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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagcagcatcaacagttatatgattaccatctttattaatgtgatttcgactttagagctatatgcactactctcttttactctctatttaattatatagCCGGCTCATGAGAAGATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAAGCAGTTCCTTCACTTGGGAACCAGGGCAAGTCAGATAATGGAAGAGCAC

Basic information

species Zea mays
transcript GRMZM2G006507_T03
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006507_T03 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os02g19510.1 (Oryza sativa), 3'ss of exon 12
tagcagcatcaacagttatatgattaccatctttattaatgtgatttcgactt-----tagagctatatgcactactctcttttactctctatttaattatatagCCGGCTCATGAGAAGATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAAGCAGTTCCTTCACTTGGGAACCAGGGCAAGTCAGATAATGGAAGAGCAC
        ||  |  | |||| |||  |  |||    ||||  ||| | | |      | || |  |  ||  ||  | ||| |  | |  ||  |||||   |||| |||||||||||||||||||| || |||||||||||||||||||||||||| || || |||||||| ||||||                         
--ttgtgctccgccttcatatcattttccacttcg--aatgctattccaaatcatccatggatcactgagc-ttaaacacttctgttttacatgaaattaatcagCCTGCTCATGAGAAGATTGGAGTCGTCGATGCTCAATGGATTGTTCATCAAGCTGTGCCATCACTTGGAAACCAG-------------------------

upper sequence: GRMZM2G006507_T03 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA13G39990.1 (Glycine max), 3'ss of exon 12
--tagcagcat-caacagttatatgattaccatctttattaatgtgatttcgactttagagctatatgcactactctcttttactctctatttaattatatagCCGGCTCATGAGAAGATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAAGCAGTTCCTTCACTTGGGAACCAGGGCAAGTCAGATAATGGAAGAGCAC
   |  || |   |  |  |||  |  | | ||||  |||| |   ||     |||   ||| || ||   ||||   ||||| | |  ||    || |  |||| || ||||| || ||||| ||  ||||| | ||||||||||||||||||| | ||||||| ||||||||||||                         
gtaaatagtaaatagtaaatatgggggtgcaatctc-attacttaaataaaatcttctaagcaatttgatttacttagttttaatttgaatcc--ttttgcagCCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAG-------------------------

upper sequence: GRMZM2G006507_T03 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA12G29800.1 (Glycine max), 3'ss of exon 12
tagcagcatcaacagttatatgattaccatct--ttattaatgtgatttcgactttagagctatatgca--ctactctcttttactctctatttaattatatagCCGGCTCATGAGAAGATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAAGCAGTTCCTTCACTTGGGAACCAGGGCAAGTCAGATAATGGAAGAGCAC
       |  |  |  |||  || ||| ||||  ||| | |  | |  ||  ||    |  |   |  |   || |    |||| | |  |||   || |  |||| || ||||| || ||||| ||  ||||| | ||||||||||||||||||| | ||||||| ||||||||||||                         
----gtaaatagtaaatatgggagtacgatctcattacttaaataaaatcttctacgtaatttggtttagtttatttagctttaatttgaattcttttttgcagCCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAG-------------------------

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|87153082|gb|DY397871.1|DY397871
EST:     ACTTGGTCCATGGATGGGGTCTTGACTTTGCTCTTAGGAAATGTGTGGAG                         CCGGCTCATGAGAAGATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
genomic: ACTTGGTCCATGGATGGGGTCTTGACTTTGCTCTTAGGAAATGTGTGGAGgtattccctg ... aattatatagCCGGCTCATGAGAAGATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
EST: gi|78106684|gb|DV525102.1|DV525102
EST:     ACTTGGTCCATGGATGGGGTCTTGACTTTGCTCTTAGGAAATGTGTGGAG                         CCGGCTCATGAGAAGATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
genomic: ACTTGGTCCATGGATGGGGTCTTGACTTTGCTCTTAGGAAATGTGTGGAGgtattccctg ... aattatatagCCGGCTCATGAGAAGATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
EST: gi|74235735|gb|DT643649.1|DT643649
EST:     ACTTGGTCCATGGATGGGGTCTTGACTTTGCTCTTAGGGAATGTGTGGAG                         CCGGCTCATGAGAAGATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
genomic: ACTTGGTCCATGGATGGGGTCTTGACTTTGCTCTTAGGAAATGTGTGGAGgtattccctg ... aattatatagCCGGCTCATGAGAAGATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
EST: gi|32928781|gb|CF033593.1|CF033593
EST:     CCATGGATGGGGTCTTGACTTTGCTCTTAGGAAATGTGTGGAG                         CCGGCTCATGAGAAGATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
genomic: CCATGGATGGGGTCTTGACTTTGCTCTTAGGAAATGTGTGGAGgtattccctg ... aattatatagCCGGCTCATGAGAAGATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
EST: gi|18964823|gb|BM661216.1|BM661216
EST:     ACTTGGTCCATGGATGGGGTCTTGACTTTGCTCTTAGGAAATGTGTGGAG                         CCGGCTCATGAGAAGATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
genomic: ACTTGGTCCATGGATGGGGTCTTGACTTTGCTCTTAGGAAATGTGTGGAGgtattccctg ... aattatatagCCGGCTCATGAGAAGATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
EST: gi|31348516|gb|CD432873.1|CD432873
EST:     ACTTGGTCCATGGATGGGGTCTTTACTTTGCTCTTAGGAAATGTGTGGAG                         CCGGCTCATGAGAAGATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
genomic: ACTTGGTCCATGGATGGGGTCTTGACTTTGCTCTTAGGAAATGTGTGGAGgtattccctg ... aattatatagCCGGCTCATGAGAAGATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
EST: gi|24763232|gb|CA398411.1|CA398411
EST:     ACTTGGTCCATGGATGGGGTCTTGACTTTGCTCTTAGGAAATGTGTGGAG                         CCGGCTCATGAGAAGATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
genomic: ACTTGGTCCATGGATGGGGTCTTGACTTTGCTCTTAGGAAATGTGTGGAGgtattccctg ... aattatatagCCGGCTCATGAGAAGATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
EST: gi|22490474|gb|BU050397.1|BU050397
EST:     ACTTGGTCCATGGATGGGGTCTTGACTTTGCTCTTAGGAAATGTGTGGAG                         CCGGCTCATGAGAAGATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
genomic: ACTTGGTCCATGGATGGGGTCTTGACTTTGCTCTTAGGAAATGTGTGGAGgtattccctg ... aattatatagCCGGCTCATGAGAAGATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
EST: gi|74237173|gb|DT645087.1|DT645087
EST:     ACTTGGTCCATGGATGGGGTCTTGACTTTGCTCTTAGGAAATGTGTGGAG                         CCGGCTCATGAGAAGATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
genomic: ACTTGGTCCATGGATGGGGTCTTGACTTTGCTCTTAGGAAATGTGTGGAGgtattccctg ... aattatatagCCGGCTCATGAGAAGATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
EST: gi|32928833|gb|CF033645.1|CF033645
EST:     CCATGGATGGGGTCTTGACTTTGCTCTTAGGAAATGTGTGGAG                         CCGGCTCATGAGAAGATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
genomic: CCATGGATGGGGTCTTGACTTTGCTCTTAGGAAATGTGTGGAGgtattccctg ... aattatatagCCGGCTCATGAGAAGATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
EST: gi|88751496|gb|DY535637.1|DY535637
EST:     ACTTGGTCCATGGATGGGGTCTGGACTTTGCTCTTAGGAAATGTGTGGAG                         CCGGCTCATGAGAAGATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
genomic: ACTTGGTCCATGGATGGGGTCTTGACTTTGCTCTTAGGAAATGTGTGGAGgtattccctg ... aattatatagCCGGCTCATGAGAAGATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
EST: gi|78544004|gb|DV621502.1|DV621502
EST:     ACTTGGTCCATGGATGGGGTCTTGACTTTGCTCTTAGGAAATGTGTGGAG                         CCGGCTCATGAGAAGATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
genomic: ACTTGGTCCATGGATGGGGTCTTGACTTTGCTCTTAGGAAATGTGTGGAGgtattccctg ... aattatatagCCGGCTCATGAGAAGATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcgactttagagctatatgcactactctcttttactctctatttaattatatagCCGGCTCATGAGAAGATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAAGCAGTTCCTTCACTTGGGAACCAGGGCAAGTCAGATAATGGAAGAGCAC
                                         atttaat  putative branch site (score: 4)
                         ctctcttttactctct  CT-rich tract
                              ttttactctctattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagcagcatcaacagttatatgattaccatctttattaatgtgatttcgactttagagctatatgcactactctcttttactctctatttaattatatagCCGGCTCATGAGAAGATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAAGCAGTTCCTTCACTTGGGAACCAGGGCAAGTCAGATAATGGAAGAGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA