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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atggtttggggatctagattaacatgattgaagcaacatggctcactggtatacgtaatccattatagaagctatggcttatatgtagccaatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGGTAGTTGTGCTGTGGACTGCAAACACTGAAAGGTACAGCAATGTATGTGCTGGTCTCAACGACACAATG

Basic information

species Zea mays
transcript GRMZM2G004528_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 4
atggtttggggatctagattaacatgattgaagcaacatggctcactggta--tacgtaatccatta-tagaagctatggcttatatgtagccaatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGGTAGTTGTGCTGTGGACTGCAAACACTGAAAGGTACAGCAATGTATGTGCTGGTCTCAACGACACAATG
 | |||   |  |||  ||||| ||| ||| | ||||||| |  ||| ||   || | |  |  | |  |  ||  |||   | | | |    | | ||| |||||||| ||||| |||| ||||||||||||||| || ||| |||||||||||||||||||||||||||||||||| |||| ||| ||||| |||||||||
-tagttccag--tctgcattaagatggttggaacaacatgacaaacttgtgactatgaatgctgtaaacattagacatgatattttttttattacttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGCAAACACTGAAAGGTACAGCAATGTCTGTGTTGGGCTCAATGACACAATG

upper sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA18G02210.2 (Glycine max), 3'ss of exon 4
atggtttggggatctagattaacatgattgaagcaacatggctcactggtatacgtaatccattatagaagctatggcttatatgtagccaatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGGTAGTTGTGCTGTGGACTGCAAACACTGAAAGGTACAGCAATGTATGTGCTGGTCTCAACGACACAATG
   || |  |   |||  | ||  |   |  |   ||||  |  ||    |||| | |||  | ||   |   | |   ||  ||| | ||   |  ||||| |||||||||    | ||||||||||||||| ||||| ||||||||||| ||||| || ||||| |||||| |   ||  || || || ||||| |||
---gtatatgt-cctatttcaatctacataca--tacata-catacatacatacatgatctgt-atcttattcaggttctaactgttgacatgaactcagGGCGTTTAAGGAAGCCACCAAAGTGGACAAGGTGGTTGTCCTGTGGACTGCCAACACAGAGAGGTATAGCAATTTGGTTGTAGGCCTTAATGACACCATG

upper sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 4
lower sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 4
----------------------------------------------------------------------------atggtttggggatctagattaacatgattgaagcaacatggctcactggtatacgtaatccattatagaagctatggc--ttatatgtagccaatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGGTAGTTGTGCTGTGGACTGCAAACACTGAAAGGTACAGCAATGTATGTGCTGGTCTCAACGACACAATG
                                                                             |   ||     |||    ||| ||     ||      | | |   |  |   ||||||   |   |||   | ||    | | |  |    ||  ||  |||||||| || ||||| ||||||||||| || || || || |||||||| |||||||| ||||| |||||||||||    | |||||| |||||||| | |
gtaacacaacgtctttactattgtaataaaatattctaaggtaacataacggtttatgtttattagcaaattaaatgtaaattttctctctgctataaaatttccaaaattcattagatgtatcatgatcgtaatttttacaagacaatttgataatgaaaattttaaaaataattagGGAGTTCAAAGAGAAAAACAAAGTGGATAAAGTGGTGGTACTGTGGACGGCAAACACAGAAAGATACAGCAATGTGGTGGTTGGTCTTAACGACACGACG

upper sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 4
lower sequence: AT2G22240.1 (Arabidopsis thaliana), 3'ss of exon 3
atggtttggggatctagattaacatgattgaagcaacatggctcac-tggtatacgtaatccattatagaagctatggcttatatgtagccaatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGGTAGTTGTGCTGTGGACTGCAAACACTGAAAGGTACAGCAATGTATGTGCTGGTCTCAACGACACAATG
                                | |    | || || | | | |  || |   |||   |   ||| | |  | | |    | |     ||||||||||||||||||||||||||||| ||| | |||||| | |||||||||||||| ||  | || ||||||||   ||  || || ||||| || | |
--------------------------------gtatatagtcttacatagcaaaattagttagttagttagtgtattgat-gtgtttgaatattt--ttagGGAGTTTAAGGAGAAGAACAAAGTGGATAAGTTGGTTGTGTTATGGACTGCAAACACAGAGCGTTATAGCAATGTGATTGTAGGACTTAACGATACGACG

upper sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 4
lower sequence: PP1S267_10V6.1 (Physcomitrella patens), 3'ss of exon 4
--atggtttggggatctaga-ttaacatgattgaagcaacatggctc-actggtatacgtaatccatt---atagaagc-tatg---gcttatatgtagccaatgaaa---cagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGGTAGTTGTGCTGTGGACTGCAAACACTGAAAGGTACAGCAATGTATGTGCTGGTCTCAACGACACAATG
  | ||  |  |  |||| | ||     ||      || | ||  || |  |   |||| ||     |   || || || | ||   ||| |  |  |  || ||  |   |||||| |||||||   ||||||| ||||||||| | ||||||||||||||||| ||||| ||| | |||||  ||||    | ||||||||| ||||| | |
gtagggcgtccgattctatacttcttccgagccctacagcctgtttctagagagttacggaaattgatcgcatcgatgcgtttgaatgctgaggtcaaaacattgtgattgcagGGACTTTAAGGCTCAGAACAAGGTGGACAAGATCGTTGTGCTGTGGACTGCTAACACCGAACGATACAGTGATGTGATCGTTGGTCTCAATGACACGAAG

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|211242966|gb|FL282599.1|FL282599
EST:     ATCAAGGGCACCAAGAAAGAACAGGTGGAGCAGATCATCAAAGATATCAG                         GGAGTTTAAGGAGAAGAACAAAGTGGACAAGGTAGTTGTGCTGTGGACTGC
genomic: ATCAAGGGCACCAAGAAAGAACAGGTGGAGCAGATCATCAAAGATATCAGgtattcggac ... aatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGGTAGTTGTGCTGTGGACTGC
EST: gi|211037209|gb|FK948218.1|FK948218
EST:     ATCAAGGGCACCAAGAAAGAACAGGTGGAGCAGATCATCAAAGATATCAG                         GGAGTTTAAGGAGAAGAACAAAGTGGACAAGGTAGTTGTGCTGTGGACTGC
genomic: ATCAAGGGCACCAAGAAAGAACAGGTGGAGCAGATCATCAAAGATATCAGgtattcggac ... aatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGGTAGTTGTGCTGTGGACTGC
EST: gi|13516068|gb|BG518344.1|BG518344
EST:     ATCAAGGGCACCAAGAAAGAACAGGTGGAGCAGATCATCAAAGATATCAG                         GGAGTTTAAGGAGAAGAACAAAGTGGACAAGGTAGTTGTGCTGTGGACTGC
genomic: ATCAAGGGCACCAAGAAAGAACAGGTGGAGCAGATCATCAAAGATATCAGgtattcggac ... aatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGGTAGTTGTGCTGTGGACTGC
EST: gi|31359455|gb|CD443812.1|CD443812
EST:     ATCAAGGGCACCAAGAAAGAACAGGTGGAGCAGATCATCAAAGATATCAG                         GGAGTTTAAGGAGAAGAACAAAGTGGACAAGGTAGTTGTGCTGTGGACTGC
genomic: ATCAAGGGCACCAAGAAAGAACAGGTGGAGCAGATCATCAAAGATATCAGgtattcggac ... aatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGGTAGTTGTGCTGTGGACTGC
EST: gi|31364344|gb|CD448699.1|CD448699
EST:     ATCAAGGGCACCAAGAAAGAACAGGTGGAGCAGATCATCAAAGATATCAG                         GGAGTTTAAGGAGAAGAACAAAGTGGACAAGGTAGTTGTGCTGTGGACTGC
genomic: ATCAAGGGCACCAAGAAAGAACAGGTGGAGCAGATCATCAAAGATATCAGgtattcggac ... aatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGGTAGTTGTGCTGTGGACTGC
EST: gi|60346856|gb|DN213829.1|DN213829
EST:     ATCAAGGGCACCAAGAAAGAACAGGTGGAGCAGATCATCAAAGATATCAG                         GGAGTTTAAGGAGAAGAACAAAGTGGACAAGGTAGTTGTGCTGTGGACTGC
genomic: ATCAAGGGCACCAAGAAAGAACAGGTGGAGCAGATCATCAAAGATATCAGgtattcggac ... aatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGGTAGTTGTGCTGTGGACTGC
EST: gi|211032313|gb|FK948194.1|FK948194
EST:     ATCAAGGGCACCAAGAAAGAACAGGTGGRGCAGATCATCAAAGATATCAG                         GGAGTTTAAGGAGAAGAACAAAGTGGACAAGGTAGTTGTGCTGTGGACTGC
genomic: ATCAAGGGCACCAAGAAAGAACAGGTGGAGCAGATCATCAAAGATATCAGgtattcggac ... aatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGGTAGTTGTGCTGTGGACTGC
EST: gi|67029746|gb|CO458495.1|CO458495
EST:     ATCAAGGGCACCAAGAAAGAACAGGTGGAGCAGATCATCAAGGATATCAG                         GGAGTTTAAGGAGAAGAACAAAGTGGACAAGGTAGTTGTGCTGTGGACTGC
genomic: ATCAAGGGCACCAAGAAAGAACAGGTGGAGCAGATCATCAAAGATATCAGgtattcggac ... aatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGGTAGTTGTGCTGTGGACTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggtatacgtaatccattatagaagctatggcttatatgtagccaatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGGTAGTTGTGCTGTGGACTGCAAACACTGAAAGGTACAGCAATGTATGTGCTGGTCTCAACGACACAATG
                attatagaa  TA-rich tract