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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAGgtaatagtatattctttctactctatttttattggcaaggttcagttattgtctccttggaactataatcagttttctggttgccaacttttag

Basic information

species Zea mays
transcript GRMZM2G108829_T02
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108829_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os02g47225.1 (Oryza sativa), 5'ss of exon 11
TCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAGgtaatagtatattctttctactctatttttattggcaaggttcagttattgtctccttggaactataatcagttttctggttgccaacttttag
||||| ||||||||||| ||| |||||||||||||||| |||||||| ||||||||||| || |||||||||| | ||   | ||   ||||  ||  | |||       || ||   | | |    | |  || |||||  ||| |  |||||| |   |||
TCACTGTGCTCATGGGACCCTTGCAAGAGACCAAAGGCTGCAGAAGTTCTCCAGCATACTTTCTTTCAGgtaaaattac--tattcgaactccgttgctgttg-------tctgtacctctgttgcagaagata-aatcaaatttatttttgccatccactag
















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|60349468|gb|DN216441.1|DN216441
EST:     CTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAG                         GGTTGTACATGTGTTCCACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCT
genomic: CTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAGgtaatagtat ... caacttttagGGTTGTACATGTGTTCCACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCT
EST: gi|211496287|gb|FL041699.1|FL041699
EST:     CTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAG                         GGTTGTACATGTGTTCCACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCT
genomic: CTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAGgtaatagtat ... caacttttagGGTTGTACATGTGTTCCACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCT
EST: gi|32870331|gb|CF010013.1|CF010013
EST:     CTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAG                         GGTTGTACATGTGTTCCACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCT
genomic: CTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAGgtaatagtat ... caacttttagGGTTGTACATGTGTTCCACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCT
EST: gi|32788458|gb|CD940694.1|CD940694
EST:     CTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAG                         GGTTGTACATGTGTTCCACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCT
genomic: CTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAGgtaatagtat ... caacttttagGGTTGTACATGTGTTCCACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCT
EST: gi|32869779|gb|CF009461.1|CF009461
EST:     CTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAG                         GGTTGTACATGTGTTCCACTCCCTGTCCGTCCAAAAGCTTCATCAC
genomic: CTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAGgtaatagtat ... caacttttagGGTTGTACATGTGTTCCACTCCCTGTCCGTCCAAAAGCTTCATCAC
EST: gi|67011156|gb|CO439905.1|CO439905
EST:     CTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTNTTTCAG                         GGNTGTACATGTGTTCCACTTNCTGTCCGTCCAAAAGCTTCATCACTTNCT
genomic: CTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAGgtaatagtat ... caacttttagGGTTGTACATGTGTTCCACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCT
EST: gi|5325074|gb|AI783265.1|AI783265
EST:     TAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCNNNNNNNCAG                         GGTTGTACATGTGTTCCACTTCCTGTCCGTCCAAAAGCTTCATCACTTCC
genomic: TAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACC-TTTTTTCAGgtaatagtat ... caacttttagGGTTGTACATGTGTTCCACTCCCTGTCCGTCCAAAAGCTTCATCACTTCC
EST: gi|5846886|gb|AI999969.1|AI999969
EST:     TAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCNNNNNNNCAG                         GGTTGTACATGTGTTCCACTTCCTGTCCGTCCAAAAGCTTCATCACTTCC
genomic: TAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACC-TTTTTTCAGgtaatagtat ... caacttttagGGTTGTACATGTGTTCCACTCCCTGTCCGTCCAAAAGCTTCATCACTTCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAGgtaatagtatattctttctactctatttttattggcaaggttcagttattgtctccttggaactataatcagttttctggttgccaacttttag

- - - - - - - - - -  AGCAAG
- - - - - - - - - - - GCAAGA
- - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - -  AGAAGT