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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcaacgttgtctaaattatgtccctgacttccttgtatagttatattcataccggatttgactgcccccattcatatgagctaactgaaaattttatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTACACTGTAACACTGTTTGCTAAGGTTGTTGACAATTTTAAGGTCCGTGCTC

Basic information

species Zea mays
transcript GRMZM2G128995_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128995_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g51530.1 (Oryza sativa), 3'ss of exon 6
---gtcaacgttgtctaaattatgtccctgacttccttgtatagttatattcataccggatttgactgcccccattcatatgagctaactgaaaattttatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTACACTGTAACACTGTTTGCTAAGGTTGTTGACAATTTTAAGGTCCGTGCTC
   ||     ||  |   | ||  |       |   | ||||   ||  |   |     |||||| |||     | | |  || |||| |    |||| ||||||||| || || |||||||| || ||||| |||||||| |||||||||||||| |||||| |||||||||||||||||||||| |||||||||||||| |
cttgtttttttttccagcactacatgttgatgtgattagtattcgtaattggttgttatatttgagtgcttttttcctt--gaactaattattgattt-atagGTACCGAGATCGTCTAAAAAACTTTATGAGGACAATGAGTATGCTCTCTACACGGTAACATTGTTTGCTAAGGTTGTTGACAACTTTAAGGTCCGTGCAC

upper sequence: GRMZM2G128995_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA19G27360.1 (Glycine max), 3'ss of exon 6
gtcaacgttgtctaaattatgtccctgacttccttgtatagttatattcataccggatttgactgcccccattcatat----gagctaactga---aaattttatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTACACTGTAACACTGTTTGCTAAGGTTGTTGACAATTTTAAGGTCCGTGCTC
        | |   ||| ||||   ||||    ||| ||| ||||   ||| | |  |||    ||     | | |||       || | |     |||| || ||||| || ||||| ||||| ||| | ||||| || |||||||||||||| || ||||||||||| ||   |   ||||  || |||||||      |||| |
-------atattccaatgatgtttttgacactattgaataattatgagcatgctgttttttctagctttattccttattctgattcttattaggataaatgttttagGTCCCCAGGTCTTCTAAGAAGTTGTATGAGGATAATGAATATGCTCTTTATACTGTAACACTCTTCAGTCGTGTTGCGGATAATTTTAGAACTAGTGCAC

upper sequence: GRMZM2G128995_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv17s0000g00460.t01 (Vitis vinifera), 3'ss of exon 6
---gtcaacgttgtctaaatta-tgtccctgacttccttgtatagttatattcataccggatttgactgcccccattcatatgagctaactgaaaattttatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTACACTGTAACACTGTTTGCTAAGGTTGTTGACAATTTTAAGGTCCGTGCTC
    |  || |||| ||| ||| |||              |  |  | | ||| |      ||  |        | |||| |||   ||||   |||||| ||||| || |||||||| || ||| |  | || |||||||||||||||||||| ||||||||  | |||| |   |||| |||||||||||||    | || |
atgctttactttgtttaagttaatgtttaaagtaataaaattcaccttttttcttttgaagttgaataaattttactcat-tgactgaact---aattttttagGTCCCCAGGTCATCCAAGAAGTTGCACGAGGACAATGAATATGCTCTCTATACTGTAACTATATTTGGTCGTGTTGCTGACAATTTTAAGACTAGCGCAC

upper sequence: GRMZM2G128995_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv14s0068g01280.t01 (Vitis vinifera), 3'ss of exon 6
----------------------------------------------------------------------------------------gt-caacgttgtctaaattatgtccctgacttccttgtatagttatattcataccggatttgactgcccccattcatatgagctaactgaaaattttatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTACACTGTAACACTGTTTGCTAAGGTTGTTGACAATTTTAAGGTCCGTGCTC
                                                                                        ||   | ||  |     |||  |  |||   |  ||| |||  | | ||          || | ||    | | |  || |  | |   ||  | ||  |||| || |||||||| || |||||  ||||||||||||| |||||||| ||||||||||| ||||||      |||| |||||||||||       ||| |
gtaagaactattttttctggctatatattctaacttaagcgaattatggtcctgaagatatcatctgcagtaggttggtaactggctcgtgtgatgtcataccttttaaatttctggagtatttgaatacat-tgtttgactttttgttcattgtaatcttcctgattaattgagctaacctctttcagGTCCCCAGGTCATCCAAGAAGCTGCATGAAGACAATGAGTATGCTCTATACACTGTAACCCTGTTTCACCGTGTTGCTGACAATTTTAGAACAAATGCAC

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|32907249|gb|CF012062.1|CF012062
EST:     ACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTG                         GTACCTAGGTCCTCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
genomic: ACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTGgtaaggttaa ... aattttatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
EST: gi|19351863|gb|BM896395.1|BM896395
EST:     ACTCCCAAAAAGACTGGTTGTCA-GCTATGAGAAAATTGACACATTCGTG                         GTACCTAGGTCCTCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
genomic: ACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTGgtaaggttaa ... aattttatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
EST: gi|40334835|gb|CK368905.1|CK368905
EST:     CCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTG                         GTACCTAGGTCCTCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
genomic: CCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTGgtaaggttaa ... aattttatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
EST: gi|60358961|gb|DN225934.1|DN225934
EST:     ACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTG                         GTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
genomic: ACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTGgtaaggttaa ... aattttatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
EST: gi|22491457|gb|BU051380.1|BU051380
EST:     ACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTG                         GTACCTAGGTC
genomic: ACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTGgtaaggttaa ... aattttatagGTACCTAGGTC
EST: gi|78076481|gb|DV504915.1|DV504915
EST:     AAGCTATGAGAAAATTGACACATTCGTG                         GTACNTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
genomic: AAGCTATGAGAAAATTGACACATTCGTGgtaaggttaa ... aattttatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
EST: gi|67013699|gb|CO442448.1|CO442448
EST:     ACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTG                         GTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
genomic: ACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTGgtaaggttaa ... aattttatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
EST: gi|71427969|gb|DR809019.1|DR809019
EST:     AATTGACACATTCGTG                         GTCCCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
genomic: AATTGACACATTCGTGgtaaggttaa ... aattttatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcataccggatttgactgcccccattcatatgagctaactgaaaattttatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTACACTGTAACACTGTTTGCTAAGGTTGTTGACAATTTTAAGGTCCGTGCTC
                                  agctaac  putative branch site (score: 2)
                                     taactgaaaattttat  TA-rich tract