTGCCAAACAGCCAATGGTGCTTTGTTCCTTCTATCCACAAATGATAAAACCATCAAATTTTGGAAGgtatg-aaatgaattctcacttgtgggatgctgaatgctatttttttattcaatttatatatgaatgacacacatggttacatt---tctgtcg-aactaagttt

upper sequence: GRMZM2G069631_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 5'ss of exon 4
GGAAATAGAAGAGAAGATTAACAAGATCAAGTGGTGCCAAACAACCAACAATGCACTCTTTCTCTTGTCTACAAATGACAAAACAATCAAGTATTGGAAGgtatgtataaaag--------aggttgctc---gttggtttactttcatatgtttacaa----cttcataggtcatcctttgttta-actagactagacctgttat--gccttggtgt-----------------------------------------------
||||||||| ||||| || || ||||| |  ||||| |||||| | ||||||||| | |||||  | || || ||||||||||| ||||||| |||||||||| | |  | |         | |||  |    ||||||  | | |||| |||  |||      |  |  | ||||  ||| || | | | |   | |||| ||    | |||| |                                                 
GGAAATAGAGGAGAAAATCAATAAGATTAGATGGTGTCAAACAGCTAACAATGCATTGTTTCTTCTCTCCACCAATGACAAAACCATCAAGTTTTGGAAGgtaggaaagagaactattttaaagttttttaaagttggtg-attatcatttgtaaacagaatgttctaaggttcatgttttcttcatagttggtcacaccttttggtgggcttgttaagtacactttatgtgtctctttgctgttctgctttgagtgttgaacag

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|211079477|gb|FL398611.1|FL398611
EST:     AATCAAGTATTGGAAG                         GTTCAAGAGAAAAAGGTGAAACGGGTTTCAGTGATGAATTTGGACACCTCC
genomic: AATCAAGTATTGGAAGgtatgtataa ... tattctatagGTTCAAGAGAAAAAGGTGAAACGCGTTTCAGTGATGAATTTGGACACCTCC
EST: gi|211374954|gb|FL429396.1|FL429396
EST:     AATCAAGTATTGGAAG                         GTTCAAGAGAAAAAGGTGAAACGGGTTTCAGTGATGAATTTGGACACCTCC
genomic: AATCAAGTATTGGAAGgtatgtataa ... tattctatagGTTCAAGAGAAAAAGGTGAAACGCGTTTCAGTGATGAATTTGGACACCTCC
EST: gi|67012325|gb|CO441074.1|CO441074
EST:     ATGCACTCTTTCTCTTGTCTACAAATGACAAAACAATCAAGTATTGGAAG                         GTTCAAGAGAAAAAGGTGAAACGCGTTTCAGTGATGAATTTGGACACCTCC
genomic: ATGCACTCTTTCTCTTGTCTACAAATGACAAAACAATCAAGTATTGGAAGgtatgtataa ... tattctatagGTTCAAGAGAAAAAGGTGAAACGCGTTTCAGTGATGAATTTGGACACCTCC
EST: gi|60340196|gb|DN207169.1|DN207169
EST:     ATGCACTCTTTCTCTTGTCTACAAATGACAAAACAATCAAGTATTGGAAG                         GTTCAAGAGAAAAAGGTGAAACGGGTTTCAGTGATGAATTTGGACACCTCC
genomic: ATGCACTCTTTCTCTTGTCTACAAATGACAAAACAATCAAGTATTGGAAGgtatgtataa ... tattctatagGTTCAAGAGAAAAAGGTGAAACGCGTTTCAGTGATGAATTTGGACACCTCC
EST: gi|148939774|gb|EC884472.2|EC884472
EST:     ATGCACTCTTTCTCTTGTCTACAAATGACAAAACAATCAAGTATTGGAAG                         GTTCAAGAGAAAAAGGTGAAACGCGTTTCAGTGATGAATTTGGACACCTCC
genomic: ATGCACTCTTTCTCTTGTCTACAAATGACAAAACAATCAAGTATTGGAAGgtatgtataa ... tattctatagGTTCAAGAGAAAAAGGTGAAACGCGTTTCAGTGATGAATTTGGACACCTCC
EST: gi|148991720|gb|EE033282.2|EE033282
EST:     ATGCACTCTTTCTCTTGTCTACAAATGACAAAACAATCAAGTATTGGAAG                         GTTCAAGAGAAAAAGGTGAAACGCGTTTCAGTGATGAATTTGGACACCTCC
genomic: ATGCACTCTTTCTCTTGTCTACAAATGACAAAACAATCAAGTATTGGAAGgtatgtataa ... tattctatagGTTCAAGAGAAAAAGGTGAAACGCGTTTCAGTGATGAATTTGGACACCTCC
EST: gi|94472892|gb|EB701850.1|EB701850
EST:     ATGCACTCTTTCTCTTGTCTACAAATGACAAAACAATCAAGTATTGGAAG                         GTTCAAGAGAAAAAGGTGAAACGCGTTTCAGTGATGAATTTGGACACCTCC
genomic: ATGCACTCTTTCTCTTGTCTACAAATGACAAAACAATCAAGTATTGGAAGgtatgtataa ... tattctatagGTTCAAGAGAAAAAGGTGAAACGCGTTTCAGTGATGAATTTGGACACCTCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAAATAGAAGAGAAGATTAACAAGATCAAGTGGTGCCAAACAACCAACAATGCACTCTTTCTCTTGTCTACAAATGACAAAACAATCAAGTATTGGAAGgtatgtataaaagaggttgctcgttggtttactttcatatgtttacaacttcataggtcatcctttgtttaactagactagacctgttatgccttggtgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ataaaaga