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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtgcttcttcccttcgcaagtcgttaggctatgtcttaactgttatcaaattgtggaacttattcatgtaaatttcaactaattaccagtcaaatgtagGTATGTGCTGTCAAAGCTCCTGGATTTGGTGAAAATAGAAGGCACAATCTAGATGACATGGCTGTGATGACTGGAGGAGAG

Basic information

species Zea mays
transcript GRMZM2G074790_T03
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074790_T03 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os05g46290.1 (Oryza sativa), 3'ss of exon 8
----------------------------------------------------------agtgct-tcttcccttcgcaagtcgttaggctatgtcttaactgttatcaaat------tgtggaactt----attcatgtaaatttcaactaattaccagtcaaatgtagGTATGTGCTGTCAAAGCTCCTGGATTTGGTGAAAATAGAAGGCACAATCTAGATGACATGGCTGTGATGACTGGAGGAGAG
                                                            || | | |  || | |  |||      || |  |  | ||  |  ||||        | |||| | |    ||||  |||||||   | | || |    || | | ||| |||||||||||||||||||||||||||||||||| |||||   |||||| |||||| |||||||| |||| |||||||||
gtgatattaactactggtcctactgtatacaatactgaattgcgtatacaagctgcttgatgatatgtgtccgttgttagttaaagtgcaagcttcttaccttcttcaagctagagctatggatcgttgatattctggtaaattagtaattatcatgcatcgattatagATATGTGCTGTCAAAGCTCCTGGATTTGGTGAAAACAGAAGAGCCAATCTGGATGACGTGGCTGTGTTGACAGGAGGAGAG
















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|18450678|gb|BM428956.1|BM428956
EST:     CGTGCTGGACTCAAG                         GTATGTGCTGTCAAAGCTCCTGGATTTGGTGAAAATAGAAGGCACAATCTA
genomic: CGTGCTGGACTCAAGgtgctaaggg ... tcaaatgtagGTATGTGCTGTCAAAGCTCCTGGATTTGGTGAAAATAGAAGGCACAATCTA
EST: gi|87152753|gb|DY397542.1|DY397542
EST:     GAGATGCTCTGTCAATGCTTGTACTGAACAAGCATCGTGCTGGACTCAAG                         GTATGTGCTGTCAAAGCTCCTGGATTTGGTGAAAATAGAAGGCACAATCTA
genomic: GAGATGCTCTGTCAATGCTTGTACTGAACAAGCATCGTGCTGGACTCAAGgtgctaaggg ... tcaaatgtagGTATGTGCTGTCAAAGCTCCTGGATTTGGTGAAAATAGAAGGCACAATCTA
EST: gi|166610019|gb|EG159989.1|EG159989
EST:     CTCTGTCAATGCTTGTACTGAACAAGCATCGTGCTGGACTCAAG                         GTATGTGCTGTCAAAGCTCCTGGATTTGGTGAAA-TAGAAGGCACAA
genomic: CTCTGTCAATGCTTGTACTGAACAAGCATCGTGCTGGACTCAAGgtgctaaggg ... tcaaatgtagGTATGTGCTGTCAAAGCTCCTGGATTTGGTGAAAATAGAAGGCACAA
EST: gi|19822484|gb|BQ048508.1|BQ048508
EST:     GAGATGCTCTGTCAATGCTTGTACTGAACAAGCATCGTGCTGGACTCAAG                         GTATGTGCTGTCAAAGCTCCTGGATTTGGTGAAAATAGAAGGCACAATCTA
genomic: GAGATGCTCTGTCAATGCTTGTACTGAACAAGCATCGTGCTGGACTCAAGgtgctaaggg ... tcaaatgtagGTATGTGCTGTCAAAGCTCCTGGATTTGGTGAAAATAGAAGGCACAATCTA
EST: gi|31351656|gb|CD436013.1|CD436013
EST:     GAGATGCTCTGTCAATGCTTGTACTGAACAAGCATCGTGCTGGACTCAAG                         GTATGTGCTGTCAAAGCTCCTGGATTTGGTGAAAATAGAAGGCACAATCTA
genomic: GAGATGCTCTGTCAATGCTTGTACTGAACAAGCATCGTGCTGGACTCAAGgtgctaaggg ... tcaaatgtagGTATGTGCTGTCAAAGCTCCTGGATTTGGTGAAAATAGAAGGCACAATCTA
EST: gi|31350305|gb|CD434662.1|CD434662
EST:     GAGATGCTCTGTCAATGCTTGTACTGAACAAGCATCGTGCTGGACTCAAG                         GTATGTGCTGTCAAAGCTCCTGGATTTGGTGAAAATAGAAGGCACAATCTA
genomic: GAGATGCTCTGTCAATGCTTGTACTGAACAAGCATCGTGCTGGACTCAAGgtgctaaggg ... tcaaatgtagGTATGTGCTGTCAAAGCTCCTGGATTTGGTGAAAATAGAAGGCACAATCTA
EST: gi|6021191|gb|AW066119.1|AW066119
EST:     GAGATGCTCTGTCAATGCTTGTACTGAACAAGCATCGTGCTGGACTCAAG                         GTATGTGCTGTCAAAGCTCCTGGATTTGGTGAAAATAGAAGGCACAATC
genomic: GAGATGCTCTGTCAATGCTTGTACTGAACAAGCATCGTGCTGGACTCAAGgtgctaaggg ... tcaaatgtagGTATGTGCTGTCAAAGCTCCTGGATTTGGTGAAAATAGAAGGCACAATC
EST: gi|22489691|gb|BU049614.1|BU049614
EST:     GAGATGCTCTGTCAATGCTTGTACTGAACAAGCATCGTGCTGGACTCAAG                         GTATGTGCTGTCAAAGCTCCTGGATTTGGTGAAAATAGAAGGCACAATCTA
genomic: GAGATGCTCTGTCAATGCTTGTACTGAACAAGCATCGTGCTGGACTCAAGgtgctaaggg ... tcaaatgtagGTATGTGCTGTCAAAGCTCCTGGATTTGGTGAAAATAGAAGGCACAATCTA
EST: gi|87153562|gb|DY398351.1|DY398351
EST:     GAGATGCTCTGTCAATGCTTGTACTGAACAAGCATCGTGCTGGACTCAAG                         GTATGTGCTGTCAAAGCTCCTGGATTTGGTGAAAATAGAAGGCACAATCTA
genomic: GAGATGCTCTGTCAATGCTTGTACTGAACAAGCATCGTGCTGGACTCAAGgtgctaaggg ... tcaaatgtagGTATGTGCTGTCAAAGCTCCTGGATTTGGTGAAAATAGAAGGCACAATCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcaaattgtggaacttattcatgtaaatttcaactaattaccagtcaaatgtagGTATGTGCTGTCAAAGCTCCTGGATTTGGTGAAAATAGAAGGCACAATCTAGATGACATGGCTGTGATGACTGGAGGAGAG
                                aactaat  putative branch site (score: 2)
                        taaatttcaactaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtgcttcttcccttcgcaagtcgttaggctatgtcttaactgttatcaaattgtggaacttattcatgtaaatttcaactaattaccagtcaaatgtagGTATGTGCTGTCAAAGCTCCTGGATTTGGTGAAAATAGAAGGCACAATCTAGATGACATGGCTGTGATGACTGGAGGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- tgcttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caactaa