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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcgttatttttattgcacatgcttatcattacatgtactaaaactgatgaataatagcttcgactataatatctgtaactcatccttttcttttttgaagGTTCGCACTATTAAAGTGGAAAAGAGGATCAATGAGATTGTGAACCGCTTGAATAAGACAAAGGTGGAACGGAAACCTGATTTAAAGG

Basic information

species Zea mays
transcript GRMZM2G157332_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157332_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g13440.1 (Oryza sativa), 3'ss of exon 4
-tcgttatttttattgcacatgcttat-cattacatgtactaaaactgatgaataatagcttcgactataatatctgtaactcatccttttcttttttgaagGTTCGCACTATTAAAGTGGAAAAGAGGATCAATGAGATTGTGAACCGCTTGAATAAGACAAAGGTGGAACGGAAACCTGATTTAAAGG
 |   |      |   ||    ||||     || |||||      ||  ||||| ||   |||   | |  ||| | |   |  || |||  |  |||  ||||||| | | | ||||| |||||  |||| |||||||||||||||||  ||||||||||||| ||||| || || ||||| |||||||
attactggacacagcccaataacttaggtcctagatgtatctc--cttttgaatgatcttttcagtttttttatgtatcctttgtcatttgttcatttacagGTTCGGATTGTCAAAGTAGAAAAACGGATTAATGAGATTGTGAACCGGCTGAATAAGACAAAAGTGGAGCGCAAGCCTGACTTAAAGG

upper sequence: GRMZM2G157332_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA04G08530.3 (Glycine max), 3'ss of exon 4
---------------------------------------------------tcgttattttt-attgcacatgcttatcattacat-gtactaaaactgatgaataat--agcttcgactataatatctgtaactcatccttttctttt-ttgaagGTTCGCACTATTAAAGTGGAAAAGAGGATCAATGAGATTGTGAACCGCTTGAATAAGACAAAGGTGGAACGGAAACCTGATTTAAAGG
                                                     ||| ||||| |||   | |  || |  || ||  ||    |    |||||||  |  ||||||   | | | |     |  |  |  ||||| | | ||  ||||||| ||| | | ||| || |||||||| ||||||||||| ||| |  | || |||||||| |||||| ||||||||||||| || |
gtgatttcttttacatttggatcttttccatattctttcagtttttttttccagttcttttttattttgcctttttgttttttcacagtgggtaggtagatgaatggttgagcttctgttttcagagtatcattttctggttttcatgtattttagGTTCGAACTGTAAGAGTTGAGAAGAGGATAAATGAGATTGTTAACAGGCTAAACAAGACAAAAGTGGAAAGGAAACCTGATTTGAAAG
















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|32910716|gb|CF015528.1|CF015528
EST:     AGACGCCTTCAATGGATGTGGGCCAAGTTGGTTTTCACAATCCTAAATTG                         GTTCGCACTATTAAAGTGGAAAAGAGGATCAATGAGATTGTGAACCGCTTG
genomic: AGACCCCTTCAATGGATGTAGGCCAAGTTGGTTTTCACAACCCTAAATTGgtgagagctc ... ttttttgaagGTTCGCACTATTAAAGTGGAAAAGAGGATCAATGAGATTGTGAACCGCTTG
EST: gi|32824357|gb|CD964079.1|CD964079
EST:     AGACGCCTTCAATGGATGTGGGCCAAGTTGGTTTTCACAACCCTAAATTG                         GTTCGCACTATTA
genomic: AGACCCCTTCAATGGATGTAGGCCAAGTTGGTTTTCACAACCCTAAATTGgtgagagctc ... ttttttgaagGTTCGCACTATTA
EST: gi|211490912|gb|FK946181.1|FK946181
EST:     AGACCCCTTCAATGGATGTAGGCCAAGTTGGTTTTCACAACCCTAAATTG                         GTTCGCACTATTAAAGTGGAAAAGAGGATCAATGAGATTGTGAACCGCTTG
genomic: AGACCCCTTCAATGGATGTAGGCCAAGTTGGTTTTCACAACCCTAAATTGgtgagagctc ... ttttttgaagGTTCGCACTATTAAAGTGGAAAAGAGGATCAATGAGATTGTGAACCGCTTG
EST: gi|149109676|gb|EE293462.2|EE293462
EST:     GACCCCTTCAATGGATGTAGGCCAAGTTGGTTTTCACAACCCCTAAATTG                         GTTCGCACTATTAAAGTGGAAAAGAGGATCAATGAAATTGTGAACCGCTTG
genomic: GACCCCTTCAATGGATGTAGGCCAAGTTGGTTTTCACAACCC-TAAATTGgtgagagctc ... ttttttgaagGTTCGCACTATTAAAGTGGAAAAGAGGATCAATGAGATTGTGAACCGCTTG
EST: gi|60399482|gb|DN232294.1|DN232294
EST:     AGACGCCTTCAATGGATGTGGGCCAAGTTGGTTTTCACAACCCTAAATTG                         GTTCGCACTATTAAAGTGGAAAAGAGGATCAATGAGATTGTGAACCGCTTG
genomic: AGACCCCTTCAATGGATGTAGGCCAAGTTGGTTTTCACAACCCTAAATTGgtgagagctc ... ttttttgaagGTTCGCACTATTAAAGTGGAAAAGAGGATCAATGAGATTGTGAACCGCTTG
EST: gi|211496693|gb|FK946217.1|FK946217
EST:     AGACCCCTTCAATGGATGTAGGCCAAGTTGGTTTTCACAACCCTAAATTG                         GTTCGCACTATTAAAGTGGAAAAGAGGATCAATGAGATTGTGAACCGCTTG
genomic: AGACCCCTTCAATGGATGTAGGCCAAGTTGGTTTTCACAACCCTAAATTGgtgagagctc ... ttttttgaagGTTCGCACTATTAAAGTGGAAAAGAGGATCAATGAGATTGTGAACCGCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgaataatagcttcgactataatatctgtaactcatccttttcttttttgaagGTTCGCACTATTAAAGTGGAAAAGAGGATCAATGAGATTGTGAACCGCTTGAATAAGACAAAGGTGGAACGGAAACCTGATTTAAAGG
                           ctgtaac  putative branch site (score: 3)
                              taactcatccttttct  CT-rich tract
                   tataatatctgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcgttatttttattgcacatgcttatcattacatgtactaaaactgatgaataatagcttcgactataatatctgtaactcatccttttcttttttgaagGTTCGCACTATTAAAGTGGAAAAGAGGATCAATGAGATTGTGAACCGCTTGAATAAGACAAAGGTGGAACGGAAACCTGATTTAAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA