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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACTTATCAAATAGGCAAAAACCTGGATGTGGAAAAGGTTCTGCCGTGGACCGATCAAGAGAGCAAACTACTGGgtaaatttgcatttcttctcagagcctttagttatgctgcttgctttcatgaattttttaatcaatatgttttccaattttcacag

Basic information

species Zea mays
transcript GRMZM2G330772_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G330772_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os07g07000.1 (Oryza sativa), 5'ss of exon 6
AACTTATCAAATAGGCAAAAACCTGGATGTGGAAAAGGTTCTGCCGTGGACCGATCAAGAGAGCAAACTACTGGgtaaatttgc-----atttcttctcagagcct--ttagttatgctgcttgctttcatgaat---tttttaatcaatatgttttccaattttcacag
||||||||||| || ||||| ||||||||||| ||||| ||||| || || ||||||||||| || |||||||||||||||| |     |||| || |     |||  ||   ||   ||| |     |||||||   | || |  || |||| || | || ||  ||||
AACTTATCAAACAGACAAAAGCCTGGATGTGGGAAAGGATCTGCGGTAGATCGATCAAGAGAACAGACTACTGGgtaaatttactggcgatttgtttttttttcctggttctgtagagtgcataaagccatgaatagttgttcatccactatgcttgctaaattctacag

upper sequence: GRMZM2G330772_T01 (Zea mays), 5'ss of exon 6
lower sequence: AT5G08080.1 (Arabidopsis thaliana), 5'ss of exon 6
AACTTATCAAATAGGCAAAAACCTGGATGTGGAAAAGGTTCTGCCGTGGACCGATCAAGAG-AGCAA-ACTACTGGgtaaatttgcatttcttctcagagcctttagttatgctgc--ttgctttcatgaattttttaatcaatatgttttccaattttcacag--------------------------------------------------------------------------
|||||  ||||||| |||||||||||||||| |||||| ||||  ||||| |||||||||  ||||| |  |||| |   |||   |||| |    |      ||  || ||   |  ||| ||| | |      || | |  |   |  | ||| |     ||                                                                          
AACTTGGCAAATAGACAAAAACCTGGATGTGCAAAAGGATCTGGTGTGGATCGATCAAGAACAGCAACAACACTgtgagcattcttatttttcaataagataatttattctgacacctttgtttttagggtagggttcagctgttgttaattcaaatgctgtagaacttggtaaacagataatgtatatataaatattctttggtatgacctttatgagctttcattctgtgcaacag
















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|211110807|gb|FL361656.1|FL361656
EST:     GGATGTGGAAAAGGTTCTGCCGTGGACCGATCAAGAGAGCAAACTACTGG                         AGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAG
genomic: GGATGTGGAAAAGGTTCTGCCGTGGACCGATCAAGAGAGCAAACTACTGGgtaaatttgc ... attttcacagAGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAG
EST: gi|211495566|gb|FL127190.1|FL127190
EST:     GGATGTGGAAAAGGTTCTGCCGTGGACCGATCAAGAGAGCAAACTACTGG                         AGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAG
genomic: GGATGTGGAAAAGGTTCTGCCGTGGACCGATCAAGAGAGCAAACTACTGGgtaaatttgc ... attttcacagAGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAG
EST: gi|60359751|gb|DN226724.1|DN226724
EST:     GGATGTGGAAAAGGTTCTGCCGTGGACCGATCAAGAGAGCAAACTACTGG                         AGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAG
genomic: GGATGTGGAAAAGGTTCTGCCGTGGACCGATCAAGAGAGCAAACTACTGGgtaaatttgc ... attttcacagAGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAG
EST: gi|67020224|gb|CO448973.1|CO448973
EST:     GGATGTGGAAAAGGTTCTGCCGTGGACCGATCAAGAGAGCAAACTACTGG                         AGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAG
genomic: GGATGTGGAAAAGGTTCTGCCGTGGACCGATCAAGAGAGCAAACTACTGGgtaaatttgc ... attttcacagAGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAG
EST: gi|211425646|gb|FL363236.1|FL363236
EST:     GGATGTGGAAAAGGTTCTGCCGTGGACCGATCAAGAGAGCAAACTACTGG                         AGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAG
genomic: GGATGTGGAAAAGGTTCTGCCGTGGACCGATCAAGAGAGCAAACTACTGGgtaaatttgc ... attttcacagAGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAG
EST: gi|211262997|gb|FL346818.1|FL346818
EST:     GATGGTGGAAAAGGTTCTGCCGTGGACCGATCAAGAGAGCAAACTACTGG                         AGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAG
genomic: GATG-TGGAAAAGGTTCTGCCGTGGACCGATCAAGAGAGCAAACTACTGGgtaaatttgc ... attttcacagAGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAG
EST: gi|67020710|gb|CO449459.1|CO449459
EST:     GGATGTGGAAAAGGTTCTGCCGTGGACCGATCAAGAGAGCAAACTACTGG                         AGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAG
genomic: GGATGTGGAAAAGGTTCTGCCGTGGACCGATCAAGAGAGCAAACTACTGGgtaaatttgc ... attttcacagAGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAG
EST: gi|9732911|gb|BE511663.1|BE511663
EST:     GGATGTGGAAAAGGTTCTGCCGTGGACCGATCAAGAGAGCAAACTACTGG                         AGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAG
genomic: GGATGTGGAAAAGGTTCTGCCGTGGACCGATCAAGAGAGCAAACTACTGGgtaaatttgc ... attttcacagAGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAG
EST: gi|211531082|gb|FL312439.1|FL312439
EST:     GGATGTGGAAAAGGTTCTGCCGTGGACCGATCAAGAGAGCAAACTACTGG                         AGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAG
genomic: GGATGTGGAAAAGGTTCTGCCGTGGACCGATCAAGAGAGCAAACTACTGGgtaaatttgc ... attttcacagAGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAG

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: 46 (upstream exon), 46 (downstream exon)
Score: 383

AACTTATCAAATAGGCAAAAACCTGGATGTGGAAAAGGTTCTGCCGTGGACCGATCAAGAGAGCAAACTACTGGgtaaatttgc ... attttcacagAGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAG


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 404

AACTTATCAAATAGGCAAAAACCTGGATGTGGAAAAGGTTCTGCCGTGGACCGATCAAGAGAGCAAACTACTGGgtaaatttgc ... attttcacagAGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 440

AACTTATCAAATAGGCAAAAACCTGGATGTGGAAAAGGTTCTGCCGTGGACCGATCAAGAGAGCAAACTACTGGgtaaatttgc ... attttcacagAGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAG


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 288

AACTTATCAAATAGGCAAAAACCTGGATGTGGAAAAGGTTCTGCCGTGGACCGATCAAGAGAGCAAACTACTGGgtaaatttgc ... attttcacagAGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACTTATCAAATAGGCAAAAACCTGGATGTGGAAAAGGTTCTGCCGTGGACCGATCAAGAGAGCAAACTACTGGgtaaatttgcatttcttctcagagcctttagttatgctgcttgctttcatgaattttttaatcaatatgttttccaattttcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA