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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATGGCAAGGATGATCTGATGAATTTTGAGATCACCATCCGACCTGATGAAGGATATTACATgtaagtgccactcttgagggtagttgctatgctgcacaaagcataattaagggagccttttccaactgcaataatatgtatgttgtggttctagtggaaa...

Basic information

species Zea mays
transcript GRMZM2G115939_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G115939_T04 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os10g11260.3 (Oryza sativa), 5'ss of exon 3
AGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATGGCAAGGATGATCTGATGAATTTTGAGATCACCATCCGACCTGATGAAGGATATTACATgtaagt-----gccactcttgagggtagttgctatgctgcacaaagcataattaagggagccttttccaactgcaataatatgtatgttgtggttctagtggaaa-
|||| ||||| || |||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| | ||||||||||||||||||||||| |||||||     ||  ||||     ||  ||  |||| ||  |   |||  |       ||  | |  ||| |  || ||  |  |     |  || ||   ||   
AGCTAAACCTACCCAAGAGCACATCAATTTCTTTTCCCAATGGCAAGGATGATCTGATGAATTTTGAGATCATCGTCCGACCTGATGAAGGATATTACCTgtaagtagaatgcatctctgttttgtgtttattatgttgttct--gcactacctcacaagtttatgtcaatttaaagaaccttcac----tatttttaaaagatca

upper sequence: GRMZM2G115939_T04 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA01G38470.2 (Glycine max), 5'ss of exon 1
AGCTCAACCTGCCGAAGACCACAT-CAATTTCTTTTCCCAATGGCAAGGATGATCTGATGAATTTTGAGATCACCATCCGACCTGATGAAGGATATTACATgtaagtgccactcttgagggtagttgctatgctgcacaaagcataattaagggagccttttccaactgcaataatatgtatgttgtggttctagtggaaa----
|||| || || || || | ||  | | ||    || ||||||||||| |||||||||||||| |||||  |  | || ||||||||||| ||||||||| |||||||  ||      ||  |   || |||  |   || |  ||  ||||    |  |  || ||||  ||| |  | | ||  |    || ||  |  |    
AGCTGAATCTACC-AAAATCATGTACCATGCAATTCCCCAATGGCAAAGATGATCTGATGAACTTTGAAGTTTCAATTCGACCTGATGATGGATATTACTTgtaagttgcaagg--aagtttccatgttattatctgcatacaatttttaactttg--tgatcaaactttaatcaactctttgaaggcactcaagctgctatgtt

upper sequence: GRMZM2G115939_T04 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA11G06830.1 (Glycine max), 5'ss of exon 3
AGCTCAACCTGCCGAAGACCACAT-CAATTTCTTTTCCCAATGGCAAGGATGATCTGATGAATTTTGAGATCACCATCCGACCTGATGAAGGATATTACATgtaagtgccactcttgagggta-gttgctatgctgcacaaagcat--aattaagggagccttttccaactgcaataatatgtatgttgtggttctagtggaaa
|||| || || || || | ||  | | ||    || ||||||||||| ||||| |||||||| |||||  |  | || ||||||||||| ||||||||| |||||||   |     |    || |||  ||| ||||| | |   |  || |  | || ||   |  || ||        || | |   |    ||  |     
AGCTGAATCTACC-AAAATCATGTACCATGCAATTCCCCAATGGCAAAGATGACCTGATGAACTTTGAAGTTTCAATTCGACCTGATGATGGATATTACTTgtaagttgtaaggaagtttctatgttattat-ctgcatacaattttcaactttgtgatccaactttaattgactcttgttgaaggcactcaagctgctatg--

upper sequence: GRMZM2G115939_T04 (Zea mays), 5'ss of exon 3
lower sequence: AT2G18600.1 (Arabidopsis thaliana), 5'ss of exon 3
AGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATGGCAAGGATGATCTGATGAATTTTGAGATCACCATCCGACCTGATGAAGGATATTACATgtaagtgccactcttgagggtagttgctatgctgcacaaagcataattaagggagcctt--ttccaactgcaata-atatgtatgttgtggttctagtggaaa--
|||| ||| | || ||| |       || |||||||| ||||| ||| ||||  |||||||||||||  | |||||   ||||||||||||||||||| |||||||          |    | |  ||||  | ||       |  ||  |||  |||   ||    |   || | |    |  ||| | ||| ||    ||   
AGCTGAACTTACCAAAGTCTTGTAAGATATCTTTTCCGAATGGGAAGAATGACTTGATGAATTTTGAAGTAACCATTAAACCTGATGAAGGATATTACTTgtaagta---------aacaaaatctctatctttcat---ttttgtttttgggtccctgaatttgcgcaaaaacacactcattcgttcttgttatacctaaacag

upper sequence: GRMZM2G115939_T04 (Zea mays), 5'ss of exon 3
lower sequence: Vv03s0063g02110.t01 (Vitis vinifera), 5'ss of exon 4
AGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATGGCAAGGATGATCTGATGAATTTTGAGATCACCATCCGACCTGATGAAGGATATTACATgtaagtgccactcttgagggtagttgctatgctgcacaaagcataattaaggga-gccttttccaactgcaataatatgtat-gttgtggttctagtggaaa
| || || || || || ||    |  || || |||||||||||||||||||| |||||||  |||||| | ||||| || |||||||||||||| ||  ||||||||    | |  |  ||  ||  | | |      || |||  ||||  |  |   ||||| | || |   |  |  |  |  |   ||  ||| ||  
AACTGAATCTACCCAAAACTTGTTGCATATCATTTCCCAATGGCAAGGATGACCTGATGAGCTTTGAGGTTACCATTCGGCCTGATGAAGGATACTATTTgtaagtgattttttgcacagttctt--tgtacattcttaatcatgtttaaatgttgttctttcctattgtatctactttcaccgaagatctttgagttgact

upper sequence: GRMZM2G115939_T04 (Zea mays), 5'ss of exon 3
lower sequence: Vv18s0001g12010.t01 (Vitis vinifera), 5'ss of exon 2
AGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATGGCAAGGATGATCTGATGAATTTTGAGATCACCATCCGACCTGATGAAGGATATTACATgtaagtg-ccact--------cttgagggtagttgct--atgctgcacaaagcataattaagggagccttttccaactgcaataatatgtatgttgtggttctagtggaaa
|| | ||||| ||  |  |       || || || |||||||| |||||||||||  |||| ||||||||||| || || ||||||||||||| |||   ||||||   || |        | | || | | ||| |  ||| |  ||||    ||    || | |  |  || ||  ||  | | ||  |   ||  |||          
AGTTGAACCTACCTGAATCTTGTGGCATATCATTCCCCAATGGGAAGGATGATCTCTTGAACTTTGAGATCACTATTCGGCCTGATGAAGGATTTTATGGgtaagtaatcatttccaagtaccttagagaatttgttcaatgttagacaacttttatgctagtgtga-taatctaatggcgtttaaatacactctgcagtt----------

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|211259767|gb|FL311710.1|FL311710
EST:     GATCTGATGAATTTTGAGATCACCATCCGACCTGATGAAGGATATTACAT                         GGGAGGCGCTTTCGTTTTCACCTTTCAAGTGTCCCCATCTTATCCTCATGA
genomic: GATCTGATGAATTTTGAGATCACCATCCGACCTGATGAAGGATATTACATgtaagtgcca ... tcttttttagGGGAGGCGCTTTCGTTTTCACCTTTCAAGTGTCCCCATCTTATCCTCATGA
EST: gi|211398788|gb|FL318386.1|FL318386
EST:     GATCTGATGAATTTTGAGATCACCATCCGACCTGATGAAGGATATTACAT                         GGGAGGCGCTTTCGTTTTCACCTTTCAAGTGT
genomic: GATCTGATGAATTTTGAGATCACCATCCGACCTGATGAAGGATATTACATgtaagtgcca ... tcttttttagGGGAGGCGCTTTCGTTTTCACCTTTCAAGTGT
EST: gi|211472923|gb|FL342170.1|FL342170
EST:     GATCTGATGAATTTTGAGATCACCATCCGACCTGATGAAGGATATTACAT                         GGGAGGCGCTTTCGTTTTCACCTTTCAAGTGTCCCCATCTTATCCTCATGA
genomic: GATCTGATGAATTTTGAGATCACCATCCGACCTGATGAAGGATATTACATgtaagtgcca ... tcttttttagGGGAGGCGCTTTCGTTTTCACCTTTCAAGTGTCCCCATCTTATCCTCATGA
EST: gi|211118985|gb|FL350356.1|FL350356
EST:     GATCTGATGAATTTTGAGATCACCATCCGACCTGATGAAGGATATTACAT                         GGGAGGCGCTTTCGTTTTCACCTTTCAAGTGTCCCCATCTTATCCTCATGA
genomic: GATCTGATGAATTTTGAGATCACCATCCGACCTGATGAAGGATATTACATgtaagtgcca ... tcttttttagGGGAGGCGCTTTCGTTTTCACCTTTCAAGTGTCCCCATCTTATCCTCATGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATGGCAAGGATGATCTGATGAATTTTGAGATCACCATCCGACCTGATGAAGGATATTACATgtaagtgccactcttgagggtagttgctatgctgcacaaagcataattaagggagccttttccaactgcaataatatgtatgttgtggttctagtggaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA