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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caacaggctgcacatgtctgatctacattttgagcctttcctgtaggatcacagaggcaatatgggcaatatttagagtttatcaaactgttgtttgcagGTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATATGCATTGCAAGGTCCACCCCTATTCTTGCACCAGATCTTCTTTCTCATG

Basic information

species Zea mays
transcript GRMZM2G158627_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158627_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os06g43760.1 (Oryza sativa), 3'ss of exon 24
---------------------------------------------------------------------------------------caacaggctgcacatg-tctgatctacattttgagcctttcctgtaggatcacagaggcaatatgggcaatatttagagtttatcaaactgttgtttgcagGTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATATGCATTGCAAGGTCCACCCCTATTCTTGCACCAGATCTTCTTTCTCATG
                                                                                       || || | |  |     | | |||  ||      |   ||       | | | |  |  |  |        || |     | ||    ||| | || |||||||||  |  | |||||||||||||||||||| |||||||| |||||||| | ||||||||||    | ||  |  |  ||   ||||| |||   ||||
gtgagtttggatattctccctgtttcagtttactgttaactgacttttatctctatcaattggaggatttgatttttcttacatgaacaccaagttatatgcactatcatcaccaccaattggtgttgacacgagttgaaatggatataaaacatttaatctcattgtcatttgtctggt-ttggcagGTAATGATCTGTGAGGAGTCTCACAATGTACAAGACATGTCGTTTGTCATTTACATTGCAAGGGTTTCTCCAGTGGTCACAGATGATCTCCTTGTCCATG
















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|166516458|gb|EG268171.1|EG268171
EST:     AATTATGCCAAAAGAAATGGCACCAACAGATGAT                         GTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTG-CATA
genomic: AATTATGCCAAAAGAAATGGCACCAACAGATGATgtaagtttcg ... ttgtttgcagGTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATA
EST: gi|6056632|gb|AW091037.1|AW091037
EST:     ACGCACTTGGTTCGCCAATTATGCCAAAAGAAATGGCACCAACAGATGAT                         GTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATA
genomic: ACGCACTTGGTTCACCAATTATGCCAAAAGAAATGGCACCAACAGATGATgtaagtttcg ... ttgtttgcagGTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATA
EST: gi|60345148|gb|DN212121.1|DN212121
EST:     ACGCACTTGGTTCACCAATTATGCCAAAAGAAATGGCACCAACAGATGAT                         GTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATA
genomic: ACGCACTTGGTTCACCAATTATGCCAAAAGAAATGGCACCAACAGATGATgtaagtttcg ... ttgtttgcagGTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATA
EST: gi|37373885|gb|CF623267.1|CF623267
EST:     ACGCACTTGGTTCACCAATTATGCCAAAAGAAATGGCACCAACAGATGAT                         GTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATA
genomic: ACGCACTTGGTTCACCAATTATGCCAAAAGAAATGGCACCAACAGATGATgtaagtttcg ... ttgtttgcagGTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATA
EST: gi|113702485|gb|EE679989.1|EE679989
EST:     ACGCACTTGGTTCACCAATTATGCCAAAAGAAATGGCACCAACAGATGAT                         GTATTACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATA
genomic: ACGCACTTGGTTCACCAATTATGCCAAAAGAAATGGCACCAACAGATGATgtaagtttcg ... ttgtttgcagGTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATA
EST: gi|78022271|gb|DV490658.1|DV490658
EST:     ACGCACTTGGTTCGCCAATTATGCCAAAAGAAATGGCACCAACAGATGAT                         GTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATA
genomic: ACGCACTTGGTTCACCAATTATGCCAAAAGAAATGGCACCAACAGATGATgtaagtttcg ... ttgtttgcagGTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATA
EST: gi|60337676|gb|DN204649.1|DN204649
EST:     ACGCACTTGGTTCACCAATTATGCCAAAAGAAATGGCACCAACAGATGAT                         GTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATA
genomic: ACGCACTTGGTTCACCAATTATGCCAAAAGAAATGGCACCAACAGATGATgtaagtttcg ... ttgtttgcagGTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatcacagaggcaatatgggcaatatttagagtttatcaaactgttgtttgcagGTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATATGCATTGCAAGGTCCACCCCTATTCTTGCACCAGATCTTCTTTCTCATG
                      aatatttagagtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caacaggctgcacatgtctgatctacattttgagcctttcctgtaggatcacagaggcaatatgggcaatatttagagtttatcaaactgttgtttgcagGTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATATGCATTGCAAGGTCCACCCCTATTCTTGCACCAGATCTTCTTTCTCATG

- - - gctgcac
- - - - - - -atgtctg
- - - - - - - - - - - -tacattt