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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGAGCTTGCTGCTATTTTCAAGAAAATTGGTGACAAGCAAACATGTACCATTGGCCTCTATGAACTGTATCGGATAACTCAGCTCTACCCAAAGgtattattcctagtgtacttccacattaacattcgtattcctttggggaactatttgtaaaatggcggtcttcattgcagattttaatcatgcactttgcatgttttcattgcaagtgttttgtttattgagcattctttcctgtttacaatctgatctgccatcattatctcag

Basic information

species Zea mays
transcript GRMZM2G068755_T01
intron # 50
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068755_T01 (Zea mays), 5'ss of exon 50
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 49
CAAGAGCTTGCTGCTATTTTCAAGAAAATTGGTGACAAGCAAACATGTACCATTGGCCTCTATGAACTGTATCGGATAACTCAGCTCTACCCAAAGgta--ttattcctagtgtacttccacattaacattcgtattcctttggggaactatttgtaaaatggcggtcttcattgcagatt-ttaatcatgcactttgcatgttttcattgcaagtgttttgtttattgagcattctttcctgtttacaatctgatctgccatcattatctcag
||||||||||||||| | |||||||||||||||||||| ||||||||||| ||||| || |||||||| || |||||||| || || ||||| ||||||  |||||| | ||| |  | ||   | |  ||  |||          || || |||  |      |||| |   | ||  || || ||| | ||| | |      |  ||  |||||                                                          
CAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAGgtatattattcatcgtgaaagtgcaacatgatgtt-atat---------aaagtaattgcca------ggtcctg--tacaatttgttcatctttcacctggtcctggtggat--caagt----------------------------------------------------------

upper sequence: GRMZM2G068755_T01 (Zea mays), 5'ss of exon 50
lower sequence: GLYMA10G35140.1 (Glycine max), 5'ss of exon 52
CAAGAGCTTGCTGCTATTTTCAAGAAAATTGGTGACAAGCAAACATGTACCATTGGCCTCTATGAACTGTATCGGATAACTCAGCTCTACCCAAAGgtatta-ttcctagtgtacttccacattaacattcgtattcctttggggaactatttgtaaaatggcggtcttcattgcagattttaatcatgcactttgcatgttttcattgcaagtgttttgtttattgagcattctttcctgtttacaatctgatctgccatcattatctcag
||||||||||||||||| || ||||| ||||| || |||||||| || || ||||| || |||||||| |||||||| || ||  | ||||||||||||  | ||  | || || ||    |||       | |         | || ||      ||| |     | |   |    |||||  |  |    || | | |     | || |||                                                           
CAAGAGCTTGCTGCTATATTTAAGAAGATTGGAGAGAAGCAAACTTGCACAATTGGTCTATATGAACTATATCGGATTACCCAATTGTACCCAAAGgtaagaattaatggtatatttg---attgggg---gaa-------aagaaaataaagaagaaaggaaacacattgctatgcattttc-ttgtttggttggtaaga---aagtggaag-----------------------------------------------------------

upper sequence: GRMZM2G068755_T01 (Zea mays), 5'ss of exon 50
lower sequence: GLYMA20G32430.1 (Glycine max), 5'ss of exon 51
CAAGAGCTTGCTGCTATTTTCAAGAAAATTGGTGACAAGCAAACATGTACCATTGGCCTCTATGAACTGTATCGGATAACTCAGCTCTACCCAAAGgtatta-ttcctagtgtacttccacattaacattcgtattcctttggggaactatttgtaaaatggcggtcttcattgcagattttaatcatgcactttgcatgttttcattgcaagtgttttgtttattgagcattctttcctgtttacaatctgatctgccatcattatctcag
|||||||| |||||||| || ||||| ||||| || |||||||| || || ||||| || |||||||| ||||| || || ||  | ||||||||||||  | ||  | ||||| ||  |       |   | |       ||| ||  |     | | ||  |   ||  |||     ||     | | |  | | |                                                                          
CAAGAGCTGGCTGCTATATTTAAGAAGATTGGGGAGAAGCAAACTTGCACAATTGGTCTATATGAACTATATCGTATTACCCAATTGTACCCAAAGgtaagaattaatggtgta-tttgattgggggaaaagaaaataaaagggaaaggaaacacatagtgatgtattttcttgtttggttgg--taagaaagtggaag-------------------------------------------------------------------------

upper sequence: GRMZM2G068755_T01 (Zea mays), 5'ss of exon 50
lower sequence: Vv00s0652g00030.t01 (Vitis vinifera), 5'ss of exon 21
CAAGAGCTTGCTGCTATTTTCAAGAAAATTGGTGACAAGCAAACATGTACCATTGGCCTCTATGAACTGTATCGGATAACTCAGCTCTACCCAAAGgta--ttatt-----cctagtgtacttccacattaacattcgtattcctttggggaactatttgtaaaatggcggtcttcattgcagattttaatcatgcactttgcatgttttcattgcaagtgttttgtttattgagcattctttcctgtttacaatctgatctgccatcattatctcag
|| || ||||||||||| ||||||||||||||||||||||||||||| || |||||  | |||||||| || || || ||||| || ||||| ||||||   |||      | | || ||  |  | |  ||  ||          | |       ||||| |  |||  |   ||    || |  ||  | |  || |    || | || |||  |  | | ||   | |  |      || || |     ||  | || ||  ||   ||| ||||
CAGGAACTTGCTGCTATATTCAAGAAAATTGGTGACAAGCAAACATGCACTATTGGTTTATATGAACTATACCGTATTACTCAACTGTACCCCAAGgtaaactataaattgcatggtatatgtttaaaagaagtttaagtagtgaatagcatgaggtttgttat-tggttgagctcgggccaaagattgctaacacaatg---atctcttaattagatctatctt-cctgtctactgcatttgccaga----aagttaatttgtgatttctatttcag

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|6095379|gb|AW120046.1|AW120046
EST:     GGATAACTCAGCTCTACCCAAAG                         GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCGTTTAGAACCTAT
genomic: GGATAACTCAGCTCTACCCAAAGgtattattcc ... attatctcagGTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCGTTTAGAACCTAT
EST: gi|93014606|gb|EB640126.1|EB640126
EST:     GTACCATTGGCCTCTATGAACTGTATCGGATAACTCAGCTCTACCCAAAG                         GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCGTTTAGAACCTAT
genomic: GTACCATTGGCCTCTATGAACTGTATCGGATAACTCAGCTCTACCCAAAGgtattattcc ... attatctcagGTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCGTTTAGAACCTAT
EST: gi|26456806|gb|CA828389.1|CA828389
EST:     GTACCATTGGCCTCTATGAACTGTATCGGATAACTCAGCTCTACCCAAAG                         GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCGTTTAGAACCTAT
genomic: GTACCATTGGCCTCTATGAACTGTATCGGATAACTCAGCTCTACCCAAAGgtattattcc ... attatctcagGTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCGTTTAGAACCTAT
EST: gi|20512828|gb|BQ280026.1|BQ280026
EST:     GTACCATTGGCCTCTATGAACTGTATCGGATAACTCAGCTCTACCCAAAG                         GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCGTTTAGAACCTAT
genomic: GTACCATTGGCCTCTATGAACTGTATCGGATAACTCAGCTCTACCCAAAGgtattattcc ... attatctcagGTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCGTTTAGAACCTAT
EST: gi|37424588|gb|CF650027.1|CF650027
EST:     GTACCATTGGCCTCTATGAACTGTATCGGATAACTCAGCTCTACCCAAAG                         GTTGATATATTTGCTCAGCTTCAAAATGCTAGTGAAGCGTTTAGAACCTAT
genomic: GTACCATTGGCCTCTATGAACTGTATCGGATAACTCAGCTCTACCCAAAGgtattattcc ... attatctcagGTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCGTTTAGAACCTAT
EST: gi|71444352|gb|DR825402.1|DR825402
EST:     GTACCATTGGCCTCTATGAACTGTATCGGATAACTCAGCTCTACCCAAAG                         GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCGTTTAGAACCTAT
genomic: GTACCATTGGCCTCTATGAACTGTATCGGATAACTCAGCTCTACCCAAAGgtattattcc ... attatctcagGTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCGTTTAGAACCTAT
EST: gi|67015335|gb|CO444084.1|CO444084
EST:     GTACCATTGGCCTTTATGAACTGTATCGGATAACTCAGCTCTACCCAAAG                         GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCGTTTAGAACCTAT
genomic: GTACCATTGGCCTCTATGAACTGTATCGGATAACTCAGCTCTACCCAAAGgtattattcc ... attatctcagGTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCGTTTAGAACCTAT
EST: gi|60395928|gb|DN228798.1|DN228798
EST:     GTACCATTGGCCTCTATGAACTGTATCGGATAACTCAGCTCTACCCAAAG                         GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCGTTTAGAACCTAT
genomic: GTACCATTGGCCTCTATGAACTGTATCGGATAACTCAGCTCTACCCAAAGgtattattcc ... attatctcagGTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCGTTTAGAACCTAT
EST: gi|71444353|gb|DR825403.1|DR825403
EST:     GTACCATTGGCCTCTATGAACTGTATCGGATAACTCAGCTCTACCCAAAG                         GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCGTTTAGAACCTAT
genomic: GTACCATTGGCCTCTATGAACTGTATCGGATAACTCAGCTCTACCCAAAGgtattattcc ... attatctcagGTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCGTTTAGAACCTAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGAGCTTGCTGCTATTTTCAAGAAAATTGGTGACAAGCAAACATGTACCATTGGCCTCTATGAACTGTATCGGATAACTCAGCTCTACCCAAAGgtattattcctagtgtacttccacattaacattcgtattcctttggggaactatttgtaaaatggcggtcttcattgcagattttaatcatgcactttgcatgttttcattgcaagtgttttgtttattgagcattctttcctgtttacaatctgatctgccatcattatctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC