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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATAGTGAGCGTGTCGATGAGTATGGACTCGGGGTTAGAGAAAGTTTGGCTGAGGCTGTCAATGCTGTCATTAATATCCTTGGAATGCAGCCGTGTGAGgtcagtttccaattctcaatttcagaaatcgtcaaatccccccccccccccccacccccaccccccacgcatcattaggtatttctgggctataacattg...

Basic information

species Zea mays
transcript GRMZM2G012501_T02
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G012501_T02 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os03g12590.1 (Oryza sativa), 5'ss of exon 17
AGATAGTGAGCGTGTCGATGAGTATGGACTCGGGGTTAGAGAAAGTTTGGCTGAGGCTGTCAATGCTGTCATTAATATCCTTGGAATGCAGCCGTGTGAGgtcagtttccaattctcaatttcagaaatcgtcaaatccccccccccccccccacccccaccccccacgcatcattaggtatttctgggctataa-cattg-------------------------
||| |||||||||||||||||||||||||| || |||||||| || |||||||||||||| | ||||||||||| ||||||||| |||||||| ||||||||||||||||| ||||   |   |   ||||| |    |||  |  |            |           ||||| ||| |||  |   | |||   | |                         
AGAAAGTGAGCGTGTCGATGAGTATGGACTTGGTGTTAGAGAGAGCTTGGCTGAGGCTGTGAGTGCTGTCATTAGTATCCTTGGTATGCAGCCTTGTGAGgtcagtttccacttct-gttcctattcatcgtaattggccctacatcatttggtttttgagaaatttaaattcatttggtttttgagaaatttaaatgtcgctaaatccttgcgcatgtttggcag

upper sequence: GRMZM2G012501_T02 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA11G12610.1 (Glycine max), 5'ss of exon 17
AGATAGTGAGCGTGTCGATGAGTATGGACTCGGGGTTAGAGAAAGTTTGGCTGAGGCTGTCAATGCTGTCATTAATATCCTTGGAATGCAGCCGTGTGAGgtcagtttccaattctcaatttcagaaatcgtcaaatccccccccccccccccacccccaccccccacgcatcattaggt-atttctgggctataacattg---
 ||  ||||||| || ||||| ||||| || ||    || || ||||||||||| ||||| ||| | ||||||||| | ||||| |||||||| |||||||| || |    ||  |||||  | |   | ||  ||               |||  ||||          ||  ||  || |||| |    | |   | ||   
TGACTGTGAGCGAGTGGATGAATATGGTCTTGGCCCCAGGGAGAGTTTGGCTGAAGCTGTAAATACCGTCATTAATCTTCTTGGGATGCAGCCTTGTGAGgtaagctaatgatg-tcaatagctgctttggt--aaatgtttgttaggagaccagacccattatattaaaatggttgagtcatttgtacaatttt-tactgcaa
















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|211362769|gb|FL362321.1|FL362321
EST:     CTGAGGCTGTCAATGCTGTCATTAATATCCTTGGAATGCAGCCGTGTGAG                         GGCACTGAGGTTGTACCGAAAAATGCAAGATCGCACACCTGCCTTCTATCT
genomic: CTGAGGCTGTCAATGCTGTCATTAATATCCTTGGAATGCAGCCGTGTGAGgtcagtttcc ... tacttttcagGGCACTGAGGTTGTACCGAAAAATGCAAGATCGCACACCTGCCTTCTATCT
EST: gi|31350725|gb|CD435082.1|CD435082
EST:     CTGAGGCTGTCAATGCTGTCATTAATATCCTTGGAATGCAGCCGTGTGAG                         GGCACTGAGGTTGTACCGAAAAATGCAAAATCGCACACCTGCCTTCTATCT
genomic: CTGAGGCTGTCAATGCTGTCATTAATATCCTTGGAATGCAGCCGTGTGAGgtcagtttcc ... tacttttcagGGCACTGAGGTTGTACCGAAAAATGCAAGATCGCACACCTGCCTTCTATCT
EST: gi|33093956|gb|CF053950.1|CF053950
EST:     CTGAGGCTGTCAATGCTGTCATTAATATCCTTGGAATGCAGCCGTGTGAG                         GGCACTGAGGTTGTACC
genomic: CTGAGGCTGTCAATGCTGTCATTAATATCCTTGGAATGCAGCCGTGTGAGgtcagtttcc ... tacttttcagGGCACTGAGGTTGTACC
EST: gi|211483291|gb|FL326634.1|FL326634
EST:     CTGAGGCTGTCAATGCTGTCATTAATATCCTTGGAATGCAGCCGTGTGAG                         GGCACTGAGGTTGTACCGAAAAATGCAAGATCGCACACCTGCCTTCTATCT
genomic: CTGAGGCTGTCAATGCTGTCATTAATATCCTTGGAATGCAGCCGTGTGAGgtcagtttcc ... tacttttcagGGCACTGAGGTTGTACCGAAAAATGCAAGATCGCACACCTGCCTTCTATCT
EST: gi|32910290|gb|CF015102.1|CF015102
EST:     CTGAGGCTGTCAATGCTGTCATTAATATCCTTGGAATGCAGCCGTGTGAG                         GGCACTGAGGTTGTACCGAAAAATGCAAGATCGCACACCTGCCTTCTATCT
genomic: CTGAGGCTGTCAATGCTGTCATTAATATCCTTGGAATGCAGCCGTGTGAGgtcagtttcc ... tacttttcagGGCACTGAGGTTGTACCGAAAAATGCAAGATCGCACACCTGCCTTCTATCT
EST: gi|5343172|gb|AI795357.1|AI795357
EST:     CTGAGGCTGTCAATGCTGTCATTAATATCCTTGGAATGCAGCCGTGTGAG                         GGCACTGAGGTTGTACCGAAAAATGCAAGATCGCACACCTGCCTTCTATCT
genomic: CTGAGGCTGTCAATGCTGTCATTAATATCCTTGGAATGCAGCCGTGTGAGgtcagtttcc ... tacttttcagGGCACTGAGGTTGTACCGAAAAATGCAAGATCGCACACCTGCCTTCTATCT
EST: gi|91049226|gb|EB159644.1|EB159644
EST:     CTGAGGCTGTCAATGCTGTCATTAATATCCTTGGAATGCAGCCGTGTGAG                         GGCACTGAGGTTGTACCGAAAAATGCAAGATCGCACACCTGCCTTCTATCT
genomic: CTGAGGCTGTCAATGCTGTCATTAATATCCTTGGAATGCAGCCGTGTGAGgtcagtttcc ... tacttttcagGGCACTGAGGTTGTACCGAAAAATGCAAGATCGCACACCTGCCTTCTATCT
EST: gi|148946069|gb|EC891365.2|EC891365
EST:     CTGAGGCTGTCAATGCTGTCATTAATATCCTTGGAATGCAGCCGTGTGAG                         GGCACTGAGGTTGTACCGAAAAATGCAAGATCGCACACCTGCCTTCTATTT
genomic: CTGAGGCTGTCAATGCTGTCATTAATATCCTTGGAATGCAGCCGTGTGAGgtcagtttcc ... tacttttcagGGCACTGAGGTTGTACCGAAAAATGCAAGATCGCACACCTGCCTTCTATCT
EST: gi|211394483|gb|FL357133.1|FL357133
EST:     CTGAGGCTGTCAATGCTGTCATTAATATCCTTGGAATGCAGCCGTGTGAG                         GGCACTGAGGTTGTACC
genomic: CTGAGGCTGTCAATGCTGTCATTAATATCCTTGGAATGCAGCCGTGTGAGgtcagtttcc ... tacttttcagGGCACTGAGGTTGTACC
EST: gi|32910289|gb|CF015101.1|CF015101
EST:     CTGAGGCTGTCAATGCTGTCATTAATATCCTTGGAATGCAGCCGTGTGAG                         GGCACTGAGGTTGTACCGAAAAATGCAAGATCGCACACCTGCCTTCTATCT
genomic: CTGAGGCTGTCAATGCTGTCATTAATATCCTTGGAATGCAGCCGTGTGAGgtcagtttcc ... tacttttcagGGCACTGAGGTTGTACCGAAAAATGCAAGATCGCACACCTGCCTTCTATCT
EST: gi|6194545|gb|AW146649.1|AW146649
EST:     CTGAGGCTGTCAATGCTGTCATTAATATCCTTGGAATGCAGCCGTGTGAG                         GGCACTGAGGTTGTACCGAAAAATGCAAGATCGCACACCTGCCTTCTATCT
genomic: CTGAGGCTGTCAATGCTGTCATTAATATCCTTGGAATGCAGCCGTGTGAGgtcagtttcc ... tacttttcagGGCACTGAGGTTGTACCGAAAAATGCAAGATCGCACACCTGCCTTCTATCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATAGTGAGCGTGTCGATGAGTATGGACTCGGGGTTAGAGAAAGTTTGGCTGAGGCTGTCAATGCTGTCATTAATATCCTTGGAATGCAGCCGTGTGAGgtcagtttccaattctcaatttcagaaatcgtcaaatccccccccccccccccacccccaccccccacgcatcattaggtatttctgggctataacattg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccacgc