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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttccactgaggcacaagcgacagaacttttttcttgataacattgcttaatgtctaaggtattcttatgtttttagGTTCTTGGGAACAAATACCAAAGTAAGCTGCTTGAAATAATTGACGCCAG

Basic information

species Zea mays
transcript GRMZM2G171354_T03
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171354_T04 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA11G12260.1 (Glycine max), 3'ss of exon 6
----gtaagtttccactgaggcacaagcgacagaacttttttcttgataacat-----tgct--taatgtctaaggtattctt----atgtt-tttagGTTCTTGGGAACAAATACCAAAGTAAGCTGCTTGAAATAATTGACGCCAG
    ||||   | |  |   | |   |||  ||  || ||||| ||||    |     ||||   ||||  |   |  |  ||    || ||  ||||||||| || ||||| |||||||| ||  |||||||||||||||| |||||
gtatgtaaaaatgctatattgtagctgcgttagg-ctcttttcatgatggtttatggctgctgacaatgcttggtgcctctttggaaatattgcttagGTTCTCGGAAACAAGTACCAAAGCAAATTGCTTGAAATAATTGATGCCAG
















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|160481336|gb|EY254270.1|EY254270
EST:     GGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATACAT                         GTTCTTGGGAACAAATACCAAAGTAAGCTGCTTGAAATAATTGACGCCAG
genomic: GGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATACATgtaagtttcc ... atgtttttagGTTCTTGGGAACAAATACCAAAGTAAGCTGCTTGAAATAATTGACGCCAG
EST: gi|32933167|gb|CF037979.1|CF037979
EST:     GGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATACAT                         GTTCTTGGGAACAAATACCAAAGTAAGCTGCTTGAAATAATTGAC
genomic: GGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATACATgtaagtttcc ... atgtttttagGTTCTTGGGAACAAATACCAAAGTAAGCTGCTTGAAATAATTGAC
EST: gi|211297306|gb|FK975033.1|FK975033
EST:     GGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATACAT                         GTTCTTGGGAACAAATACCAAAGTAAGCTGCTTGAAATAATTGACGCCAG
genomic: GGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATACATgtaagtttcc ... atgtttttagGTTCTTGGGAACAAATACCAAAGTAAGCTGCTTGAAATAATTGACGCCAG
EST: gi|71447517|gb|DR828567.1|DR828567
EST:     GTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATACAT                         GTTCTTGGGAACAAATACCAAAGTAAGCTGCTTGAAATAATTGACGCCAG
genomic: GTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATACATgtaagtttcc ... atgtttttagGTTCTTGGGAACAAATACCAAAGTAAGCTGCTTGAAATAATTGACGCCAG
EST: gi|6564181|gb|AW231803.1|AW231803
EST:     GGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATACAT                         GTTCTTGGGAACAAATACCAAAGTAAGCTGCTTGAAATAATTGACGCCAG
genomic: GGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATACATgtaagtttcc ... atgtttttagGTTCTTGGGAACAAATACCAAAGTAAGCTGCTTGAAATAATTGACGCCAG
EST: gi|211297305|gb|FK975032.1|FK975032
EST:     GGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATACAT                         GTTCTTGGGAACAAATACCAAAGTAAGCTGCTTGAAATAATTGACGCCAG
genomic: GGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATACATgtaagtttcc ... atgtttttagGTTCTTGGGAACAAATACCAAAGTAAGCTGCTTGAAATAATTGACGCCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaacttttttcttgataacattgcttaatgtctaaggtattcttatgtttttagGTTCTTGGGAACAAATACCAAAGTAAGCTGCTTGAAATAATTGACGCCAG
                                        ttcttat  CT-rich tract
                                      tattcttatgttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttccactgaggcacaagcgacagaacttttttcttgataacattgcttaatgtctaaggtattcttatgtttttagGTTCTTGGGAACAAATACCAAAGTAAGCTGCTTGAAATAATTGACGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT