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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAGAAGCGGATATACCTCGTCTTCGAGTACCTGGATCTGGACCTCAAGAAGTTCATGGACTCTTGCCCGGAGTTTGCTAAGAATCCCACTTTGATTAAGgtgaagaagcacatgatatgttagtttgtgactgctagtctgcgccttgcttctgtcctgctccgcatatagataaactcgagccatgactcatgcattt...

Basic information

species Zea mays
transcript GRMZM2G143213_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143213_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g02680.1 (Oryza sativa), 5'ss of exon 2
CGAGAAGCGGATATACCTCGTCTTCGAGTACCTGGATCTGGACCTCAAGAAGTTCATGGACTCTTGCCCGGAGTTTGCTAAGAATCCCACTTTGATTAAGgtgaagaagcacatgatatgttagtttgtgactgctagtctgcgccttgcttctgtcctgctccgcatatagataaactcga-gccatgactcatgcattt--------
 |||||||| ||||| || ||||| ||||| |||||||||||||| |||||||||||||||||||| || |||||||| || || |||||||| |||||||||| |  || |   ||     | | |||   ||  |      | ||  ||||| |  |  || |||||| | | ||||||| |   || ||   |||||         
TGAGAAGCGCATATATCTTGTCTTTGAGTATCTGGATCTGGACCTAAAGAAGTTCATGGACTCTTGTCCAGAGTTTGCGAAAAACCCCACTTTAATTAAGgtga-gtggccctaaatgcaaaaatatgt---tgtca-----tgactcacttctattattttctgcatatggttgaactcgaagtgttggcttgagcattattgatcaa

upper sequence: GRMZM2G143213_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g01850.1 (Oryza sativa), 5'ss of exon 4
CGAGAAGCGGATATACCTCGTCTTCGAGTACCTGGATCTGGACCTCAAGAAGTTCATGGACTCTTGCCCGGAGTTTGCTAAGAATCCCACTTTGATTAAGgtgaagaagcacatgatatgttagtttgtgactgctagtctgcgccttgcttctgtcctgctccgcatatagataaactcgagccat-gactcatgcattt--------
 |||||||| |||   || ||||| ||||| |||||||||||||| |||||||||||||||||||| || |||||||| || || |||||||| |||||||||| |  || |   ||     ||| |       || |||   | ||  ||| | | ||  || |||||| | | ||||| |  ||| | ||   |||||         
TGAGAAGCGCATAGGTCTTGTCTTTGAGTATCTGGATCTGGACCTGAAGAAGTTCATGGACTCTTGTCCAGAGTTTGCAAAAAACCCCACTTTAATTAAGgtga-gcggccctaaatgcaaaagtat-------cttgtc-atgactcacttttattcttttctgcatatggttgaactcaaagcattggcttgagcattattgatcaa
















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|78093070|gb|DV521444.1|DV521444
EST:     TCATGGACTCTTGCCCGGAGTTTGCTAAGAATCCCACTTTGATTAAG                         TCATACCTCTACCAGATACTCCGTGGCGTTGCGTACTGCCATTCTCATAGA
genomic: TCATGGACTCTTGCCCGGAGTTTGCTAAGAATCCCACTTTGATTAAGgtgaagaagc ... tgttctccagTCATACCTCTACCAGATACTCCGTGGCGTTGCGTACTGCCATTCTCATAGA
EST: gi|60397283|gb|DN230099.1|DN230099
EST:     AGTTCATGGACTCTTGCCCGGAGTTTGCTAAGAATCCCACTTTGATTAAG                         TCATACCTCTACCAGATACTCCGTGGCGTTGCGTACTGCCATTCTCATAGA
genomic: AGTTCATGGACTCTTGCCCGGAGTTTGCTAAGAATCCCACTTTGATTAAGgtgaagaagc ... tgttctccagTCATACCTCTACCAGATACTCCGTGGCGTTGCGTACTGCCATTCTCATAGA
EST: gi|61118495|gb|DN559456.1|DN559456
EST:     AGTTCATGGACTCTTGCCCGGAGTTTGCTAAGAATCCCACTTTGATTAAG                         TCATACCTCTACCAGATACTCCGTGGTGTTGCGTACTGCCATTCTCATAGA
genomic: AGTTCATGGACTCTTGCCCGGAGTTTGCTAAGAATCCCACTTTGATTAAGgtgaagaagc ... tgttctccagTCATACCTCTACCAGATACTCCGTGGCGTTGCGTACTGCCATTCTCATAGA
EST: gi|5847313|gb|AW000392.1|AW000392
EST:     AGTTCATGGACTCTTGCCCGGAGTTTGCTAAGAATCCCACTTTGATTAAG                         TCATACCTCTACCAGATACTCCGTGGTGTTGCGTACTGCCATTCTCATAGA
genomic: AGTTCATGGACTCTTGCCCGGAGTTTGCTAAGAATCCCACTTTGATTAAGgtgaagaagc ... tgttctccagTCATACCTCTACCAGATACTCCGTGGCGTTGCGTACTGCCATTCTCATAGA
EST: gi|32916297|gb|CF021109.1|CF021109
EST:     GGACTCTTGCCCGGAGTTTGCTAAGAATCCCACTTTGATTAAG                         TCATACCTCTACCAGATACTCCGTGGCGTTGCGTACTGCCATTCTCATAGA
genomic: GGACTCTTGCCCGGAGTTTGCTAAGAATCCCACTTTGATTAAGgtgaagaagc ... tgttctccagTCATACCTCTACCAGATACTCCGTGGCGTTGCGTACTGCCATTCTCATAGA
EST: gi|22542162|gb|BU092600.1|BU092600
EST:     AGTTCATGGACTCTTGCCCGGAGTTTGCTAAGAATCCCACTTTGATTAAG                         TCATACCTCTACCAGATACTCCGTGGCGTTGCGTACTGCCATTCTCATAGA
genomic: AGTTCATGGACTCTTGCCCGGAGTTTGCTAAGAATCCCACTTTGATTAAGgtgaagaagc ... tgttctccagTCATACCTCTACCAGATACTCCGTGGCGTTGCGTACTGCCATTCTCATAGA
EST: gi|6020558|gb|AW065591.1|AW065591
EST:     AGTTCATGGACTCTTGCCCGGAGTTTGCTAAGAATCCCACTTTGATTAAG                         TCATACCTCTACCAGATACTCCGTGGTGTTGCGTACTGCCATTCTCATAGA
genomic: AGTTCATGGACTCTTGCCCGGAGTTTGCTAAGAATCCCACTTTGATTAAGgtgaagaagc ... tgttctccagTCATACCTCTACCAGATACTCCGTGGCGTTGCGTACTGCCATTCTCATAGA
EST: gi|67024512|gb|CO453261.1|CO453261
EST:     AAGAATCCTACTTTGATTAAG                         TCATACCTCTACCAGATACTCCGTGGCGTTGCGTACTGCCATTCTCATAGA
genomic: AAGAATCCCACTTTGATTAAGgtgaagaagc ... tgttctccagTCATACCTCTACCAGATACTCCGTGGCGTTGCGTACTGCCATTCTCATAGA
EST: gi|21390004|gb|BQ528053.1|BQ528053
EST:     AGTTCATGGACTCTTGCCCGGAGTTTGCTAAGAATCCCACTTTGATTAAG                         TCATACCTCTACCAGATACTCCGTGGCGTTGCGTACTGCCATTCTCATAGA
genomic: AGTTCATGGACTCTTGCCCGGAGTTTGCTAAGAATCCCACTTTGATTAAGgtgaagaagc ... tgttctccagTCATACCTCTACCAGATACTCCGTGGCGTTGCGTACTGCCATTCTCATAGA
EST: gi|60398446|gb|DN231262.1|DN231262
EST:     AGTTCATGGACTCTTGCCCGGAGTTTGCTAAGAATCCCACTTTGATTAAG                         TCATACCTCTACCAGATACTCCGTGGCGTTGCGTACTGCCATTCTCATAGA
genomic: AGTTCATGGACTCTTGCCCGGAGTTTGCTAAGAATCCCACTTTGATTAAGgtgaagaagc ... tgttctccagTCATACCTCTACCAGATACTCCGTGGCGTTGCGTACTGCCATTCTCATAGA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 109

CGAGAAGCGGATATACCTCGTCTTCGAGTACCTGGATCTGGACCTCAAGAAGTTCATGGACTCTTGCCCGGAGTTTGCTAAGAATCCCACTTTGATTAAGgtgaagaagc ... tgttctccagTCATACCTCTACCAGATACTCCGTGGCGTTGCGTACTGCCATTCTCATAGAGTTCTTCACCGAGATTTGAAACCTCAGAACTTGTTGATAGATCGGCGTA


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 52

CGAGAAGCGGATATACCTCGTCTTCGAGTACCTGGATCTGGACCTCAAGAAGTTCATGGACTCTTGCCCGGAGTTTGCTAAGAATCCCACTTTGATTAAGgtgaagaagc ... tgttctccagTCATACCTCTACCAGATACTCCGTGGCGTTGCGTACTGCCATTCTCATAGAGTTCTTCACCGAGATTTGAAACCTCAGAACTTGTTGATAGATCGGCGTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 98

CGAGAAGCGGATATACCTCGTCTTCGAGTACCTGGATCTGGACCTCAAGAAGTTCATGGACTCTTGCCCGGAGTTTGCTAAGAATCCCACTTTGATTAAGgtgaagaagc ... tgttctccagTCATACCTCTACCAGATACTCCGTGGCGTTGCGTACTGCCATTCTCATAGAGTTCTTCACCGAGATTTGAAACCTCAGAACTTGTTGATAGATCGGCGTA


Block sizes: 44 (upstream exon), 44 (downstream exon)
Score: 28

CGAGAAGCGGATATACCTCGTCTTCGAGTACCTGGATCTGGACCTCAAGAAGTTCATGGACTCTTGCCCGGAGTTTGCTAAGAATCCCACTTTGATTAAGgtgaagaagc ... tgttctccagTCATACCTCTACCAGATACTCCGTGGCGTTGCGTACTGCCATTCTCATAGAGTTCTTCACCGAGATTTGAAACCTCAGAACTTGTTGATAGATCGGCGTA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGAGAAGCGGATATACCTCGTCTTCGAGTACCTGGATCTGGACCTCAAGAAGTTCATGGACTCTTGCCCGGAGTTTGCTAAGAATCCCACTTTGATTAAGgtgaagaagcacatgatatgttagtttgtgactgctagtctgcgccttgcttctgtcctgctccgcatatagataaactcgagccatgactcatgcattt

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