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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGAATCCTAGGATAGTAATGCAGTGCTCACACCATTTCCACCTTGGCTGTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGTCTGTGGAAAGgtaatttgtttatctctttgcttacccttataatttattattgctgtcacacatatgtgaagcccgacacaaaatttatgtcacctgttctacgatgaag...

Basic information

species Zea mays
transcript GRMZM2G468260_T04
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G468260_T04 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os11g41140.1 (Oryza sativa), 5'ss of exon 4
TGAGAATCCTAGGATAGTAATGCAGTGCTCACACCATTTCCACCTTGGCTGTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGTCTGTGGAAAGgtaattt--gtttatctctttgcttacccttataatttattattgctgtcacacatatgtgaagcccgacacaaaatttatgtcacct--gttctacgatgaag
||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||||||||||||||   |||| |||||  |||    ||     |||| |||  |||| ||  ||| ||         || |  |||   |   ||  || |||||   || 
TGAGAATCCTAGGATAGTAATGCAGTGCTCACATCATTTCCACCTTGGCTGTATTTATGAGTGGATGGAAAGAAGTGAAGCATGCCCTGTTTGTGGAAAGgtaattttgctttagctcttc-cttttttttcctccttataatttttgtc-cagttatatgctttgttg-actatgtttgctttttctaggtactacgtacaa-

upper sequence: GRMZM2G468260_T04 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA18G50950.1 (Glycine max), 5'ss of exon 4
TGAGAATCCTAGGATAGTAATGCAGTGCTCACACCATTTCCACCTTGGCTGTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGTCTGTGGAAAGgtaatttgtttatctctttgcttacccttataatttattattgctgtcacacatatgtgaagcccgacacaaaatttatgtcacctgttctacgatgaag----
 |||||||| | |||||| |   | ||||| || ||||| || ||| | |||||||||||||||||||||||||||||    || || || ||||| |||||||| | ||  |    ||   |    ||||   | | |         |     ||    |    ||  ||   | ||  | | | |   || || ||      
-GAGAATCCGAAGATAGTGACAAAATGCTCTCATCATTTTCATCTTTGTTGTATTTATGAGTGGATGGAAAGAAGTGACAACTGTCCCGTTTGTGGGAAGGtaatattttcttggtattttctgaa-ttatttctcactgaaatgactaagttcat-cagaatttgatgcatgttctacataaac-gaggtaggaagactggct

upper sequence: GRMZM2G468260_T04 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA08G27730.1 (Glycine max), 5'ss of exon 4
TGAGAATCCTAGGATAGTAATGCAGTGCTCACACCATTTCCACCTTGGCTGTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGTCTGTGGAAAGgtaatttgtttatctctttgcttacccttataatttattattgctgtcacacatatgtgaagcccg-acacaaaatttatgtcacctgttctacgatgaag-
 |||||||| | |||||| |   | ||||| || ||||| || ||||| || ||||||||||||||||||||||||||    || ||||| ||||| |||||||  | ||||  |  |   ||    ||||   | | |        ||     |   |||    |  || | ||   ||   | | ||   | ||  |   
AGAGAATCCGAAGATAGTGACAAAATGCTCTCATCATTTTCATCTTGGTTGCATTTATGAGTGGATGGAAAGAAGTGACAGCTGTCCTGTTTGTGGGAAGgtaa--tatttacttggtattttcgaattatttctcactgaaatgaccaagttcaacagaaattagtgcatagaacacatcaaagcagtaggatgagaacct

upper sequence: GRMZM2G468260_T04 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA13G06840.1 (Glycine max), 5'ss of exon 3
TGAGAATCCTAGGATAGTAATGCAGTGCTCACACCATTTCCACCTTGGCTGTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGTCTGTGGAAAGgtaatttgtttatctctttgcttacccttataatttattattgctgtcacacatatgtgaagcccgacacaaaatttatgtcacctgttctacgatgaag--
 |||||||| | |||| | |   | ||||| || ||||| |||||||| || ||||||||||||||||| ||||||||    || |||||||||||||||||| |   |     | | |   |||  |   ||    || ||  |     |  ||| | ||       |  |   ||   |  |     ||   || ||   
AGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTCACCTTGGTTGCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGTCTGTGGAAAGgtactacatagtattttctaaatact-taggaaaacgttttttttagtttatttatttaaaatatttgaagatgattcaattgca-acactgtaataaaata

upper sequence: GRMZM2G468260_T04 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA19G04340.1 (Glycine max), 5'ss of exon 4
TGAGAATCCTAGGATAGTAATGCAGTGCTCACACCATTTCCACCTTGGCTGTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGTCTGTGGAAAGgtaatttgtttatctctttgcttacccttataatttattattgctgtcacacatatgtgaagcccgacacaaaatttatgtcacctgttctacgatgaag-
 |||||||| | |||| | |   | ||||| || ||||| |||||||| || ||||||||||||||||| ||||||||    || || || ||||||||||||||   ||  | | ||         || |  ||| ||| | |  |  ||   | |   |    ||||  ||  |         ||||||  || |    
AGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTCACCTTGGTTGCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCAGTTTGTGGAAAGgtaatac-ttagtattttctaaggattttttttttttttacttcattagcaatgaagcagaaatggacaggaatatatcaaattttgttctgagaagtgaa

upper sequence: GRMZM2G468260_T04 (Zea mays), 5'ss of exon 1
lower sequence: AT3G02290.2 (Arabidopsis thaliana), 5'ss of exon 3
TGAGAATCCTAGGATAGTAATGCAGTGCTCACACCATTTCCACCTTGGCTGTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGTCTGTGGAAAGgtaatttgtttatctctttgcttacccttataatttattattgctgtcacacatatgtgaagcccgacacaaaatttatgtcacctgttctacgatgaag----
 ||||| || | ||| || |   | || |||||||||||||||||| | || ||||||||||||||||| ||||||||    || || ||||| ||||||||||    ||| | | | |||  |  |||| ||   | |     |   || |   |   ||||   |  | | ||   | ||     ||  ||| |  ||    
AGAGAACCCAAAGATTGTGACAAAATGTTCACACCATTTCCACCTTAGTTGCATTTATGAGTGGATGGAGAGAAGTGAAAACTGTCCAGTCTGCGGAAAGgtaaccactttttttttctgc--attcttagaacgaagtgcgtataaaactcccgt-caaagcaaaaggccatatgcttttcgaa-attgcacggtctagatga

upper sequence: GRMZM2G468260_T04 (Zea mays), 5'ss of exon 1
lower sequence: AT5G38895.1 (Arabidopsis thaliana), 5'ss of exon 4
TGAGAATCCTAGGATAGTAATGCAGTGCTCACACCATTTCCACCTTGGCTGTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGTCTGTGGAAAGgtaatttgtttatctctttgcttacccttataatttattattgctgtcacacatatgtgaagcccgaca-caaaatttatgtcacct-gttctacgatgaag
 |||||||| | |||| | |   |||| || ||||||||||||||| ||||||||||||| |||||||| ||||||||  | ||||| |||||||||||||||| | ||    || | | |  | | ||| ||       ||| |   |          |   ||  || | | ||| |     | |  || |    |  | 
GGAGAATCCGAAGATAATCACCAAGTGTTCTCACCATTTCCACCTTAGCTGTATTTATGAATGGATGGAGAGAAGTGAAACTTGCCCCGTCTGTGGAAAGgtaactcgtc--gctttctacaaaactttaaaacccggatttggtcgaatgttccatcaatctccttcatcgatattaaaagtgcatcattttgtattagaa

upper sequence: GRMZM2G468260_T04 (Zea mays), 5'ss of exon 1
lower sequence: AT5G15790.2 (Arabidopsis thaliana), 5'ss of exon 4
TGAGAATCCTAGGATAGTAATGCAGTGCTCACACCATTTCCACCTTGGCTGTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGTCTGTGGAAAGgtaatttgtttatctctttgcttacccttataatttattattgctgtcacacatatgtgaagcccgacacaaaatttatgtcacctgt-tctacgatgaag
 ||||| || | ||| || |   |||| || ||||||||||||||  | || |||||||| |||||||| ||||||||    |||||||| |||||||||||||    |||   | ||     |  |   |  |    |  |  | |   |    |    || | ||| || |    ||  | | |   |  ||||   | 
AGAGAACCCGAAGATTGTTACAAAGTGTTCTCACCATTTCCACCTCAGTTGCATTTATGAATGGATGGAGAGAAGTGAAAACTGCCCTGTTTGTGGAAAGgtaaacacttttcatgttcttccaagccagttttcggcttctcatttactagtgtttcagagtcagactcagacaccatcacgcgtaaatagacgagtga-

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|211285705|gb|FL480404.1|FL480404
EST:     GTATTTATGAGTGGATGGAAAGAAGTGAAGCATGCCCTGTCTGTGGAAAG                         AAGATGGAGTTTGACGAGACAACATAATCCTCTGGCTGGACTCTACACCAT
genomic: GTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGTCTGTGGAAAGgtaatttgtt ... ttcaatgcagAAGATGGAGTTTGACGAGACAACATAATCCTCTGGCTGGACTCTACACCAT




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGAATCCTAGGATAGTAATGCAGTGCTCACACCATTTCCACCTTGGCTGTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGTCTGTGGAAAGgtaatttgtttatctctttgcttacccttataatttattattgctgtcacacatatgtgaagcccgacacaaaatttatgtcacctgttctacgatgaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT