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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgagtgttaaccacttcctcatgcttccttctcctttttcagttccattgctatcatccaatggtaatacatatatgtttgacatatttatcttcttgtttccgttgccacagGATTATACTGCTAAGCTGTCTGACTTTGGCCTGGCAAAAGCTGGCCCTGAAGGTGATCAGACCCATGTATCAACACGGGTGATGGGAACCTACGGTTATG

Basic information

species Zea mays
transcript GRMZM2G007283_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G007283_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g02810.1 (Oryza sativa), 3'ss of exon 4
gttgagtgttaaccacttcctcatgcttccttctcctttttcagttccattgctatcatccaatggtaatacatatatgtttgacata------tttatcttcttgtttccgttgccacagGATTATACTGCTAAGCTGTCTGACTTTGGCCTGGCAAAAGCTGGCCCTGAAGGTGATCAGACCCATGTATCAACACGGGTGATGGGAACCTACGGTTATG
|||||||   |    |||    |||  |  || |  |||| |  || |  | ||||   |   ||| ||||  || || |||  ||||      |||||||| || ||| |  |  ||||||||||||||||||| || ||||||||||| ||||||||||||||||| ||||| ||||| ||||||||||||||||||||||||||||| || |||||||
gttgagtagcattt-cttgtcaatgtcttgttttttttttcc--tttctcttctatg--ctgttgggaatatgtaaatatttttcataataacatttatctt-ttatttacacttacacagGATTATACTGCTAAACTCTCTGACTTTGGTCTGGCAAAAGCTGGCCCAGAAGGCGATCAAACCCATGTATCAACACGGGTGATGGGAACATATGGTTATG

upper sequence: GRMZM2G007283_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g02830.2 (Oryza sativa), 3'ss of exon 4
gttgagtgttaaccacttcctcatgcttccttctcctttttcagttccattgctatcatccaatggtaatacatatatgtttgacata------tttatcttcttgtttccgttgccacagGATTATACTGCTAAGCTGTCTGACTTTGGCCTGGCAAAAGCTGGCCCTGAAGGTGATCAGACCCATGTATCAACACGGGTGATGGGAACCTACGGTTATG
|||||||    | || ||| |     |  ||| |  ||||||  |||  ||     ||||   ||| ||||  || || |||  ||||      |||||||| || ||| |  |  ||||||||||||||||||| || ||||||||||| ||||||||||||||||| ||||| ||||| |||||||||||||| |||||||||||||| || |||||||
gttgagt----agcatttcttgccaatatcttgttttttttcctttctcttctatgcatctgttgggaatatgtaaatatttttcataatagcatttatctt-ttatttgcacttacacagGATTATACTGCTAAACTCTCTGACTTTGGTCTGGCAAAAGCTGGCCCAGAAGGCGATCAAACCCATGTATCAACTCGGGTGATGGGAACATATGGTTATG

upper sequence: GRMZM2G007283_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv08s0056g00150.t01 (Vitis vinifera), 3'ss of exon 4
gttgagtgttaaccacttcctcatgcttccttctcc----tttttcagttccattgctatcatccaatggtaatacatatatgtttgacatatttatcttcttgtttccgttgccacagGATTATACTGCTAAGCTGTCTGACTTTGGCCTGGCAAAAGCTGGCCCTGAAGGTGATCAGACCCATGTATCAACACGGGTGATGGGAACCTACGGTTATG
     ||    | || ||| | |  |  | ||  ||      |||   |  |||||| |||||   |   |  | ||    |||||  | |  | |||           |   | |||||||||||| || ||||| ||||||||||| || ||||||||||| ||  |||||||| |||||||||||||||| || || ||||| ||||| |||||||
-----gtaagtagcatttcttaaaaccacattagccaagacatttttttctcattgccatcatgggagaatgcttcactcctgtttaccctgctaatc-----accggtgaatctacagGATTATACAGCCAAGCTTTCTGACTTTGGGCTTGCAAAAGCTGGACCACAAGGTGATGAGACCCATGTATCAACTCGTGTAATGGGTACCTATGGTTATG

upper sequence: GRMZM2G007283_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S31_254V6.1 (Physcomitrella patens), 3'ss of exon 4
gttgagtgttaaccacttcctcatgcttccttctcctttttcagttccattgc-tatcatccaatggtaatacatatatgtttgacatatt-tatcttc----ttgtttccgttgccacagGATTATACTGCTAAGCTGTCTGACTTTGGCCTGGCAAAAGCTGGCCCTGAAGGTGATCAGACCCATGTATCAACACGGGTGATGGGAACCTACGGTTATG
                      ||  ||  | | |  |    | || | || | |||  ||   |  |  ||      |   || |||  | | || ||     |  |||    |   |||||||| || |||||||| ||||| |||||||| || |||| ||| |||||||| ||  | || || ||||||||||| || ||||| ||||| || ||||
---------------------aatattttgtacgcaatagagactttcgtttcgtatagtctgttccttgtatgggacttgatgtcatcctctgtcctcaaacctagttcttgggtgtcagGATTACACAGCTAAGCTATCTGATTTTGGCCTAGCGAAAGATGGGCCTGAAGGAGACAAAACTCACGTATCAACACGTGTCATGGGCACCTATGGCTATG

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|67022281|gb|CO451030.1|CO451030
EST:     GGCCTGTCATCTACAGAGATTTCAAGACATCAAATATTCTACTGGACTCT                         GATTATACTGCTAAGCTGTCTGACTTTGGCCTGNCAAAAGCTGGCCCTGAA
genomic: GGCCTGTCATCTACAGAGATTTCAAGACATCAAATATTCTACTGGACTCTgttgagtgtt ... gttgccacagGATTATACTGCTAAGCTGTCTGACTTTGGCCTGGCAAAAGCTGGCCCTGAA
EST: gi|148957429|gb|EC903492.2|EC903492
EST:     GGCCTGTCATCTACAGAGATTTCAAGACATCAAATATTCTACTGGACTCT                         GATTATACTGCTAAGCTGTCTGACTTTGGCCTGGCAAAAGCTGGCCCTGAA
genomic: GGCCTGTCATCTACAGAGATTTCAAGACATCAAATATTCTACTGGACTCTgttgagtgtt ... gttgccacagGATTATACTGCTAAGCTGTCTGACTTTGGCCTGGCAAAAGCTGGCCCTGAA
EST: gi|74234771|gb|DT642685.1|DT642685
EST:     GGCCTGTCATCTACAGAGATTTCAAGACATCAAATATTCTACTGGACTCT                         GATTATACTGCTAAGCTGTCTGACTTTGGTCTGGCAAAAGCTGGCCCTGAA
genomic: GGCCTGTCATCTACAGAGATTTCAAGACATCAAATATTCTACTGGACTCTgttgagtgtt ... gttgccacagGATTATACTGCTAAGCTGTCTGACTTTGGCCTGGCAAAAGCTGGCCCTGAA
EST: gi|78081509|gb|DV509921.1|DV509921
EST:     GGCCTGTCATCTACAGAGATTTCAAGACATCAAATATTCTACTGGACTCT                         GATTATACTGCTAAGCTGTCTGACTTTGGCCTGGCAAAAGCTGGCCCTGAA
genomic: GGCCTGTCATCTACAGAGATTTCAAGACATCAAATATTCTACTGGACTCTgttgagtgtt ... gttgccacagGATTATACTGCTAAGCTGTCTGACTTTGGCCTGGCAAAAGCTGGCCCTGAA
EST: gi|74234770|gb|DT642684.1|DT642684
EST:     GGCCTGTCATCTACAGAGATTTCAAGACATCAAATATTCTACTGGACTCT                         GATTATACTGCTAAGCTGTCTGACTTTGGCCTGGCAAAAGCTGGCCCTGAA
genomic: GGCCTGTCATCTACAGAGATTTCAAGACATCAAATATTCTACTGGACTCTgttgagtgtt ... gttgccacagGATTATACTGCTAAGCTGTCTGACTTTGGCCTGGCAAAAGCTGGCCCTGAA
EST: gi|149102573|gb|EE188233.2|EE188233
EST:     GGCCTGTCATCTACAGAGATTTCAAGACATCNAATATTCTACTGGACTCT                         GATTATACTGCTAAGCTGTCTGACTTTGGCCTGGCAAAAGCTGGCCC
genomic: GGCCTGTCATCTACAGAGATTTCAAGACATCAAATATTCTACTGGACTCTgttgagtgtt ... gttgccacagGATTATACTGCTAAGCTGTCTGACTTTGGCCTGGCAAAAGCTGGCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatggtaatacatatatgtttgacatatttatcttcttgtttccgttgccacagGATTATACTGCTAAGCTGTCTGACTTTGGCCTGGCAAAAGCTGGCCCTGAAGGTGATCAGACCCATGTATCAACACGGGTGATGGGAACCTACGGTTATG
                  gtttgac  putative branch site (score: 4)
                                tcttcttgtttccgtt  putative PPT
      taatacatatatgttt  TA-rich tract