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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacccgatgcagcatacgtaccctttgcgaaagctaaaatctgatcgactagtcagtgaactccgctgttctgatttttactgagcatacatggtgcagGATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTGTTGGAGTCTCAAACTACAATG

Basic information

species Zea mays
transcript GRMZM2G111954_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G111954_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g04990.1 (Oryza sativa), 3'ss of exon 5
-----gtacccgatgcagcatacgtac-------cctttgcgaaagctaaaatctgatcgactagtcagt---gaactccgctgttctgatttttactgagcatacatggtgcagGATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTGTTGGAGTCTCAAACTACAATG
         || ||| |   |||  |          |||  |||   | | ||     |  ||||   |     |||| |    ||||||  |    |||||||      | |||| ||||||||||| || || ||||| |||||||||||||| || ||||||||||||||||||||||||||||
gtacacagtccaatgaaaattacccatataaccatttttatgaattattagatagttccttctagcatgacaaaaacttcaacattctgacatc-gttgagcatt----attcagGGTATCTTGATGGACTTGCAGATGCCTATGAGCAAGGCCTTGTAAAGGCTGTTGGAGTCTCAAACTACAATG

upper sequence: GRMZM2G111954_T03 (Zea mays), 3'ss of exon 5
lower sequence: AT1G06690.1 (Arabidopsis thaliana), 3'ss of exon 5
-----gtacccgatgcagcatacgtaccctttgcgaaagctaaaatctgatcgactagtcagtgaactccgctgttctgatttttactgagcatacatggtgcagGATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTGTTGGAGTCTCAAACTACAATG
      |       ||||||   | | |   |   ||  ||| | |  |    |||  |  ||||  |           |||   | || |  |      |  |||||||||||||||||| | |||||||  ||| ||||| || |||||||||||||| || || |||||||  |
gttttttcttaagagcagcac-tgaatctacttttaa--ctagagttcgtgtcactt-ttggtga-ttatatcaaatccattgacattgtgagttatgtttttagGATATCTTGATGGTCTTGGGGATGCTGTTGAACAAGGACTTGTCAAGGCTGTTGGTGTTTCTAACTACAGCG
















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|76281356|gb|DV020924.1|DV020924
EST:     TGGCCAGGGATTTGGGGGAACGAAG                         GATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG
genomic: TGGCCAGGGATTTGGGGGAACGAAGgtacccgatg ... catggtgcagGATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG
EST: gi|149077171|gb|EE165834.2|EE165834
EST:     TGGCCAGGGATTTGGGGGAACGAAG                         GATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG
genomic: TGGCCAGGGATTTGGGGGAACGAAGgtacccgatg ... catggtgcagGATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG
EST: gi|148931921|gb|EC875135.2|EC875135
EST:     TGGCCAGGGATTTGGGGGAACGAAG                         GATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG
genomic: TGGCCAGGGATTTGGGGGAACGAAGgtacccgatg ... catggtgcagGATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG
EST: gi|148935240|gb|EC879277.2|EC879277
EST:     TGGCCAGGGATTTGGGGGAACGAAG                         GATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG
genomic: TGGCCAGGGATTTGGGGGAACGAAGgtacccgatg ... catggtgcagGATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG
EST: gi|149063769|gb|EE157636.2|EE157636
EST:     TGGCCAGGGATTTGGGGGAACGAAG                         GATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG
genomic: TGGCCAGGGATTTGGGGGAACGAAGgtacccgatg ... catggtgcagGATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG
EST: gi|149013468|gb|EE042982.2|EE042982
EST:     TGGCCAGGGATTTGGGGGAACGAAG                         GATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG
genomic: TGGCCAGGGATTTGGGGGAACGAAGgtacccgatg ... catggtgcagGATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG
EST: gi|148972626|gb|EE023587.2|EE023587
EST:     TGGCCAGGGATTTGGGGGAACGAAG                         GATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG
genomic: TGGCCAGGGATTTGGGGGAACGAAGgtacccgatg ... catggtgcagGATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG
EST: gi|148982464|gb|EE028329.2|EE028329
EST:     TGGCCAGGGATTTGGGGGAACGAAG                         GATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG
genomic: TGGCCAGGGATTTGGGGGAACGAAGgtacccgatg ... catggtgcagGATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG
EST: gi|148936271|gb|EC880349.2|EC880349
EST:     TGGCCAGGGATTTGGGGGAACGAAG                         GATATCTTGATGGTCT
genomic: TGGCCAGGGATTTGGGGGAACGAAGgtacccgatg ... catggtgcagGATATCTTGATGGTCT
EST: gi|149111659|gb|EE190803.2|EE190803
EST:     TGGCCAGGGATTTGGGGGAACGAAG                         GATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG
genomic: TGGCCAGGGATTTGGGGGAACGAAGgtacccgatg ... catggtgcagGATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgactagtcagtgaactccgctgttctgatttttactgagcatacatggtgcagGATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTGTTGGAGTCTCAAACTACAATG
                        ttctgat  putative branch site (score: 3)
                           tgattttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacccgatgcagcatacgtaccctttgcgaaagctaaaatctgatcgactagtcagtgaactccgctgttctgatttttactgagcatacatggtgcagGATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTGTTGGAGTCTCAAACTACAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG