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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agagtccattgttgcagaatccttcaatgccttatggtgttacatatttcagattgctgaaggttgactataatagtactgttgatgatttttttaatagGGTGATGAAAATGTTGGGGTTGCACTTTTGACTTATCCTGTTCTAATGGCTTCTGACATTCTTTTGTACCAG

Basic information

species Zea mays
transcript GRMZM2G177970_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G177970_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g54020.2 (Oryza sativa), 3'ss of exon 6
-agagtccattgttgcagaatccttcaatgccttatggtgttacatatttcagattgctgaaggttgactataatagtactgttgatgatttttttaatagGGTGATGAAAATGTTGGGGTTGCACTTTTGACTTATCCTGTTCTAATGGCTTCTGACATTCTTTTGTACCAG
   |  || |     |   ||       ||   ||  || | |    |   |  |||   ||  || | | |  | |   | ||  |   || |||| |||||||||||||||||||| || ||||||||||||||||||||| |||||||||||||||||||  ||||||||
gcaaaaccctcaactccttatatcatggtgttgtactgtttaatccgtcctattttggcaaatttttattttgttgggtttatttttttcttattta-tagGGTGATGAAAATGTTGGAGTGGCACTTTTGACTTATCCTGTTTTAATGGCTTCTGACATTCTCCTGTACCAG

upper sequence: GRMZM2G177970_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA04G09130.2 (Glycine max), 3'ss of exon 6
----agagtccattgttgcagaatccttcaatgc--cttatggtg--ttacatatttcagattgctgaaggttgactataatagtactgttgatgatttttttaatagGGTGATGAAAATGTTGGGGTTGCACTTTTGACTTATCCTGTTCTAATGGCTTCTGACATTCTTTTGTACCAG
      |   ||           | ||||| |||  || ||| ||  ||  || |||    ||    ||        |||||||     ||    |||   |   ||||| |||||| | ||||||||||| |||||||||||||||||||| ||||||||||| || ||| | || |||
tttgctaaatcaggcccatgtttttcttcagtgctcctcatgctggcttgtatgttttcatttatccaa--------ataatagattcttttggaattggatctgtagGGAGATGAAGAAGTTGGGGTTGCCCTTTTGACTTATCCTGTTCTGATGGCTTCTGATATACTTCTATATCAG

upper sequence: GRMZM2G177970_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA06G09240.2 (Glycine max), 3'ss of exon 2
agagtccattgttgcagaatccttcaatgc--cttatggtg--ttacatatttcagattgctgaaggttgactataatagtactgttgatgatttttttaatagGGTGATGAAAATGTTGGGGTTGCACTTTTGACTTATCCTGTTCTAATGGCTTCTGACATTCTTTTGTACCAG
  |   ||        |    ||||| |||  || ||| ||  ||  || |||    ||     |   |    |||||||     ||    |||   ||  ||||| |||||| | ||||||||||| |||||||||||||||||||| ||||||||||| || ||| | || |||
-taaatcaggcccatggttctcttcagtgctcctcatgctggcttgtatgttttcatttatctta---tccaaataatagattcttttggaattggatttgtagGGAGATGAAGAAGTTGGGGTTGCCCTTTTGACTTATCCTGTTCTGATGGCTTCTGATATACTTCTATATCAG

upper sequence: GRMZM2G177970_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv04s0008g00200.t01 (Vitis vinifera), 3'ss of exon 6
agagtccattgttgcagaatccttcaatgccttatggtgttacatatttcagattgctgaaggttgactataatag-tactgttgatgatttttttaatagGGTGATGAAAATGTTGGGGTTGCACTTTTGACTTATCCTGTTCTAATGGCTTCTGACATTCTTTTGTACCAG
  | |      ||| |   | |    |||  ||  |      |||  |||  | |  |  ||    | || |  || |  | || |   | | |||  ||||| |||||||||||||||||||| ||| |||||||||||||||| ||||||||||| |||||||| || |||
-tattttgcacttgtaatgttcaatcatggtttgagaatgagcattcttctaacttttccagtgccattacacaagatgttcttcaatttctgttttgtagGGAGATGAAAATGTTGGGGTTGCCCTTCTGACTTATCCTGTTCTCATGGCTTCTGATATTCTTTTATATCAG

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|71449704|gb|DR830754.1|DR830754
EST:     AGAATGATCCAGTTCAAAGAGAAGTCTCGCAAGGCGG-G--T-----G--                         ----ATGAAAATGTTGGGGTTGCACTTTTGACTTATCCTGTTCTAATGGCT
genomic: AGAATGATCCAGTTCAAAGAGAAGTCTCGCAAGGCGGTGCGTCACTTGCTgtacggcagc ... tttttaatagGGTGATGAAAATGTTGGGGTTGCACTTTTGACTTATCCTGTTCTAATGGCT
EST: gi|50331394|gb|CO526520.1|CO526520
EST:     AGAATGATCCAGTTCAAAGAGAAGTCTCGCAAGGCGG-G--T-----G--                         ----ATGAAAATGTTGGGGTTGCACTTTTGACTTATCCTGTTCTAATGGCT
genomic: AGAATGATCCAGTTCAAAGAGAAGTCTCGCAAGGCGGTGCGTCACTTGCTgtacggcagc ... tttttaatagGGTGATGAAAATGTTGGGGTTGCACTTTTGACTTATCCTGTTCTAATGGCT
EST: gi|76294199|gb|DV033767.1|DV033767
EST:     AGAATGATCCAGTTCAAAGAGAAGTCTCGCAAGGCGGTGCGTCACTTGCT                         GGTGATGAAAATGTTGGGGTTGCACTTTTGACTTATCCTGTTCTAATGGCT
genomic: AGAATGATCCAGTTCAAAGAGAAGTCTCGCAAGGCGGTGCGTCACTTGCTgtacggcagc ... tttttaatagGGTGATGAAAATGTTGGGGTTGCACTTTTGACTTATCCTGTTCTAATGGCT
EST: gi|78120428|gb|DV538812.1|DV538812
EST:     AGAATGATCCAGTTCAAAGAGAAGTCTCGCAAGGCGG-G--T-----G--                         ----ATGAAAATGTTGGGGTTGCACTTTTGACTTATCCTGTTCTAATGGCT
genomic: AGAATGATCCAGTTCAAAGAGAAGTCTCGCAAGGCGGTGCGTCACTTGCTgtacggcagc ... tttttaatagGGTGATGAAAATGTTGGGGTTGCACTTTTGACTTATCCTGTTCTAATGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcagattgctgaaggttgactataatagtactgttgatgatttttttaatagGGTGATGAAAATGTTGGGGTTGCACTTTTGACTTATCCTGTTCTAATGGCTTCTGACATTCTTTTGTACCAG
                                  tgttgat  putative branch site (score: 4)
                                           ttttttt  putative PPT
                                    ttgatgatttttttaa  TA-rich tract