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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taccgaccagcccgactaatcgcgattaatcgcgattagtcggacgacttgaaatcattgattgtaatcatagattctagtcttgactggactcctgcagACCTTGCAGATCGACGATTTAAAACTCAGCGAAATTGGGCCTAAATTTGAGCATCATGAAATGTTTCCTGCTCGCACAAACACAG

Basic information

species Zea mays
transcript GRMZM2G130332_T04
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130332_T04 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os12g37960.1 (Oryza sativa), 3'ss of exon 5
--taccgaccagcccgactaatcgcgattaatcgcgattagtcggacgacttgaaatcattgattgtaatcatagattctagtcttgactggactcctgcagACCTTGCAGATCGACGATTTAAAACTCAGCGAAATTGGGCCTAAATTTGAGCATCATGAAATGTTTCCTGCTCGCACAAACACAG
   |        |     |  | |   |  ||      ||| |   | |  |  |  |  |   | |||| ||  ||| | |||||| |||||      |||   |||||  | || |||||||| || || || |||||||||||||| ||||||||||||||||||||||| ||||| |||||||
gtgattaggttcctgtgttgtttgaactgtatatatcctagcctatccaggtccaggctgtccatataataatttattgttgtcttggctggaaaa--acagGTTTTGCATGTTGATGATTTAAAGCTTAGTGATATTGGGCCTAAATTCGAGCATCATGAAATGTTTCCTGCCCGCACCAACACAG

upper sequence: GRMZM2G130332_T04 (Zea mays), 3'ss of exon 5
lower sequence: Vv08s0040g02540.t01 (Vitis vinifera), 3'ss of exon 5
---taccgaccagcccgactaatcgcgattaat-cgcgattagtc--ggacgacttgaaatcattgattgtaatcatagattctagtcttgactggactcctgcagACCTTGCAGATCGACGATTTAAAACTCAGCGAAATTGGGCCTAAATTTGAGCATCATGAAATGTTTCCTGCTCGCACAAACACAG
    |  ||  |   | | ||   |    ||||     |||  ||  |  |  ||     ||| ||||| |  |  |  ||||     ||   || | |    ||||  |||||| | || || |||||  |    || ||||| || ||||||||||||||||  |||||||||||||| || || ||||
aaacatggatta-ttctattatatgtacataatatattatttttcttgttcatctgactgtcactgatttt--ttctctattc---ctttatgtgcaattgatcagAATTTGCAGGTTGATGAATTAAATTTAGCTGACATTGGTCCAAAATTTGAGCATCATGCTATGTTTCCTGCTCGAACTAATACAG
















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|71329026|gb|DR801212.1|DR801212
EST:     TTAGCATGGGCAACCCCCACTGTGTCACATTTGGGGCAAACGAGTTAAAG                         ACCTTGCAGATCGACGATTTAAAACTCAGCGAAATTGGGCCTAAATTTGAG
genomic: TTAGCATGGGCAACCCCCACTGTGTCACATTTGGGGCAAACGAGTTAAAGgtaatcagct ... actcctgcagACCTTGCAGATCGACGATTTAAAACTCAGCGAAATTGGGCCTAAATTTGAG
EST: gi|74233526|gb|DT641440.1|DT641440
EST:     TTAGCATGGGCAACCCCCACTGTGTCACATTTGGGGCAAACGAGTTAAAG                         ACCTTGCAGATCGACGATTTAAAACTCAGCGAAATTGGGCCTAAATTTGAG
genomic: TTAGCATGGGCAACCCCCACTGTGTCACATTTGGGGCAAACGAGTTAAAGgtaatcagct ... actcctgcagACCTTGCAGATCGACGATTTAAAACTCAGCGAAATTGGGCCTAAATTTGAG
EST: gi|71324621|gb|DR799009.1|DR799009
EST:     TTAGCATGGGCAACCCCCACTGTGTCACATTTGGGGCAAACGAGTTAAAG                         ACCTTGCAGATCGACGATTTAAAACTCAGCGAAATTGGGCCTAAATTTGAG
genomic: TTAGCATGGGCAACCCCCACTGTGTCACATTTGGGGCAAACGAGTTAAAGgtaatcagct ... actcctgcagACCTTGCAGATCGACGATTTAAAACTCAGCGAAATTGGGCCTAAATTTGAG
EST: gi|148970899|gb|EE021693.2|EE021693
EST:     TTAGCATGGGCAACCCCCACTGTGTCACATTTGGGGCAAACGAGTTAAAG                         ACCTTGCAGATCGACGATTTAAAACTCAGCGAAATTGGGCCTAAATTTGAG
genomic: TTAGCATGGGCAACCCCCACTGTGTCACATTTGGGGCAAACGAGTTAAAGgtaatcagct ... actcctgcagACCTTGCAGATCGACGATTTAAAACTCAGCGAAATTGGGCCTAAATTTGAG
EST: gi|78088914|gb|DV517307.1|DV517307
EST:     TTAGCATGGGCAACCCCCACTGTGTCACATTTGGGGCAAACGAGTTAAAG                         ACCTTGCAGATCGACGATTTAAAACTCAGCGAAATTGGGCCTAAATTTGAG
genomic: TTAGCATGGGCAACCCCCACTGTGTCACATTTGGGGCAAACGAGTTAAAGgtaatcagct ... actcctgcagACCTTGCAGATCGACGATTTAAAACTCAGCGAAATTGGGCCTAAATTTGAG
EST: gi|76014966|gb|DT942136.1|DT942136
EST:     TTAGCATGGGCAACCCCCACTGTGTCACATTTGGGGCAAACGAGTTAAAG                         A--T--C-GA-CGA---TTTAAAACTCAGCGAAATTGGGCCTAAATTTGAG
genomic: TTAGCATGGGCAACCCCCACTGTGTCACATTTGGGGCAAACGAGTTAAAGgtaatcagct ... actcctgcagACCTTGCAGATCGACGATTTAAAACTCAGCGAAATTGGGCCTAAATTTGAG
EST: gi|71769300|gb|DR967237.1|DR967237
EST:     TTAGCATGGGCAACCCCCACTGTGTCACATTTGGGGCAAACGAGTTAAAG                         ACCTTGCAGATCGACGATTTAAAACTCAGCGAAATTGGGCCTAAATTTGAG
genomic: TTAGCATGGGCAACCCCCACTGTGTCACATTTGGGGCAAACGAGTTAAAGgtaatcagct ... actcctgcagACCTTGCAGATCGACGATTTAAAACTCAGCGAAATTGGGCCTAAATTTGAG
EST: gi|71443835|gb|DR824885.1|DR824885
EST:     TTAGCATGGGCAACCCCCACTGTGTCACATTTGGGGCAAACGAGTTAAAG                         ACCTTGCAGATCGACGATTTAAAACTCAGCGAAATTGGGCCTAAATTTGAG
genomic: TTAGCATGGGCAACCCCCACTGTGTCACATTTGGGGCAAACGAGTTAAAGgtaatcagct ... actcctgcagACCTTGCAGATCGACGATTTAAAACTCAGCGAAATTGGGCCTAAATTTGAG
EST: gi|101383177|gb|EB813643.1|EB813643
EST:     TTAGCATGGGCAACCCCCACTGTGTCACATTTGGGGCAAACGAGTTAAAG                         ACCTTGCAGATCGACGATTTAA
genomic: TTAGCATGGGCAACCCCCACTGTGTCACATTTGGGGCAAACGAGTTAAAGgtaatcagct ... actcctgcagACCTTGCAGATCGACGATTTAA
EST: gi|76017579|gb|DT944749.1|DT944749
EST:     TTAGCATGGGCAACCCCCACTGTGTCACATTTGGGGCAAACGAGTTAAAG                         ACCTTGCAGATCGACGATTTAAAACTCAGCGAAATTGGGCCTAAATTTGAG
genomic: TTAGCATGGGCAACCCCCACTGTGTCACATTTGGGGCAAACGAGTTAAAGgtaatcagct ... actcctgcagACCTTGCAGATCGACGATTTAAAACTCAGCGAAATTGGGCCTAAATTTGAG
EST: gi|148961806|gb|EE012586.2|EE012586
EST:     TTAGCATGGGCAACCCCCACTGTGTCACATTTGGGGCAAACGAGTTAAAG                         AACTTGCAGATCGACGATTTAAAACTCAGCGAAATTGGGCCTAAATTTGAG
genomic: TTAGCATGGGCAACCCCCACTGTGTCACATTTGGGGCAAACGAGTTAAAGgtaatcagct ... actcctgcagACCTTGCAGATCGACGATTTAAAACTCAGCGAAATTGGGCCTAAATTTGAG
EST: gi|24773782|gb|CA409036.1|CA409036
EST:     TTAGCATGGGCAACCCCCACTGTGTCACATTTGGGGCAAACGAGTTAAAG                         ACCTTGCAGATCGACGATTTAAAACTCAGCGAAATTGGGCCTAAATTTGAG
genomic: TTAGCATGGGCAACCCCCACTGTGTCACATTTGGGGCAAACGAGTTAAAGgtaatcagct ... actcctgcagACCTTGCAGATCGACGATTTAAAACTCAGCGAAATTGGGCCTAAATTTGAG
EST: gi|211026296|gb|FL344450.1|FL344450
EST:     TTAGCATGGGCAACCCCCACTGTGTCACATTTGGGGCAAACGAGTTAAAG                         ACCTTGCAGATCGACGATTTAAAACTCAGCGAAATTGGGCCTAAATTTGAG
genomic: TTAGCATGGGCAACCCCCACTGTGTCACATTTGGGGCAAACGAGTTAAAGgtaatcagct ... actcctgcagACCTTGCAGATCGACGATTTAAAACTCAGCGAAATTGGGCCTAAATTTGAG
EST: gi|148986800|gb|EE030596.2|EE030596
EST:     TTAGCATGGGCAACCCCCACTGTGTCACATTTGGGGCAAACGAGTTAAAG                         ACCTTGCAGATCGACGATTTAAAACTCAGCGAAATTGGGCCTAAATTTGAG
genomic: TTAGCATGGGCAACCCCCACTGTGTCACATTTGGGGCAAACGAGTTAAAGgtaatcagct ... actcctgcagACCTTGCAGATCGACGATTTAAAACTCAGCGAAATTGGGCCTAAATTTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacttgaaatcattgattgtaatcatagattctagtcttgactggactcctgcagACCTTGCAGATCGACGATTTAAAACTCAGCGAAATTGGGCCTAAATTTGAGCATCATGAAATGTTTCCTGCTCGCACAAACACAG
                                   tcttgac  putative branch site (score: 3)
                                              ctcctgc  putative PPT
      aaatcatt  TA-rich tract