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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttcccagcattgaccctttattagatagaagtaaattgctgcctgaatcgtgtggaaatgttgcagGCTAGATTATGAAGCTGGACTGGAGGACTTCAAGGAACGTTTGATTAATTATGAAAAG

Basic information

species Zea mays
transcript GRMZM2G021846_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G021846_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os05g07130.2 (Oryza sativa), 3'ss of exon 12
--gtgagtttcccagcattgaccctttattagatagaagtaaatt-gctgcctgaatcgtgtggaaatgttgcagGCTAGATTATGAAGCTGGACTGGAGGACTTCAAGGAACGTTTGATTAATTATGAAAAG
  | |  | ||||   |||  ||||||  || ||| |||| |||| |   |||||||| ||||||||  || ||||| |||||||||| ||||| ||  |||||||||||||||  ||   || |||||||||
gtgaggatctcccgaaattttccctttgcta-atataagtgaatttgtgacctgaatcctgtggaaacttttcagGCCAGATTATGAAACTGGAGTGCGGGACTTCAAGGAACGCCTGGCAAACTATGAAAAG
















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|8103262|gb|AW927912.1|AW927912
EST:     GAAAGAAACATACGGCTGAAGATCCAACAAAGTCCAGACTATGCTGAACA                         GCTAGATTATGAAGCTGGACTGGAGGACTTCAAGGAACGTTTGATTAATTA
genomic: GAAAGAAACATACGGCTGAAGATCCAACAAAGTCCAGACTATGCTGAACAgtgagtttcc ... aatgttgcagGCTAGATTATGAAGCTGGACTGGAGGACTTCAAGGAACGTTTGATTAATTA
EST: gi|32840580|gb|CD980261.1|CD980261
EST:     GAAAGAAACATACGGCTGAAGATCCAACAAAGTCCAGACTATGCTGAACA                         GCTAGATTATGAAGCTGGACTGGAGGACTTCAAGGAACGTTTGATTAATTA
genomic: GAAAGAAACATACGGCTGAAGATCCAACAAAGTCCAGACTATGCTGAACAgtgagtttcc ... aatgttgcagGCTAGATTATGAAGCTGGACTGGAGGACTTCAAGGAACGTTTGATTAATTA
EST: gi|32802732|gb|CD954968.1|CD954968
EST:     GATCCAACAAAGTCCAGACTATGCTGAACA                         GCTAGATTATGAAGCTGGACTGGAGGACTTCAAGGAACGTTTGATTA
genomic: GATCCAACAAAGTCCAGACTATGCTGAACAgtgagtttcc ... aatgttgcagGCTAGATTATGAAGCTGGACTGGAGGACTTCAAGGAACGTTTGATTA
EST: gi|32840579|gb|CD980260.1|CD980260
EST:     GAAAGAAACATACGGGTGAAGATCCAACAAAGTCCAGACTATGCTGAACA                         GCTAGATTATG
genomic: GAAAGAAACATACGGCTGAAGATCCAACAAAGTCCAGACTATGCTGAACAgtgagtttcc ... aatgttgcagGCTAGATTATG
EST: gi|32825021|gb|CD964743.1|CD964743
EST:     GATCTAACAAAGTCCAGACTATGCTGAACA                         GCTAGATTATGAAGCTGGACTGGAGGACTTCAAGGAACGTTTGATTA
genomic: GATCCAACAAAGTCCAGACTATGCTGAACAgtgagtttcc ... aatgttgcagGCTAGATTATGAAGCTGGACTGGAGGACTTCAAGGAACGTTTGATTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaccctttattagatagaagtaaattgctgcctgaatcgtgtggaaatgttgcagGCTAGATTATGAAGCTGGACTGGAGGACTTCAAGGAACGTTTGATTAATTATGAAAAG
 cattgac  putative branch site (score: 3)
     tttattagatagaagt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtttcccagcattgaccctttattagatagaagtaaattgctgcctgaatcgtgtggaaatgttgcagGCTAGATTATGAAGCTGGACTGGAGGACTTCAAGGAACGTTTGATTAATTATGAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA