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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctctattacattttttgtttggtatttatgatttctgtgattgtgtctacatggattaactgttatgattccttaaatctatatttcctgaacctgaaagGGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCAG

Basic information

species Zea mays
transcript GRMZM2G107106_T06
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107106_T06 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os08g41010.4 (Oryza sativa), 3'ss of exon 5
--ctctattacattttttgtttggtatttatgatttctgtgattgtgtctacatggatt--aactgttatgattccttaaatctatatttcctgaacctgaaagGGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCAG
  || |   |    ||   ||  || |   |   |  | |  |    |  |    |||   || ||||   | || | |  | || | ||| |  |     |||||| | |||||||| |||||||| || ||||| || ||||||||||||||||
aactgtcgaagggcttcctttaagtgtcctttgatattatagtgtgataaatcacgataggaaatgtttcaactc-tcatttatacaattctttgat---gaagGGCGCGAGGGCTGGTTCATATTCCGAGGAAGGATCCCAGAAGAAGCCTGCAG
















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|32929362|gb|CF034174.1|CF034174
EST:     GAATTCCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATG                         GGCACGAGGGCTGGCTCATATTCCGATGAAGGTTCTCAGAAGAAGCCTGCA
genomic: GAATTCCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATGgtatgtgctc ... aacctgaaagGGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCA
EST: gi|38502536|gb|CF972396.1|CF972396
EST:     GAATTCCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATG                         GGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCA
genomic: GAATTCCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATGgtatgtgctc ... aacctgaaagGGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCA
EST: gi|60354809|gb|DN221782.1|DN221782
EST:     CCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATG                         GGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCA
genomic: CCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATGgtatgtgctc ... aacctgaaagGGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCA
EST: gi|71765407|gb|DR963344.1|DR963344
EST:     AATTCCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATG                         GGCACAAGGGCTGGCTCATATTTTGATGAAGGTTCTCAGAAGAAGCCTGCA
genomic: AATTCCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATGgtatgtgctc ... aacctgaaagGGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCA
EST: gi|71760238|gb|DR958175.1|DR958175
EST:     GGCCAATACCTGCTGGTCCTGGTCCAATG                         GGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCA
genomic: GGCCAATACCTGCTGGTCCTGGTCCAATGgtatgtgctc ... aacctgaaagGGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCA
EST: gi|32929980|gb|CF034792.1|CF034792
EST:     GAATTCCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATG                         GGCACAAGGGCTGGCTCATATTCCGATGAAGGTTCTCAGAAGAAGCCTGCA
genomic: GAATTCCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATGgtatgtgctc ... aacctgaaagGGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCA
EST: gi|86469486|gb|DY235856.1|DY235856
EST:     GTATGGGCCAATACCTGCTGGTCCTGGTCCAATG                         GGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCA
genomic: GTATGGGCCAATACCTGCTGGTCCTGGTCCAATGgtatgtgctc ... aacctgaaagGGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCA
EST: gi|60336833|gb|DN203806.1|DN203806
EST:     GAATTCCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATG                         GGCACAAGGGCTGGCTCATATTCCGATGAAGGTTCTCAGAAGAAGCCTGCA
genomic: GAATTCCCATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATGgtatgtgctc ... aacctgaaagGGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCA
EST: gi|71761651|gb|DR959588.1|DR959588
EST:     CATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATG                         GGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCA
genomic: CATGGACAGGTATGGGCCAATACCTGCTGGTCCTGGTCCAATGgtatgtgctc ... aacctgaaagGGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctacatggattaactgttatgattccttaaatctatatttcctgaacctgaaagGGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCAG
        gattaac  putative branch site (score: 2)
                           ttaaatctatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctctattacattttttgtttggtatttatgatttctgtgattgtgtctacatggattaactgttatgattccttaaatctatatttcctgaacctgaaagGGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG