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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCATACCCTCCTAAAAGGATTGGAGAAGATAGCTGTCAGTGCAGACATTCCTATGTTGGTCTGTGGAGATTTCAACTCAACCCCTGGGAGgtgcatctgcatttgaaaatcatggcaatatttaacaggttttattttttcttgaacaatggttgtctaagcacacaattgtacatttcag

Basic information

species Zea mays
transcript GRMZM2G118467_T03
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118467_T03 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os10g27230.1 (Oryza sativa), 5'ss of exon 9
GTTCATACCCTCCTAAAAGGATTGGAGAAGATAGCTGTCAGTGCAGACATTCCTATGTTGGTCTGTGGAGATTTCAACTCAACCCCTGGGAGgtgcatctgcatttgaaaatcatggcaatatttaacaggttttattttttcttgaacaatggttgtctaagcacacaattgtacatttcag
||||| || ||||||||||| ||||| || |||||||| ||||| |||||||| |||||||||||||| |||||||| |||  ||||||||||||  | |  || ||  | |||  | | ||||||   |||   ||| ||| |  ||| ||||   |||||| || ||||| | | ||||||
GTTCAAACTCTCCTAAAAGGGTTGGAAAAAATAGCTGTTAGTGCGGACATTCCAATGTTGGTCTGTGGGGATTTCAATTCAGTCCCTGGGAGgtgtgtataaatatgcta-tcactgtagtatttatttggtaaaattattt-tgaaaccatggacttctaagtactcaattatgc-tttcag

upper sequence: GRMZM2G118467_T03 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA02G26620.1 (Glycine max), 5'ss of exon 8
GTTCATACCCTCCTAAAAGGATTGGAGAAGATAGCTGTCAGTGCAGACATTCCTATGTTGGTCTGTGGAGATTTCAACTCAACCCCTGGGAGgtgcatctgcatttgaaaatcatggcaatattta-acaggttttattttttcttgaacaatggttgtctaagcacacaattgtacatttcag-----
|||||||| ||| ||||||| ||||| || |||||||  || ||||||||||| |||||||| ||||||||||| || |||   || || |||| | |||   | |     | |||  | |||||  |  | ||||||||| |  | |  |     | | ||     |  ||| |  | ||||      
GTTCATACTCTCTTAAAAGGGTTGGAAAAAATAGCTGCAAGCGCAGACATTCCGATGTTGGTTTGTGGAGATTTTAATTCAGTTCCAGGAAGgtacttctttttct-----ttatgtaattatttgtagtgtttttattttgtaataaggatcatatttttataatgattattttgaacttcattacag

upper sequence: GRMZM2G118467_T03 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA03G36550.1 (Glycine max), 5'ss of exon 8
GTTCATACCCTCCTAAAAGGATTGGAGAAGATAGCTGTCAGTGCAGACATTCCTATGTTGGTCTGTGGAGATTTCAACTCAACCCCTGGGAGgtgcatctgcatttgaaaatca----tggcaatatttaac------aggttttattttttcttgaacaatg-gttgtctaagcacacaattgtacatttcag---
|| || || ||| | |||||||||||||| || ||||  |||||||| ||||| |||||||| ||||| || || || ||||  || || ||||     | | |||    || |    |||  |  ||| |        ||| || | |     | || |||  |||   |||    |   |  ||  |  | |   
GTGCACACTCTCTTGAAAGGATTGGAGAAAATTGCTGCAAGTGCAGATATTCCAATGTTGGTTTGTGGGGACTTTAATTCAATTCCAGGAAGgtctgagtactttttttgattaactttggatacttttcatctgcaagggtcttttgtcagtatcaataatttgtttcttaaagttattttcttatttggctgtag

upper sequence: GRMZM2G118467_T03 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA09G15980.2 (Glycine max), 5'ss of exon 8
GTTCATACCCTCCTAAAAGGATTGGAGAAGATAGCTGTCAGTGCAGACATTCCTATGTTGGTCTGTGGAGATTTCAACTCAACCCCTGGGAGgtgcatctgcat-ttgaaaatcatggcaatatttaacaggttttattttttcttgaacaatggttgtctaagcacacaattgtacatttcag-----
|||||||| ||| ||||||| ||||| || |||||||  |||||||||||||| |||||||| ||||||||||| || |||   || || ||||       ||| ||     | |||  | |||||      |||| |||| |  | |  |     | | ||     |  ||| |  |  ||       
GTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCAAGTGCAGACATTCCGATGTTGGTTTGTGGAGATTTTAATTCAGTTCCGGGAAGgtttgatgacatctttttctttatgtaattatttttagttttttgttttgtaataaggatcatgtatttataatgattattttgaacatcgttgcag

upper sequence: GRMZM2G118467_T03 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA19G39210.1 (Glycine max), 5'ss of exon 8
GTTCATACCCTCCTAAAAGGATTGGAGAAGATAGCTGTCAGTGCAGACATTCCTATGTTGGTCTGTGGAGATTTCAACTCAACCCCTGGGAGgtgcatctgcatttgaa--aatcatggcaatatttaacaggttttattttttcttgaacaatggttgtctaag-cacacaattgtacatttcag---------
|| || || ||| | |||||||||||||| || |||| ||||||||||||||| |||||||| ||||| || || || ||||  || || ||||     | | |||  |  ||   |||  |  ||| |   |      | |||  | |  |    |  | |  | |  | | || |    ||            
GTGCACACTCTCTTGAAAGGATTGGAGAAAATTGCTGCCAGTGCAGACATTCCAATGTTGGTTTGTGGGGACTTTAATTCAATTCCAGGAAGgtctgattactttttgattaactttggatacttttcatctgcaagggtcttttgtcagtatcattaatttgcgtcttaaagttattttcttatttggctgtag

upper sequence: GRMZM2G118467_T03 (Zea mays), 5'ss of exon 9
lower sequence: AT3G58560.1 (Arabidopsis thaliana), 5'ss of exon 8
GTTCATACCCTCCTAAAAGGATTGGAGAAGATAGCTGTCAGTGCAGACATTCCTATGTTGGTCTGTGGAGATTTCAACTCAACCCCTGGGAGgtgcatctgcatttgaaa---atcatggcaatatttaacaggttttattttttcttgaacaatggttgt-----ctaagcacacaattgtacatttcag---------------
||||| ||  |  | || ||| ||||||| ||||||| ||||||||| ||||| ||| | || ||||||||||||||| ||   |||| |||||    |||  |||   |    | ||| | |  |   |   ||   | | | | || ||  ||| ||||     |||     |  |   |  | |||                 
GTTCACACATTATTGAAGGGACTGGAGAAAATAGCTGCCAGTGCAGATATTCCAATGCTTGTGTGTGGAGATTTCAACACAGTACCTGCGAGgtctggctggttttcctatttgttatgcccaagtagcaattgtcaaactctatattaaattatgattgtggtttctacctgaattaacttggagttccttcttaatattttcag

upper sequence: GRMZM2G118467_T03 (Zea mays), 5'ss of exon 9
lower sequence: Vv08s0007g07020.t01 (Vitis vinifera), 5'ss of exon 8
GTTCATACCCTCCTAAAAGGATTGGAGAAGATAGCTGTCAGTGCAGACATTCCTATGTTGGTCTGTGGAGATTTCAACTCAACCCCTGGGAGgtgcatctgcatttgaaaatcatggcaatatttaacaggttttattttttcttgaacaatggttgtctaagcacacaattgtacatttcag-----------------------------------------------
|||||||| ||| ||||||| ||||| || ||||||| ||||||||||||||| ||| |||| ||||| ||||| || |||   ||||| ||||   |||       |||||   |   ||   | || | |    |  | |  |      | |   | |  |   | | || |   ||||                                                 
GTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATTCCCATGCTGGTTTGTGGCGATTTTAATTCAGTTCCTGGAAGgtctgtctatgcactaaaatatagttgattgcttactgttccagtggtgttctagtttctagcactttgtgtg-aaagttatgtttttctagaaatgccatttcgcttatttgaaggtaattttgaaccttattgcag

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|32808456|gb|CD960690.1|CD960690
EST:     GCAGACATTCCTATGTTGGTCTGTGGAGATTTCAACTCAACCCCTGGGAG                         TTCTCCACATGCGCTTCTGGCAATGGGCAAAGTTGATCAGCATCATCCAGA
genomic: GCAGACATTCCTATGTTGGTCTGTGGAGATTTCAACTCAACCCCTGGGAGgtgcatctgc ... tacatttcagTTCTCCACATGCGCTTCTGGCAATGGGCAAAGTTGATCAGCATCATCCAGA
EST: gi|211192150|gb|FK946799.1|FK946799
EST:     GCAGACATTCCTATGTTGGTCTGTGGAGATTTCAACTCAACCCCTGGGAG                         TTCTCCACATGCGCTTCTGGCAATGGGCAAAGTTGATCAGCATCATCCAGA
genomic: GCAGACATTCCTATGTTGGTCTGTGGAGATTTCAACTCAACCCCTGGGAGgtgcatctgc ... tacatttcagTTCTCCACATGCGCTTCTGGCAATGGGCAAAGTTGATCAGCATCATCCAGA
EST: gi|211013492|gb|FL469772.1|FL469772
EST:     GCAGACATTCCTATGTT-GTCTGTGGAGATTTCAACTCAACCCCTGGGAG                         TTCTCCACATGCGCTTCTGGCAATGGGCAAAGTTGATCAGCATCATCCAGA
genomic: GCAGACATTCCTATGTTGGTCTGTGGAGATTTCAACTCAACCCCTGGGAGgtgcatctgc ... tacatttcagTTCTCCACATGCGCTTCTGGCAATGGGCAAAGTTGATCAGCATCATCCAGA
EST: gi|148934305|gb|EC878331.2|EC878331
EST:     CAACCCCTGGGAG                         TTCTCCACATGCGCTTCTGGCAATGGGCAAAGTTGATCAGCATCATCCAGA
genomic: CAACCCCTGGGAGgtgcatctgc ... tacatttcagTTCTCCACATGCGCTTCTGGCAATGGGCAAAGTTGATCAGCATCATCCAGA
EST: gi|60343893|gb|DN210866.1|DN210866
EST:     GCAGACATTCCTATGTTGGTCTGTGGAGATTTCAACTCAACCCCTGGGAG                         TTCTCCACATGCGCTTCTGGCAATGGGCAAAGTTGATCAGCATCATCCAGA
genomic: GCAGACATTCCTATGTTGGTCTGTGGAGATTTCAACTCAACCCCTGGGAGgtgcatctgc ... tacatttcagTTCTCCACATGCGCTTCTGGCAATGGGCAAAGTTGATCAGCATCATCCAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCATACCCTCCTAAAAGGATTGGAGAAGATAGCTGTCAGTGCAGACATTCCTATGTTGGTCTGTGGAGATTTCAACTCAACCCCTGGGAGgtgcatctgcatttgaaaatcatggcaatatttaacaggttttattttttcttgaacaatggttgtctaagcacacaattgtacatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT