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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAATGGAATGATATATGTCATTCAGgtaatttacgtatttggatttctcactgatgagcttataagagcatgtactagccaaagaacaggccttttttcaccatgtcaatggttcttaaaaggtt...

Basic information

species Zea mays
transcript GRMZM2G171469_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171469_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g02850.2 (Oryza sativa), 5'ss of exon 5
GCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAATGGAATGATATATGTCATTCAGgtaatttacgtatttggatttctcactgatgagcttataagagcatgtactagccaaa--gaacaggccttttttcaccatgtcaatggttcttaaaaggtt---
||||| ||| |||| |||||||||||| | |||||||| || |||||||||||| || | ||||  || ||||| | ||    ||    |||||| |||| |||   |||||  || | |     | ||     ||| |    |  | | |||| |||| |     ||   |||   
GCACGGGCAATGTCTACTGATGGGCTCAGACCAGCTTTTTATACAATCAATGGAGTGGTCTATGCAATCCAGgtgactttgccatccacatttcttactgttga---tataattgcttctctctacaaactcatacatgaaactcattatcatgacaattggaa--aacttgttact
















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|78108686|gb|DV527104.1|DV527104
EST:     GGCTCCGGCCAGCTTTCTACACAATCAATGGAATGATATATGTCATTCAG                         ATACTACTGTGGCTGCTCATGTGGTGGAAACCAGTTCAAGCCGTGGTAATT
genomic: GGCTCCGGCCAGCTTTCTACACAATCAATGGAATGATATATGTCATTCAGgtaatttacg ... aaaactccagATACTACTGTGGCTGCTCATGTGGTGGAAACCAGTTCAAGCCGTGGTAATT
EST: gi|149017006|gb|EE045660.2|EE045660
EST:     GGCTCCGGCCAGCTTTCTACACAATCAATGGAATGATATATGTCATTCAG                         ATACTACTGTGGCTGCTCATGTGGTGGAAACCAGTTCAAGCCGTGGTAATT
genomic: GGCTCCGGCCAGCTTTCTACACAATCAATGGAATGATATATGTCATTCAGgtaatttacg ... aaaactccagATACTACTGTGGCTGCTCATGTGGTGGAAACCAGTTCAAGCCGTGGTAATT
EST: gi|91873273|gb|EB403230.1|EB403230
EST:     GGCTCCGGCCAGCTTTCTACACAATCAATGGAATGATATATGTCATTCAG                         ATACTACTGTGGCTGCTCATGTGGTGGAAACCAGTTCAAGCCGTGGTAATT
genomic: GGCTCCGGCCAGCTTTCTACACAATCAATGGAATGATATATGTCATTCAGgtaatttacg ... aaaactccagATACTACTGTGGCTGCTCATGTGGTGGAAACCAGTTCAAGCCGTGGTAATT
EST: gi|78108178|gb|DV526596.1|DV526596
EST:     GGCTCCGGCCAGCTTTCTACACAATCAATGGAATGATATATGTCATTCAG                         ATACTACTGTGGCTGCTCATGTGGTGGAAACCAGTTCAAGCCGTGGTAATT
genomic: GGCTCCGGCCAGCTTTCTACACAATCAATGGAATGATATATGTCATTCAGgtaatttacg ... aaaactccagATACTACTGTGGCTGCTCATGTGGTGGAAACCAGTTCAAGCCGTGGTAATT
EST: gi|71322323|gb|DR797838.1|DR797838
EST:     GGCTCCGGCCAGCTTTCTACACAATCAATGGAATGATATATGTCATTCAG                         ATACTACTGTGGCTGCTCATGTGGTGGAAACCAGTTCAAGCCGTGGTAATT
genomic: GGCTCCGGCCAGCTTTCTACACAATCAATGGAATGATATATGTCATTCAGgtaatttacg ... aaaactccagATACTACTGTGGCTGCTCATGTGGTGGAAACCAGTTCAAGCCGTGGTAATT
EST: gi|76018861|gb|DT946031.1|DT946031
EST:     GGCTCCGGCCAGCTTTCTACACAATCAATGGAATGATATATGTCATTCAG                         ATACTACTGTGGCTGCTCATGTGGTGGAAACCAGTTCAAGCCGTGGTAATT
genomic: GGCTCCGGCCAGCTTTCTACACAATCAATGGAATGATATATGTCATTCAGgtaatttacg ... aaaactccagATACTACTGTGGCTGCTCATGTGGTGGAAACCAGTTCAAGCCGTGGTAATT
EST: gi|5895618|gb|AW036864.1|AW036864
EST:     GGCTCCGGCCAGCTTTCTATACAATCAATGGAATGATCTATGTCATTCAG                         ATACTACTGTGGCTGCTCATGTGGTGGAAACCAGTTCAAGCCGNGGTAATT
genomic: GGCTCCGGCCAGCTTTCTACACAATCAATGGAATGATATATGTCATTCAGgtaatttacg ... aaaactccagATACTACTGTGGCTGCTCATGTGGTGGAAACCAGTTCAAGCCGTGGTAATT
EST: gi|74237785|gb|DT645699.1|DT645699
EST:     GGCTCCGGCCAGCTTTCTACACAATCAATGGAATGATATATGTCATTCAG                         ATACTACTGTGGCTGCTCATGTGGTGGAAACCAGTTCAAGCCGTGGTAATT
genomic: GGCTCCGGCCAGCTTTCTACACAATCAATGGAATGATATATGTCATTCAGgtaatttacg ... aaaactccagATACTACTGTGGCTGCTCATGTGGTGGAAACCAGTTCAAGCCGTGGTAATT
EST: gi|50333507|gb|CO528633.1|CO528633
EST:     GGCTCCGGCCAGCTTTCTACACAATCAATGGAATGATATATGTCATTCAG                         ATACTACTGTGGCTGCTCATGTGGTGGAAACCAGTTCAAGCCGTGGTAATT
genomic: GGCTCCGGCCAGCTTTCTACACAATCAATGGAATGATATATGTCATTCAGgtaatttacg ... aaaactccagATACTACTGTGGCTGCTCATGTGGTGGAAACCAGTTCAAGCCGTGGTAATT
EST: gi|71770532|gb|DR968469.1|DR968469
EST:     GGCTCCGGCCAGCTTTCTACACAATCAATGGAATGATATATGTCATTCAG                         ATACTACTGTGGCTGCTCATGTGGTGGAAACCAGTTCAAGCCGTGGTAATT
genomic: GGCTCCGGCCAGCTTTCTACACAATCAATGGAATGATATATGTCATTCAGgtaatttacg ... aaaactccagATACTACTGTGGCTGCTCATGTGGTGGAAACCAGTTCAAGCCGTGGTAATT
EST: gi|149075806|gb|EE164341.2|EE164341
EST:     GGCTCCGGCCAGCTTTCTACACAATCAATGGAATGATATATGTCATTCAG                         ATACTACTGTGGCTGCTCATGTGGTGGAAACCAGTTCAAGCCGTGGTAATT
genomic: GGCTCCGGCCAGCTTTCTACACAATCAATGGAATGATATATGTCATTCAGgtaatttacg ... aaaactccagATACTACTGTGGCTGCTCATGTGGTGGAAACCAGTTCAAGCCGTGGTAATT

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: 49 (upstream exon), 47 (downstream exon)
Score: 68

GCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAATGGAATGATATATGTCATTCAGgtaatttacg ... aaaactccagATACTACTGTGGCTGCTCATGTGGTGGAAACCAGTTCAAGCCGTGGTAATTTTGTCAAAGATGTTCTTTGCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 86

GCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAATGGAATGATATATGTCATTCAGgtaatttacg ... aaaactccagATACTACTGTGGCTGCTCATGTGGTGGAAACCAGTTCAAGCCGTGGTAATTTTGTCAAAGATGTTCTTTGCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 74

GCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAATGGAATGATATATGTCATTCAGgtaatttacg ... aaaactccagATACTACTGTGGCTGCTCATGTGGTGGAAACCAGTTCAAGCCGTGGTAATTTTGTCAAAGATGTTCTTTGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 87

GCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAATGGAATGATATATGTCATTCAGgtaatttacg ... aaaactccagATACTACTGTGGCTGCTCATGTGGTGGAAACCAGTTCAAGCCGTGGTAATTTTGTCAAAGATGTTCTTTGCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAATGGAATGATATATGTCATTCAGgtaatttacgtatttggatttctcactgatgagcttataagagcatgtactagccaaagaacaggccttttttcaccatgtcaatggttcttaaaaggtt

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