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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtccttgtatcaactctttggtttcttcaccattttttggattctaaattcttttcaattaccagGAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAAGAACGTGATGAATTTCAGAAAATGGTTATAGGAAATCAG

Basic information

species Zea mays
transcript GRMZM2G147500_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147500_T04 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os08g14460.1 (Oryza sativa), 3'ss of exon 4
gtttgtccttgtatcaactctt---tggtttcttcaccattttttggattctaa--attcttttcaattaccagGAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAAGAACGTGATGAATTTCAGAAAATGGTTATAGGAAATCAG
||| || ||| |||||| ||||   ||  |||||  ||| | ||    |||||   |||  ||   |  ||||||||||||||||||||||  || ||||| |||||||||| ||||||||||| ||||| ||||| || || ||||||||||| || ||||||
gttcgttcttctatcaattcttgtttgtattctttgccaatcttgaacttctatttatttcttctgaccaccagGAGGCCAAAAACACTGCAACTTTGAAGGCTCAGATTGACAAGCTGCAACAGGAACGCGATGAGTTCCAAAAAATGGTTATTGGCAATCAG

upper sequence: GRMZM2G147500_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA17G07040.2 (Glycine max), 3'ss of exon 5
--------------------------------------------------------------------------------------------------gtttgtccttgtatcaactctttggtttcttcaccattttttggattctaaattcttttcaattacc-agGAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAAGAACGTGATGAATTTCAGAAAATGGTTATAGGAAATCAG
                                                                                                       |     | |  || |  || |      |   ||| ||  | |     |   || |  |||   |||| || ||||||||||| ||||||||| | || ||||| ||||||||||| ||  | |||||||| |||| ||||||||| || ||||||
gtaaggagatgcttggaaatctggttttggcaaacgtaaagcatgctattgtcttgcttagatgaaaagatcagaagtgtgtccattatgcaagatgcaacaatttccttttttacgcagtgatgctgctagattttgtttaactggggttgaattcctgttatttagGAAGCTAAAAACACTGCAGCTCTGAAGGCCCAAATTGAGAAGCTGCAACAGGAGAGGGATGAATTCCAGAGAATGGTTATTGGTAATCAG

upper sequence: GRMZM2G147500_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA13G00980.1 (Glycine max), 3'ss of exon 5
-----------------------------------------------------------------------------------gtttgtcct--tgtatcaactctttggtttcttcaccattttt--tggattctaaattcttttc-----aattacc-------agGAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAAGAACGTGATGAATTTCAGAAAATGGTTATAGGAAATCAG
                                                                                   ||| |||    |||| | | |   |  ||| | ||    |  |  | |||| |   ||  |||      |||| |        ||||||| ||||||||||| ||||||||| |||| ||||| ||||||||||| ||  | ||||||||||||| ||||||||| || ||||||
gtaaggagtgcttgtatttctggttttggcaaacctaaagcatgttattgtcttgcttagatgaaaagattagaagtgtgtctgttagtcaagatgtaacgatttccttatttatgcagtgatgctactagatttttgtttaatttgggtagaattccttttatatagGAGGCTAAAAACACTGCAGCTCTGAAGGCTCAAATTGAGAAGCTGCAACAGGAGAGGGATGAATTTCAGAGAATGGTTATTGGTAATCAG

upper sequence: GRMZM2G147500_T04 (Zea mays), 3'ss of exon 5
lower sequence: AT5G57410.3 (Arabidopsis thaliana), 3'ss of exon 5
gtttgtcctt----gtatcaactct--ttggtttc--ttcaccattttttggattctaaattcttttcaattaccagGAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAAGAACGTGATGAATTTCAGAAAATGGTTATAGGAAATCAG
||  |||||     || ||| ||    ||| ||||  ||   |  || || |||| | |||||  |    ||  ||||| |||||||||||||| ||| |||||||||||||||| ||| | || || ||  | |||||||| || |  ||||| || || || |||
gtgagtcctataaagtttcagctgaaattgttttcgcttaggctcttgtttgattatgaattcactgtg-ttgacagGAAGCCAAAAACACTGCAGCTTTGAAGTCTCAGATTGAAAAGTTACAGCAGGAGAGGGATGAATTCCAAAGGATGGTGATTGGTAACCAG

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|31611780|gb|CD568402.1|CD568402
EST:     ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACG                         GAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAA
genomic: ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACGgtttgtcctt ... caattaccagGAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAA
EST: gi|211122097|gb|FL004251.1|FL004251
EST:     ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACG                         GAGGCCAAAAACACTGCTGCTCTGAAGTCTCA
genomic: ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACGgtttgtcctt ... caattaccagGAGGCCAAAAACACTGCTGCTCTGAAGTCTCA
EST: gi|33094171|gb|CF054165.1|CF054165
EST:     ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACG                         GAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAA
genomic: ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACGgtttgtcctt ... caattaccagGAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAA
EST: gi|211122868|gb|FL004257.1|FL004257
EST:     ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACG                         GAGGCCAAAAA
genomic: ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACGgtttgtcctt ... caattaccagGAGGCCAAAAA
EST: gi|211122100|gb|FL004254.1|FL004254
EST:     ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACG                         GAGGCCAAAAACACTGCTG
genomic: ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACGgtttgtcctt ... caattaccagGAGGCCAAAAACACTGCTG
EST: gi|33102758|gb|CF062718.1|CF062718
EST:     ATGCTCAATTAGTAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACG                         GAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAA
genomic: ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACGgtttgtcctt ... caattaccagGAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAA
EST: gi|211124442|gb|FL004297.1|FL004297
EST:     ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACG                         GAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAA
genomic: ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACGgtttgtcctt ... caattaccagGAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAA
EST: gi|22715261|gb|BU197668.1|BU197668
EST:     ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACG                         GAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAA
genomic: ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACGgtttgtcctt ... caattaccagGAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAA
EST: gi|211122872|gb|FL004261.1|FL004261
EST:     ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACG                         GAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAA
genomic: ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACGgtttgtcctt ... caattaccagGAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAA
EST: gi|211122877|gb|FL004266.1|FL004266
EST:     ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACG                         GAGGCCAAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAAC
genomic: ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACGgtttgtcctt ... caattaccagGAGGCCAAAAA-CACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAAC
EST: gi|211124436|gb|FL004291.1|FL004291
EST:     ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACG                         GAGGCCAAAAAC
genomic: ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACGgtttgtcctt ... caattaccagGAGGCCAAAAAC
EST: gi|211122095|gb|FL004249.1|FL004249
EST:     ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACG                         GAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTG
genomic: ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACGgtttgtcctt ... caattaccagGAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTG
EST: gi|211124441|gb|FL004296.1|FL004296
EST:     ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACG                         GAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAA
genomic: ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACGgtttgtcctt ... caattaccagGAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAA
EST: gi|211124440|gb|FL004295.1|FL004295
EST:     ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACG                         GAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAA
genomic: ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACGgtttgtcctt ... caattaccagGAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAA
EST: gi|26559425|gb|CA831660.1|CA831660
EST:     ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACG                         GAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAA
genomic: ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACGgtttgtcctt ... caattaccagGAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAA
EST: gi|211122101|gb|FL004255.1|FL004255
EST:     ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACG                         GAGGCCAAAAACACTGCTGCTCTGAAGTCTCANATAGATAAGCTGCAACAA
genomic: ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACGgtttgtcctt ... caattaccagGAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAA
EST: gi|33095529|gb|CF055523.1|CF055523
EST:     ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACG                         GAGGCCGGAGGCACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAA
genomic: ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACGgtttgtcctt ... caattaccagGAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAA
EST: gi|211125213|gb|FL004301.1|FL004301
EST:     ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACG                         GAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAA
genomic: ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACGgtttgtcctt ... caattaccagGAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAA
EST: gi|211124432|gb|FL004287.1|FL004287
EST:     ATGCTCAATTAGCAGCSAAAGATCGAGAGCTAGCCACTCTTACTCGAACG                         GAGGCCAAAAACACTG
genomic: ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACGgtttgtcctt ... caattaccagGAGGCCAAAAACACTG
EST: gi|211124434|gb|FL004289.1|FL004289
EST:     ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACG                         GAGGCCAAAAACACTGCT
genomic: ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACGgtttgtcctt ... caattaccagGAGGCCAAAAACACTGCT
EST: gi|148964224|gb|EE015404.2|EE015404
EST:     ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACG                         GAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAA
genomic: ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACGgtttgtcctt ... caattaccagGAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAA
EST: gi|26558350|gb|CA830585.1|CA830585
EST:     ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACG                         GAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAA
genomic: ATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACGgtttgtcctt ... caattaccagGAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caactctttggtttcttcaccattttttggattctaaattcttttcaattaccagGAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAAGAACGTGATGAATTTCAGAAAATGGTTATAGGAAATCAG
                               ttctaaa  putative branch site (score: 2)
                                      ttcttttc  CT-rich tract
                              attctaaattcttttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtccttgtatcaactctttggtttcttcaccattttttggattctaaattcttttcaattaccagGAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAAGAACGTGATGAATTTCAGAAAATGGTTATAGGAAATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC