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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatcacaaatctgtcactttacccagttacttagtttgtcctgaattgtaattgaatttgattgtgatgtttctgttggtctggtgcataataactatacctatttactataatatcttttttttatgttgaagcatgtctataattctcatcttaatgttcaacagGTTGAACTATCAAATCCTGATACTGAGCTCCGCTTGCTTGAAGTATTTTACCACAAGATTTATAAG

Basic information

species Zea mays
transcript GRMZM2G014805_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 25
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 25
gtgatcacaaatctgtcactttacccagttacttagtttgtcctgaattgtaattgaatttgattgtgatgtttctgt-tggtctggtgcataataactatacctatttactataatatcttttttttatgttgaagcatgtctataattctcatc-------------ttaatgttcaacagGTTGAACTATCAAATCCTGATACTGAGCTCCGCTTGCTTGAAGTATTTTACCACAAGATTTATAAG
|||||||| |||||| ||| || ||| | || || || || || || | | |||| | || ||| || | | || || || ||||||||| | |||| ||| | ||||| || ||| || || ||| ||||||| |||||||||||||| || ||||||||| |||| |||||||||||||||||||| || |||||||||||||||
gtgatcacttatctgt---ttttccggtttatcca--ttctcttgcatcgt--ttatcctgaaaactgataacttggtgctatctattgagttctctct-tatcttgttactataagctgttttatttttcatgaagagtgcctactatcctgatccaatcctgatcttttaatgt-caacagGTTGAACTGTCCAATCCTGATGCTGAACTCCGCTTGCTTGAAGTATTCTATCACAAGATTTATAAG
















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|32933255|gb|CF038067.1|CF038067
EST:     TTCCAAGAAACAGCACCATCAGTGATGTGATCACTGATTTGAAAACCAAG                         GTTGAACTATCAAATCCTGATACTGAGCTCCGCTTGCTTGAAGTATTTTAC
genomic: TTCCAAGAAACAGCACCATCAGTGACGTGATCACTGATTTGAAAACCAAGgtgatcacaa ... tgttcaacagGTTGAACTATCAAATCCTGATACTGAGCTCCGCTTGCTTGAAGTATTTTAC
EST: gi|32934023|gb|CF038835.1|CF038835
EST:     TTCCAAGAAACAGCACCATCAGTGATGTGATCACTGATTTGAAAACCAAG                         GTTGAACTATCAAATCCTGATACTGAGCTCCGCTTGCTTGAAGTATTTTAC
genomic: TTCCAAGAAACAGCACCATCAGTGACGTGATCACTGATTTGAAAACCAAGgtgatcacaa ... tgttcaacagGTTGAACTATCAAATCCTGATACTGAGCTCCGCTTGCTTGAAGTATTTTAC
EST: gi|60354119|gb|DN221092.1|DN221092
EST:     TTCCAAGAAACAGCACCATCAGTGACGTGATCACTGATTTGAAAACCAAG                         GTTGAACTATCAAATCCTGATACTGAGCTCCGCTTGCTTGAAGTATTTTAC
genomic: TTCCAAGAAACAGCACCATCAGTGACGTGATCACTGATTTGAAAACCAAGgtgatcacaa ... tgttcaacagGTTGAACTATCAAATCCTGATACTGAGCTCCGCTTGCTTGAAGTATTTTAC
EST: gi|76019060|gb|DT946230.1|DT946230
EST:     TTCCAAGAAACAGCACCATCAGTGACGTGATCACTGATTTGAAAACCAAG                         GTTGAACTATCAAATCCTGATACTGAGCTCCGCTTGCTTGAAGTATTTTAC
genomic: TTCCAAGAAACAGCACCATCAGTGACGTGATCACTGATTTGAAAACCAAGgtgatcacaa ... tgttcaacagGTTGAACTATCAAATCCTGATACTGAGCTCCGCTTGCTTGAAGTATTTTAC
EST: gi|13178629|gb|BG349887.1|BG349887
EST:     TTCCAAGAAACAGCACCATCAGTGACGTGATCACTGATTTGAAAACCAAG                         GTTGAACTATCAAATCCTGATACTGAGCTCCGCTTGCTTGAAGTATTTTAC
genomic: TTCCAAGAAACAGCACCATCAGTGACGTGATCACTGATTTGAAAACCAAGgtgatcacaa ... tgttcaacagGTTGAACTATCAAATCCTGATACTGAGCTCCGCTTGCTTGAAGTATTTTAC
EST: gi|16378289|gb|BI992373.1|BI992373
EST:     TTCCAAGAAACAGCACCATCAGTGACGTGATCACTGATTTGAAAACCAAG                         GTTGAACTATCAAATCCTGATACTGAGCTCCGCTTGCTTGAAGTATTTTAC
genomic: TTCCAAGAAACAGCACCATCAGTGACGTGATCACTGATTTGAAAACCAAGgtgatcacaa ... tgttcaacagGTTGAACTATCAAATCCTGATACTGAGCTCCGCTTGCTTGAAGTATTTTAC
EST: gi|94476779|gb|EB705737.1|EB705737
EST:     TTCCAAGAAACAGCACCATCAGTGACGTGATCACTGATTTGAAAACCAAG                         GTTGAACTATCAAATCCTGATACTGAGCTCCGCTTGCTTGAAGTATTTTAC
genomic: TTCCAAGAAACAGCACCATCAGTGACGTGATCACTGATTTGAAAACCAAGgtgatcacaa ... tgttcaacagGTTGAACTATCAAATCCTGATACTGAGCTCCGCTTGCTTGAAGTATTTTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatcttttttttatgttgaagcatgtctataattctcatcttaatgttcaacagGTTGAACTATCAAATCCTGATACTGAGCTCCGCTTGCTTGAAGTATTTTACCACAAGATTTATAAG
                                       tcttaat  putative branch site (score: 3)
 ttttttttatgttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatcacaaatctgtcactttacccagttacttagtttgtcctgaattgtaattgaatttgattgtgatgtttctgttggtctggtgcataataactatacctatttactataatatcttttttttatgttgaagcatgtctataattctcatcttaatgttcaacagGTTGAACTATCAAATCCTGATACTGAGCTCCGCTTGCTTGAAGTATTTTACCACAAGATTTATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG