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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttatttgtttgctcagggagttcatgtttgctatttcagtatgatatttttcagagacatacttttcgtcatatgcttcactttatttgaacattccagTCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCTGAATGGATACACCCCACCCAATAAAGAG

Basic information

species Zea mays
transcript GRMZM2G170291_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G170291_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g18200.1 (Oryza sativa), 3'ss of exon 4
tttatttgtttgctcagggagttcatgtttgctattt-cagtatgatatttttcagagacatacttttcgtcatatgcttcactt-tatttgaa-cattccagTCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCTGAATGGATACACCCCACCCAATAAAGAG
      | |||||| |     |  ||  |    ||   |    ||| |  || || | ||   | ||   ||  || |||  ||| ||||||||  ||| |||||||||||||||||| || |||||||||||||| |||||||| ||||| || |||||||||| ||| || |||||||||
--ctcatatttgct-acaccatgaatagtaataatccactacttgacaccttccataaaccagccttagctctaatactttgcttgtatttgaaatatttcagTCATGAAGAAATCGATGTTAGCCATCCTGATTTTTTTAGCAGTGCTAAACTCAATGGATACATCCCTCCAAATAAAGAG
















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|78105400|gb|DV523818.1|DV523818
EST:     GTTCAACACGTGGATAAACCCTTAATCTGGTGTGGGGACTTGAATGTCAG                         TCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
genomic: GTTCAACACGTGGATAAACCCTTAATCTGGTGTGGGGACTTGAATGTCAGgtaatcgtga ... aacattccagTCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
EST: gi|76021195|gb|DT948365.1|DT948365
EST:     GTTCAACACGTGGATAAACCCTTAATCTGGTGTGGGGACTTGAATGTCAG                         TCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
genomic: GTTCAACACGTGGATAAACCCTTAATCTGGTGTGGGGACTTGAATGTCAGgtaatcgtga ... aacattccagTCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
EST: gi|91872354|gb|EB402311.1|EB402311
EST:     GTTCAACACGTGGATAAACCCTTAATCTGGTGTGGGGACTTGAATGTCAG                         TCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
genomic: GTTCAACACGTGGATAAACCCTTAATCTGGTGTGGGGACTTGAATGTCAGgtaatcgtga ... aacattccagTCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
EST: gi|76010860|gb|DT938030.1|DT938030
EST:     GTTCAACACGTGGATAAACCCTTAATCTGGTGTGGGGACTTGAATGTCAG                         TCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
genomic: GTTCAACACGTGGATAAACCCTTAATCTGGTGTGGGGACTTGAATGTCAGgtaatcgtga ... aacattccagTCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
EST: gi|149095617|gb|EE168978.2|EE168978
EST:     GTTCAACACGTGGATAAACCCTTAATCTGGTGTGGGGACTTGAATGTCAG                         TCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
genomic: GTTCAACACGTGGATAAACCCTTAATCTGGTGTGGGGACTTGAATGTCAGgtaatcgtga ... aacattccagTCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
EST: gi|76018500|gb|DT945670.1|DT945670
EST:     GTTCAACACGTGGATAAACCCTTAATCTGGTGTGGGGACTTGAATGTCAG                         TCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
genomic: GTTCAACACGTGGATAAACCCTTAATCTGGTGTGGGGACTTGAATGTCAGgtaatcgtga ... aacattccagTCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
EST: gi|76016190|gb|DT943360.1|DT943360
EST:     GGGACTTGAATGTCAG                         TCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
genomic: GGGACTTGAATGTCAGgtaatcgtga ... aacattccagTCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
EST: gi|71771442|gb|DR969379.1|DR969379
EST:     GTTCAACACGTGGATAAACCCTTAATCTGGTGTGGGGACTTGAATGTCAG                         TCATGAAGAAATCGACCTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
genomic: GTTCAACACGTGGATAAACCCTTAATCTGGTGTGGGGACTTGAATGTCAGgtaatcgtga ... aacattccagTCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
EST: gi|50332549|gb|CO527675.1|CO527675
EST:     GGTGTGGGGACTTGAATGTCAG                         TCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
genomic: GGTGTGGGGACTTGAATGTCAGgtaatcgtga ... aacattccagTCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
EST: gi|76014034|gb|DT941204.1|DT941204
EST:     GTTCAACACGTGGATAAACCCTTAATCTGGTGTGGGGACTTGAATGTCAG                         TCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
genomic: GTTCAACACGTGGATAAACCCTTAATCTGGTGTGGGGACTTGAATGTCAGgtaatcgtga ... aacattccagTCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
EST: gi|91872355|gb|EB402312.1|EB402312
EST:     GTTCAACACGTGGATAAACCCTTAATCTGGTGTGGGGACTTGAATGTCAG                         TCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
genomic: GTTCAACACGTGGATAAACCCTTAATCTGGTGTGGGGACTTGAATGTCAGgtaatcgtga ... aacattccagTCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
EST: gi|84980468|gb|DW530817.1|DW530817
EST:     GTTCAACACGTGGATAAACCCTTAATCTGGTGTGGGGACTTGAATGTCAG                         TCATGAAGAAATCGACGTCAGCCATCCTGA
genomic: GTTCAACACGTGGATAAACCCTTAATCTGGTGTGGGGACTTGAATGTCAGgtaatcgtga ... aacattccagTCATGAAGAAATCGACGTCAGCCATCCTGA
EST: gi|74236587|gb|DT644501.1|DT644501
EST:     GTTCAACACGTGGATAAACCCTTAATCTGGTGTGGGGACTTGAATGTCAG                         TCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
genomic: GTTCAACACGTGGATAAACCCTTAATCTGGTGTGGGGACTTGAATGTCAGgtaatcgtga ... aacattccagTCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
EST: gi|78105399|gb|DV523817.1|DV523817
EST:     GGGACTTGAATGTCAG                         TCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
genomic: GGGACTTGAATGTCAGgtaatcgtga ... aacattccagTCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
EST: gi|211321950|gb|FK966256.1|FK966256
EST:     GTTCAACACGTGGATAAACCCTTAATCTGGTGTGGGGACTTGAATGTCAG                         TCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
genomic: GTTCAACACGTGGATAAACCCTTAATCTGGTGTGGGGACTTGAATGTCAGgtaatcgtga ... aacattccagTCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
EST: gi|60351954|gb|DN218927.1|DN218927
EST:     TCAACACGTGGATAAACCCTTAATCTGGTGTGGGGACTTGAATGTCAG                         TCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
genomic: TCAACACGTGGATAAACCCTTAATCTGGTGTGGGGACTTGAATGTCAGgtaatcgtga ... aacattccagTCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
EST: gi|76016191|gb|DT943361.1|DT943361
EST:     GTTCAACACGTGGATAAACCCTTAATCTGGTGTGGGGACTTGAATGTCAG                         TCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
genomic: GTTCAACACGTGGATAAACCCTTAATCTGGTGTGGGGACTTGAATGTCAGgtaatcgtga ... aacattccagTCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
EST: gi|74236588|gb|DT644502.1|DT644502
EST:     GTTCCACACGTGGATAAACCCTTAATCTGGTGTGGGGACTTGAATGTCAG                         TCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
genomic: GTTCAACACGTGGATAAACCCTTAATCTGGTGTGGGGACTTGAATGTCAGgtaatcgtga ... aacattccagTCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
EST: gi|18661354|gb|BM501369.1|BM501369
EST:     GTTCAACACGTGGATAAACCCTTAATCTGGTGTGGGGACTTGAATGTCAG                         TCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
genomic: GTTCAACACGTGGATAAACCCTTAATCTGGTGTGGGGACTTGAATGTCAGgtaatcgtga ... aacattccagTCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
EST: gi|60356095|gb|DN223068.1|DN223068
EST:     CTGGTGTGGGGACTTGAATGTCAG                         TCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
genomic: CTGGTGTGGGGACTTGAATGTCAGgtaatcgtga ... aacattccagTCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCT
EST: gi|76010861|gb|DT938031.1|DT938031
EST:     TTCAACACGTGGATAAACCCTTAATCTGGTGTGGGGACTTTGA-TGTCAG                         TCATGAAGAAATCGACGTCAGCCATCC
genomic: TTCAACACGTGGATAAACCCTTAATCTGGTGTGGGGACTT-GAATGTCAGgtaatcgtga ... aacattccagTCATGAAGAAATCGACGTCAGCCATCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttttcagagacatacttttcgtcatatgcttcactttatttgaacattccagTCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCTGAATGGATACACCCCACCCAATAAAGAG
                                     tttatttgaacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttatttgtttgctcagggagttcatgtttgctatttcagtatgatatttttcagagacatacttttcgtcatatgcttcactttatttgaacattccagTCATGAAGAAATCGACGTCAGCCATCCTGATTTCTTTAGCAGCGCTAAGCTGAATGGATACACCCCACCCAATAAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA