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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggccttagcgcacctagatgccttatgcaggaagcaccttgtagctgccgtggggttaatataattttttttctcacactggaatgtttacctatgcagGAAGCACCCTGTGGCGATTTGACGACACACTTATTCTGTCACTTGTGTGCTATATGCCAGGAGTACAGGGAGATCCGTGAGAGAACAGGCAGTGGCTCCT

Basic information

species Zea mays
transcript GRMZM5G892035_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G892035_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g16210.1 (Oryza sativa), 3'ss of exon 3
gggccttagcgcacctagat-gccttatgcaggaagcaccttgtagctgccgtggggttaatataattttttttctcacactgga-atgtttacctatgcagGAAGCACCCTGTGGCGATTTGACGACACACTTATTCTGTCACTTGTGTGCTATATGCCAGGAGTACAGGGAGATCCGTGAGAGAACAGGCAGTGGCTCCT
 |    | | | || |   | |   | |   |        |  | ||     | |  ||| |     |    |  |||      | || ||| | | ||||||||||||| ||||||||||| || || ||||||||||||||| ||||||||||||| || ||||||||||||||||| ||||| |||| ||| |||||||
-gatactggagtacatcactagggctgtatggttgttgagtcatggcaaatctagt-ttactgattctaacatgttcatttcaaatatattttcttttgcagGAAGCACCATGTGGCGATTTAACAACGCACTTATTCTGTCACCTGTGTGCTATATGTCAAGAGTACAGGGAGATCCGCGAGAGGACAGACAGCGGCTCCT

upper sequence: GRMZM5G892035_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT2G40935.1 (Arabidopsis thaliana), 3'ss of exon 3
gggccttagcgcacctagatgccttatgcaggaagcaccttgtagctgccgtggggttaatataattttttttctcacactggaatgtttacctatgcagGAAGCACCCTGTGGCGATTTGACGACACACTTATTCTGTCACTTGTGTGCTATATGCCAGGAGTACAGGGAGATCCGTGAGAGAACAGGCAGTGGCTCCT---
                  ||  || |  |   |   |  | |    | || |  |||   |||       ||        |  ||  ||     || ||||| || || ||||| |||||    |||||||| ||||||||||||||||| || ||||| || ||||| ||||| || ||   ||   ||||||| || |   
------------gttagaatttctcaaacgacacatatgtggataataccattaggtatgtatgtggcgcttctgactgatttaacattctttgattcagGAGGCTCCATGTGGGGATTTTGTAACACACTTCTTCTGTCACTTGTGTGCCATTTGCCAAGAATACAGAGAGATTCGAGAACAAA---GCAGTGGTTCATATC
















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|76284761|gb|DV024329.1|DV024329
EST:     GTTATGCTTGCGGATATCGCAGTGCACTAAGAACAAAGTACAATCTTCCG                         GAAGCACCCTGTGGCGATTTGACGACACACTTATTCTGTCACTTGTGTGCT
genomic: GTTATGCTTGCGGATATCGCAGTGCACTAAGAACAAAGTACAATCTTCCGgtatgtggtt ... acctatgcagGAAGCACCCTGTGGCGATTTGACGACACACTTATTCTGTCACTTGTGTGCT
EST: gi|71765696|gb|DR963633.1|DR963633
EST:     GTTATGCTTGCGGATATCGCAGTGCACTAAGAACAAAGTACAATCTTCCG                         GAAGCACCCTGTGGCGATTTGACGACACACTTATTCTGTCACTTGTGTGCT
genomic: GTTATGCTTGCGGATATCGCAGTGCACTAAGAACAAAGTACAATCTTCCGgtatgtggtt ... acctatgcagGAAGCACCCTGTGGCGATTTGACGACACACTTATTCTGTCACTTGTGTGCT
EST: gi|116826785|gb|EC870620.1|EC870620
EST:     GTTATGCTTGCGGATATCGCAGTGCACTAAGAACAAAGTACAATCTTCCG                         GAAGCACCCTGTGGCGATTTGACGACACACTTATTCTGTCACTTGTGTGCT
genomic: GTTATGCTTGCGGATATCGCAGTGCACTAAGAACAAAGTACAATCTTCCGgtatgtggtt ... acctatgcagGAAGCACCCTGTGGCGATTTGACGACACACTTATTCTGTCACTTGTGTGCT
EST: gi|71765695|gb|DR963632.1|DR963632
EST:     GTTATGCTTGCGGATATCGCAGTGCACTAAGAACAAAGTACAATCTTCCG                         GAAGCACCCTGTGGCGATTTGACGACACACTTATTCTGTCACTTGTGTGCT
genomic: GTTATGCTTGCGGATATCGCAGTGCACTAAGAACAAAGTACAATCTTCCGgtatgtggtt ... acctatgcagGAAGCACCCTGTGGCGATTTGACGACACACTTATTCTGTCACTTGTGTGCT
EST: gi|211110941|gb|FL028257.1|FL028257
EST:     ATATCGCAGTGCACTAAGAACAAAGTACAATCTTCCG                         GAAGCA-CCTGTGGCGATTTGACGACACACTTATTCTGTCACTTGTGTGCT
genomic: ATATCGCAGTGCACTAAGAACAAAGTACAATCTTCCGgtatgtggtt ... acctatgcagGAAGCACCCTGTGGCGATTTGACGACACACTTATTCTGTCACTTGTGTGCT
EST: gi|211409317|gb|FL444002.1|FL444002
EST:     ATATCGCAGTGCACTAAGAACAAAGTACAATCTTCCG                         GAAGCACCCTGTGGCGATTTGACGACACACTTATTCTGTCACTTGTGTGCT
genomic: ATATCGCAGTGCACTAAGAACAAAGTACAATCTTCCGgtatgtggtt ... acctatgcagGAAGCACCCTGTGGCGATTTGACGACACACTTATTCTGTCACTTGTGTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgccgtggggttaatataattttttttctcacactggaatgtttacctatgcagGAAGCACCCTGTGGCGATTTGACGACACACTTATTCTGTCACTTGTGTGCTATATGCCAGGAGTACAGGGAGATCCGTGAGAGAACAGGCAGTGGCTCCT
                          ttctcac  putative branch site (score: 2)
                                          tttacct  putative PPT
           ttaatataattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gggccttagcgcacctagatgccttatgcaggaagcaccttgtagctgccgtggggttaatataattttttttctcacactggaatgtttacctatgcagGAAGCACCCTGTGGCGATTTGACGACACACTTATTCTGTCACTTGTGTGCTATATGCCAGGAGTACAGGGAGATCCGTGAGAGAACAGGCAGTGGCTCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC