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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgattttaaaacattatgctgttaccaaaagttattttcttgtctgttattgtcaactgtacataggttcctttctgatgagttctgttgattcatttacatcgttttagGCTTTAGCTGCTCGAGGTTTGAAGAGTGGCGGTACTGTTCAACAGCGTGCAGATCGTCTTTTCTTGTTGAAG

Basic information

species Zea mays
transcript GRMZM2G178227_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178227_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g50850.2 (Oryza sativa), 3'ss of exon 7
gtttgattttaaaacattatgctgttaccaaaagttattttcttgtctgttattgtcaactgtacataggttcctttctgatgagttctgttgattcatttacatcgtt-ttagGCTTTAGCTGCTCGAGGTTTGAAGAGTGGCGGTACTGTTCAACAGCGTGCAGATCGTCTTTTCTTGTTGAAG
|| ||| ||     || || | |||||  |  |  | |||| |  | |  |||| |  |   | | | ||    ||      |    || ||||||  |||   |  ||   |||||||||||||||| || || || ||||| |||||||||||||||||||| || || |||||||||||||||
gtatgactt----gcaatacgttgttattattaccttttttttcctgtcctattattcaactttcgttgggctttt------gtaccctattgattggttttggtttttgccagGCTTTAGCTGCTCGTGGATTAAAAAGTGGTGGTACTGTTCAACAGCGTGCTGAGCGACTTTTCTTGTTGAAG
















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|8367537|gb|BE050482.1|BE050482
EST:     ACAGCACAGTTGAAGAACTTGTTGAGCTTGGCCCAGAAAAATTAAAACAG                         GCTTTAGCTGCTCGAGGTTTGAAGAGTGGCGGTACTGTTCAACAGCGTGCA
genomic: ACAGCACAGTTGAAGAACTTGTTGAGCTTGGCCCAGAAAAATTAAAACAGgtttgatttt ... atcgttttagGCTTTAGCTGCTCGAGGTTTGAAGAGTGGCGGTACTGTTCAACAGCGTGCA
EST: gi|60393978|gb|DN226848.1|DN226848
EST:     ACAGCACAGTTGAAGAACTTGTTGAGCTTGGCCCAGAAAAATTAAAACAG                         GCTTTAGCTGCTCGAGGTTTGAAGAGTGGCGGTACTGTTCAACAGCGTGCA
genomic: ACAGCACAGTTGAAGAACTTGTTGAGCTTGGCCCAGAAAAATTAAAACAGgtttgatttt ... atcgttttagGCTTTAGCTGCTCGAGGTTTGAAGAGTGGCGGTACTGTTCAACAGCGTGCA
EST: gi|6021114|gb|AW066042.1|AW066042
EST:     ACAGCACAGTTGAAGAACTTGTTGAGCTTGGCCCAGAAAAATTAAAACAG                         GCTTTAGCTGCTCGAGGTTTGAAGAGTGGCGGTACTGTTCAACAGCGTGCA
genomic: ACAGCACAGTTGAAGAACTTGTTGAGCTTGGCCCAGAAAAATTAAAACAGgtttgatttt ... atcgttttagGCTTTAGCTGCTCGAGGTTTGAAGAGTGGCGGTACTGTTCAACAGCGTGCA
EST: gi|76290494|gb|DV030062.1|DV030062
EST:     ACAGCACAGTTGAAGAACTTGTTGAGCTTGGCCCAGAAAAATTAAAACAG                         GCTTTAGCTGCTCGAGGTTTGAAGAGTGGCGGTACTGTTCAACAGCGTGCA
genomic: ACAGCACAGTTGAAGAACTTGTTGAGCTTGGCCCAGAAAAATTAAAACAGgtttgatttt ... atcgttttagGCTTTAGCTGCTCGAGGTTTGAAGAGTGGCGGTACTGTTCAACAGCGTGCA
EST: gi|20802738|gb|BQ293788.1|BQ293788
EST:     ACAGCACAGTTGAAGAACTTGTTGAGCTTGGCCCAGAAAAATTAAAACAG                         GCTTTAGCTGCTCGAGGTTTGAAGAGTGGCGGTACTGTTCAACAGCGTGCA
genomic: ACAGCACAGTTGAAGAACTTGTTGAGCTTGGCCCAGAAAAATTAAAACAGgtttgatttt ... atcgttttagGCTTTAGCTGCTCGAGGTTTGAAGAGTGGCGGTACTGTTCAACAGCGTGCA
EST: gi|31358406|gb|CD442763.1|CD442763
EST:     ACAGCACAGTTGAAGAACTTGTTGAGCTTGGCCCAGAAAAATTAAAACAG                         GCTTTAGCTGCTCGAGGTTTGAAGAGTGGCGGTACTGTTCAACAGCGTGCA
genomic: ACAGCACAGTTGAAGAACTTGTTGAGCTTGGCCCAGAAAAATTAAAACAGgtttgatttt ... atcgttttagGCTTTAGCTGCTCGAGGTTTGAAGAGTGGCGGTACTGTTCAACAGCGTGCA
EST: gi|8367536|gb|BE050481.1|BE050481
EST:     ACAGCACAGTTGAAGAACTTGTTGAGCTTGGCCCAGAAAAATTAAAACAG                         GCTTTAGCTGCTCGAGGTTTGAAGAGTGGCGGTACTGTTCAACAGCGTGCA
genomic: ACAGCACAGTTGAAGAACTTGTTGAGCTTGGCCCAGAAAAATTAAAACAGgtttgatttt ... atcgttttagGCTTTAGCTGCTCGAGGTTTGAAGAGTGGCGGTACTGTTCAACAGCGTGCA
EST: gi|26456323|gb|CA827906.1|CA827906
EST:     ACAGCACAGTTGAAGAACTTGTTGAGCTTGGCCCAGAAAAATTAAAACAG                         GCTTTAGCTGCTCGAGGTTTGAAGAGTGGCGGTACTGTTCAACAGCGTGCA
genomic: ACAGCACAGTTGAAGAACTTGTTGAGCTTGGCCCAGAAAAATTAAAACAGgtttgatttt ... atcgttttagGCTTTAGCTGCTCGAGGTTTGAAGAGTGGCGGTACTGTTCAACAGCGTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgtacataggttcctttctgatgagttctgttgattcatttacatcgttttagGCTTTAGCTGCTCGAGGTTTGAAGAGTGGCGGTACTGTTCAACAGCGTGCAGATCGTCTTTTCTTGTTGAAG
                                              tcgtttt  CT-rich tract
                                   attcattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgattttaaaacattatgctgttaccaaaagttattttcttgtctgttattgtcaactgtacataggttcctttctgatgagttctgttgattcatttacatcgttttagGCTTTAGCTGCTCGAGGTTTGAAGAGTGGCGGTACTGTTCAACAGCGTGCAGATCGTCTTTTCTTGTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG