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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggacagctcgtcttcctgctgctctacattgccgtaaacacgtagagctgtgcatgtgctatggatgggatgctgatactgtgtgtttctgcaaattaaatgcagGATCTTAAGTCCCAGCTGCGGGAACTGATTCCGGAACAGCAG

Basic information

species Zea mays
transcript GRMZM2G063909_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063909_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 3
---------------------------------gtaggacagctcgtcttcctgctgctctacattgcc-gtaaacacgt---agagctgtgcatgtgctatggatgggatgctgatactgtgtgtttctgcaaattaaatgcagGATCTTAAGTCCCAGCTGCGGGAACTGATTCCGGAACAGCAG
                                  |  |         || || | | || |       | ||    | |    | ||  | | ||||||| || |    | | || |    |||||||||  | |||| ||||||||||| ||||||||||||| |||| ||||||| ||||| |||
gtaagtcaattagtttttgttcgttcgtgctaaatgtgtggttgaaactaccagttactatgtgccatctgtggctaggctcgaaagtggggaatgtgctctgaa--aaaagatgtttgattgtgtttctaaatattatatgcagGATCTCAAGTCCCAGCTGCAGGAATTGATTCCTGAACAACAG

upper sequence: GRMZM2G063909_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g33240.3 (Oryza sativa), 3'ss of exon 2
-------------------------------------------------------------------gtaggacagctcgtcttcctgc-tgctctacattgccgtaaac-acgtagagctgtgcatgtgctatggatgggatgctgatactgtgtgtttctgcaaattaaa--tgcagGATCTTAAGTCCCAGCTGCGGGAACTGATTCCGGAACAGCAG
                                                                       || || |   ||  || | | || |   | ||    |   |  |  || ||   ||||||| || |   |||| |  |  | |||||| ||  | ||||    | |||||||||||||||||||||| |||| ||||||| || || |||
gtaagacaataatagtttgtttgtttctttgtttgtttgttcgtgctataaatatttgcatggttgaaattgatagttaccctctctaccttctgtggctggctacgattgaaattaagttggaaatgtgctctgaaaaagatgtt--tgatttgtgttcctaaatattatgctttcagGATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAG
















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|71303469|gb|DR787844.1|DR787844
EST:     CCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGCGCGTCCGACCTC                         GATCTTAAGTCCCAGCTGCGGGAACTGATTCCGGAACAGCAG
genomic: CCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGCGCGTCCGACCTCgtaggacagc ... ttaaatgcagGATCTTAAGTCCCAGCTGCGGGAACTGATTCCGGAACAGCAG
EST: gi|78076904|gb|DV505338.1|DV505338
EST:     CCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGCGCGTCCGACCTC                         GATCTTAAGTCCCAGCTGCGGGAACTGATTCCGGAACAGCAG
genomic: CCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGCGCGTCCGACCTCgtaggacagc ... ttaaatgcagGATCTTAAGTCCCAGCTGCGGGAACTGATTCCGGAACAGCAG
EST: gi|4609695|gb|AI600534.1|AI600534
EST:     CCACGCTGGGTGGTGTGAGATGGCTGCTTATGCAGAGCGCGTCCGACCTC                         GATCTTAAGTCCCAGCTGCGGGAACTGATTCCGGAACAGCAG
genomic: CCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGCGCGTCCGACCTCgtaggacagc ... ttaaatgcagGATCTTAAGTCCCAGCTGCGGGAACTGATTCCGGAACAGCAG
EST: gi|211161741|gb|FL193319.1|FL193319
EST:     CCACGCTGGGTGGTGTGAGATGGCTGCAGATGCACAGCGCGTCCGAGCTC                         GATCTTAAGTCCCAGCTGCGGGAACTGATTCCGGAACAGCAG
genomic: CCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGCGCGTCCGACCTCgtaggacagc ... ttaaatgcagGATCTTAAGTCCCAGCTGCGGGAACTGATTCCGGAACAGCAG
EST: gi|149101097|gb|EE187201.2|EE187201
EST:     CCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGCGCGTCCGACCTC                         GATCTTAAGTCCCAGCTGCGGGAACTGATTCCGGAACAGCAG
genomic: CCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGCGCGTCCGACCTCgtaggacagc ... ttaaatgcagGATCTTAAGTCCCAGCTGCGGGAACTGATTCCGGAACAGCAG
EST: gi|78088374|gb|DV516767.1|DV516767
EST:     CCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGCGCGTCCGACCTC                         GATCTTAAGTCCCAGCTGCGGGAACTGATTCCGGAACAGCAG
genomic: CCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGCGCGTCCGACCTCgtaggacagc ... ttaaatgcagGATCTTAAGTCCCAGCTGCGGGAACTGATTCCGGAACAGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatgtgctatggatgggatgctgatactgtgtgtttctgcaaattaaatgcagGATCTTAAGTCCCAGCTGCGGGAACTGATTCCGGAACAGCAG
                    tgctgat  putative branch site (score: 3)
                                          aaattaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggacagctcgtcttcctgctgctctacattgccgtaaacacgtagagctgtgcatgtgctatggatgggatgctgatactgtgtgtttctgcaaattaaatgcagGATCTTAAGTCCCAGCTGCGGGAACTGATTCCGGAACAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC