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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctccccgctgccttctccgctccatatattgtctgcactattatgcctcatgctaatatcaatgtccattacttgacacagGCTGGAGAAACAATCGAGCACAACCAGCTTCATACCCAAGTCGATTACAGAGCGTTTTACCCGTTGAGCTTCCACTCGTTTCCAGAACAATGTGACATTT

Basic information

species Zea mays
transcript GRMZM2G177914_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G177914_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g12710.1 (Oryza sativa), 3'ss of exon 7
----gttctccccgctgccttctccgctccatatattgtctgcactattatgcctcatgctaatatcaatgtccattacttgacacagGCTGGAGAAACAATCGAGCACAACCAGCTTCATACCCAAGTCGATTACAGAGCGTTTTACCCGTTGAGCTTCCACTCGTTTCCAGAACAATGTG-ACATTT
     | || || ||||||||| ||  | || || |||  ||||   |||    | || ||||   || | | | || |||||| ||||||||||||||| || | |||||||||| ||||||| ||||||||| |||||||||| | |||||||||    |   | |||    |   | || |||   
gttcttacttcctgctgccttcccc-ttgcacatgttgcgtgcatgtttacatgtaatcctaa---cagtattcgtttcttgacgcagGCTGGAGAAACAGTCAAACACAACCAGCCTCATACCGAAGTCGATTTCAGAGCGTTTCAGCCGTTGAGCCGTGAGA-GCTTCACTCATGTTATGGACAGAA

upper sequence: GRMZM2G177914_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g25110.1 (Oryza sativa), 3'ss of exon 5
--------------------gttctccccgctgccttctccgctccatatattgtctgcactattatgcctcatgctaatatcaatgtccattacttgacacagGCTGGAGAAACAATCGAGCACAACCAGCTTCATACCCAAGTCGATTACAGAGCGTTTTACCCGTTGAGCTTCCACTCGTTTCCAGAACAATGTGACATTT--
                     | || || ||||||||| ||  | || || |||   |||   |||    | || ||||   || | | | || |||||||||||||||||||||| || | |||||||||| ||||||| ||||||||| |||||||||| | ||| |||||      || |   |||||   |   |   ||  
tagaagagattgcaaggttcttacttcctgctgccttcccc-ttgcacatgttgcgagcatgtttacatgtaatcctaa---cagtattcgtttcttgacacagGCTGGAGAAACAGTCAAACACAACCAGCCTCATACCGAAGTCGATTTCAGAGCGTTTCAGCCGATGAGCCGTG--TCATGGACAGAAACTTTGAAGGCTTGA
















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|71436744|gb|DR817794.1|DR817794
EST:     TCAAAACAAGTTCAGAACAGATAATGAAATCTGTGGGAAAAGATTGAAAG                         GCTGGAGAAACAATCG
genomic: TCGAAACAAGTTCAGAACAGATAATGAAATCTGTGG-AAGAGATTGAAAGgttctccccg ... cttgacacagGCTGGAGAAACAATCG
EST: gi|71758093|gb|DR956030.1|DR956030
EST:     ATCGAAACAAGTTCAGAACAGATAATGAAATCTGTGGAAGAGATTGAAAG                         GCTGGAGAAACAATCGAGCACAACCAGCTTCATACCCAAGTCGATTACAGA
genomic: ATCGAAACAAGTTCAGAACAGATAATGAAATCTGTGGAAGAGATTGAAAGgttctccccg ... cttgacacagGCTGGAGAAACAATCGAGCACAACCAGCTTCATACCCAAGTCGATTACAGA
EST: gi|84980466|gb|DW530815.1|DW530815
EST:     ATCGAAACAAGTTCAGAACAGATAATGAAATCTGTGGAAGAGATTGAAAG                         GCTGGAGAAACAATCGAGCACAACCAGCTTCATACCCAAGTCGATTACAGA
genomic: ATCGAAACAAGTTCAGAACAGATAATGAAATCTGTGGAAGAGATTGAAAGgttctccccg ... cttgacacagGCTGGAGAAACAATCGAGCACAACCAGCTTCATACCCAAGTCGATTACAGA
EST: gi|78110300|gb|DV528715.1|DV528715
EST:     ATCGAAACAAGTTCAGAACAGATAATGAAATCTGTGGAAGAGATTGAAAG                         GCTGGAGAAACAATCGAGCACAACCAGCTTCATACCCAAGTCGATTACAGA
genomic: ATCGAAACAAGTTCAGAACAGATAATGAAATCTGTGGAAGAGATTGAAAGgttctccccg ... cttgacacagGCTGGAGAAACAATCGAGCACAACCAGCTTCATACCCAAGTCGATTACAGA
EST: gi|71771237|gb|DR969174.1|DR969174
EST:     ATCGAAACAAGTTCAGAACAGATAATGAAATCTGTGGAAGAGATTGAAAG                         GCTGGAGAAACAATCGAGCACAACCAGCTTCATACCCGAGTCGATTACAGA
genomic: ATCGAAACAAGTTCAGAACAGATAATGAAATCTGTGGAAGAGATTGAAAGgttctccccg ... cttgacacagGCTGGAGAAACAATCGAGCACAACCAGCTTCATACCCAAGTCGATTACAGA
EST: gi|19769487|gb|BQ034208.1|BQ034208
EST:     ATCGAAACAAGTTCAGAACAGATAATGAAATCTGTGGAAGAGATTGAAAG                         GCTGGAGAAACAATCGAGCACAACCAGCTTCATACCCAAGTCGATTACAGA
genomic: ATCGAAACAAGTTCAGAACAGATAATGAAATCTGTGGAAGAGATTGAAAGgttctccccg ... cttgacacagGCTGGAGAAACAATCGAGCACAACCAGCTTCATACCCAAGTCGATTACAGA
EST: gi|18162805|gb|BM332644.1|BM332644
EST:     ATCGAAACAAGTTCAGAACAGATAATGAAATCTGTGGAAGAGATTGAAAG                         GCTGGAGAAACAATCGAGCACAACCAGCTTCATACCCAAGTCGATTACAGA
genomic: ATCGAAACAAGTTCAGAACAGATAATGAAATCTGTGGAAGAGATTGAAAGgttctccccg ... cttgacacagGCTGGAGAAACAATCGAGCACAACCAGCTTCATACCCAAGTCGATTACAGA
EST: gi|9742647|gb|BE518795.1|BE518795
EST:     ATCGAAACAAGTTCAGAACAGATAATGAAATCTGTGGAACACATTGAAAG                         GCTGGAGAAACAATCGAGCACAACCAGCTTCATACCCAAGTCGATTACAGA
genomic: ATCGAAACAAGTTCAGAACAGATAATGAAATCTGTGGAAGAGATTGAAAGgttctccccg ... cttgacacagGCTGGAGAAACAATCGAGCACAACCAGCTTCATACCCAAGTCGATTACAGA
EST: gi|37379099|gb|CF626280.1|CF626280
EST:     ATCGAAACAAGTTCAGAACAGATAATGAAATCTGTGGAAGAGATTGAAAG                         GCTGGAGAAACAATCGAGCACAACCAGCTTCATACCCAAGTCGATTACAGA
genomic: ATCGAAACAAGTTCAGAACAGATAATGAAATCTGTGGAAGAGATTGAAAGgttctccccg ... cttgacacagGCTGGAGAAACAATCGAGCACAACCAGCTTCATACCCAAGTCGATTACAGA
EST: gi|78110301|gb|DV528716.1|DV528716
EST:     ATCGAAACAAGTTCAGAACAGATAATGAAATCTGTGGAAGAGATTGAAAG                         GCTGGAGAAACAATCGAGCANCA-CCAGCTTCATACCCAAGTCGATTACAG
genomic: ATCGAAACAAGTTCAGAACAGATAATGAAATCTGTGGAAGAGATTGAAAGgttctccccg ... cttgacacagGCTGGAGAAACAATCGAGCA-CAACCAGCTTCATACCCAAGTCGATTACAG
EST: gi|148948825|gb|EC894231.2|EC894231
EST:     ATCGAAACAAGTTCAGAACAGATAATGAAATCTGTGGAAGAGATTGAAAG                         GCTGGAGAAACAATCGAGCACAACCAGCTTCATACCCAAGTCGATTACAGA
genomic: ATCGAAACAAGTTCAGAACAGATAATGAAATCTGTGGAAGAGATTGAAAGgttctccccg ... cttgacacagGCTGGAGAAACAATCGAGCACAACCAGCTTCATACCCAAGTCGATTACAGA
EST: gi|149107282|gb|EE189165.2|EE189165
EST:     ATCGAAACAAGTTCAGAACAGATAATGAAATCTGTGGAAGAGATTGAAAG                         GCTGGAGAAACAATCGAGCACAACCAGCTTCATACCCAAGTCGATTACAGA
genomic: ATCGAAACAAGTTCAGAACAGATAATGAAATCTGTGGAAGAGATTGAAAGgttctccccg ... cttgacacagGCTGGAGAAACAATCGAGCACAACCAGCTTCATACCCAAGTCGATTACAGA
EST: gi|149107281|gb|EE189164.2|EE189164
EST:     ATCGAAACAAGTTCAGAACAGATAATGAAATCTGTGGAAGAGATTGAAAG                         GCTGGAGAAACAATCGAGCACAACCAGCTTCATACCCAAGTCGATTACAGA
genomic: ATCGAAACAAGTTCAGAACAGATAATGAAATCTGTGGAAGAGATTGAAAGgttctccccg ... cttgacacagGCTGGAGAAACAATCGAGCACAACCAGCTTCATACCCAAGTCGATTACAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgtctgcactattatgcctcatgctaatatcaatgtccattacttgacacagGCTGGAGAAACAATCGAGCACAACCAGCTTCATACCCAAGTCGATTACAGAGCGTTTTACCCGTTGAGCTTCCACTCGTTTCCAGAACAATGTGACATTT
                           taatatcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttctccccgctgccttctccgctccatatattgtctgcactattatgcctcatgctaatatcaatgtccattacttgacacagGCTGGAGAAACAATCGAGCACAACCAGCTTCATACCCAAGTCGATTACAGAGCGTTTTACCCGTTGAGCTTCCACTCGTTTCCAGAACAATGTGACATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT