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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAGgtaactgaattactattaaattttcttgggtaatgaaagcaatcagctaattgatctgtttagtcccagtttttaataggtatgttcgtatatgccttctatgttgattgtatgcctaaccctctttctttccatcccttgtgaccag

Basic information

species Zea mays
transcript GRMZM2G047404_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047404_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os09g12600.2 (Oryza sativa), 5'ss of exon 5
GGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAGgtaactgaattactattaaattttcttgggtaatgaaagcaatcagctaattgatctgtttagtcccagtttttaataggtatgttcgtatatgccttctatgttgattgtatgcctaaccctctttctttccatcccttgtgaccag
|||||||||||||||||||||||| |||||||| ||||||||||||||||||||| | |||||||| |||||||||||||| ||||||||||||| | ||        ||     | ||  |      || || | |       ||||| | ||| | |    | |    | | ||| | || || |  | ||                                        
GGCTGGATTTTGGAGTGCAATGGCCTCAAATGTCACCTTCCAGTCAAGGAATGTGTTGAGCAAGAAGCTTATGGTGAAGAAGGAGgtaactgaataattagagtgcggtc----atcatagatattggcaactgaattgcagaattagtacaagtgtgt----gtttctcttgaata-gtctgctttagtaata---------------------------------------
















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|211421923|gb|FL203903.1|FL203903
EST:     CCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAG                         GAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTC
genomic: CCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAGgtaactgaat ... ttgtgaccagGAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTC
EST: gi|37395421|gb|CF634991.1|CF634991
EST:     CCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAG                         GAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTC
genomic: CCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAGgtaactgaat ... ttgtgaccagGAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTC
EST: gi|8103136|gb|AW927794.1|AW927794
EST:     CCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAG                         GAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTC
genomic: CCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAGgtaactgaat ... ttgtgaccagGAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTC
EST: gi|40336776|gb|CK370846.1|CK370846
EST:     CCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAG                         GAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTC
genomic: CCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAGgtaactgaat ... ttgtgaccagGAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTC
EST: gi|60395055|gb|DN227924.1|DN227924
EST:     CCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAG                         GAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTC
genomic: CCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAGgtaactgaat ... ttgtgaccagGAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTC
EST: gi|116814527|gb|EC857099.1|EC857099
EST:     CCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAG                         GAATCTCTCGACCAACATTAACCTATTCTCGATCATTACAGTCATGTCATT
genomic: CCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAGgtaactgaat ... ttgtgaccagGAATCTCTCGAC-AACATTAACCTATTCTCGATCATTACAGTCATGTCATT
EST: gi|67026165|gb|CO454914.1|CO454914
EST:     CCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAG                         GAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTC
genomic: CCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAGgtaactgaat ... ttgtgaccagGAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTC
EST: gi|148990723|gb|EE032129.2|EE032129
EST:     CCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAG                         GAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTC
genomic: CCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAGgtaactgaat ... ttgtgaccagGAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTC
EST: gi|50325876|gb|CO521002.1|CO521002
EST:     CCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAG                         GAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTC
genomic: CCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAGgtaactgaat ... ttgtgaccagGAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTC
EST: gi|211071461|gb|FL174369.1|FL174369
EST:     CCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAG                         GAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTC
genomic: CCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAGgtaactgaat ... ttgtgaccagGAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTC
EST: gi|23199513|gb|BU582078.1|BU582078
EST:     CCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAG                         GAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTC
genomic: CCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAGgtaactgaat ... ttgtgaccagGAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTC
EST: gi|76281901|gb|DV021469.1|DV021469
EST:     CCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAG                         GAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTC
genomic: CCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAGgtaactgaat ... ttgtgaccagGAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTC
EST: gi|33103829|gb|CF063789.1|CF063789
EST:     CCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAG                         GAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTC
genomic: CCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAGgtaactgaat ... ttgtgaccagGAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTC
EST: gi|7844570|gb|AW787792.1|AW787792
EST:     TTCCAGTCAAGGAATGTGCTAAGCAAGAATATTTATGTGTGAAGAAAGAG                         GAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTC
genomic: TTCCAGTCAAGGAATGTGCTAAGCAAGAA-ACTTATG-GTGAAGAAAGAGgtaactgaat ... ttgtgaccagGAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTC
EST: gi|88753541|gb|DY537682.1|DY537682
EST:     CCTTCCAGTCAAGGAATGTGCTAAGCAAAAAACTTATGGTGAAGAAAGAG                         GAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTC
genomic: CCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAGgtaactgaat ... ttgtgaccagGAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTC
EST: gi|12046824|gb|BF728963.1|BF728963
EST:     CCTTCCAGTCAAGGAATGTGCTAAGCAAGAATCTTATGGTGAAGAAAGAG                         GAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTC
genomic: CCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAGgtaactgaat ... ttgtgaccagGAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTC
EST: gi|76281902|gb|DV021470.1|DV021470
EST:     CCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAG                         GAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTC
genomic: CCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAGgtaactgaat ... ttgtgaccagGAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTC
EST: gi|6973548|gb|AW438284.1|AW438284
EST:     CCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAG                         GAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTC
genomic: CCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAGgtaactgaat ... ttgtgaccagGAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTC

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: 48 (upstream exon), 48 (downstream exon)
Score: 532

GGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAGgtaactgaat ... ttgtgaccagGAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTCTTCCTGTTGGCCCCAGTAACCTTACTTACAGAAGGTGTTAAAGTTAGTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 332

GGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAGgtaactgaat ... ttgtgaccagGAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTCTTCCTGTTGGCCCCAGTAACCTTACTTACAGAAGGTGTTAAAGTTAGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 423

GGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAGgtaactgaat ... ttgtgaccagGAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTCTTCCTGTTGGCCCCAGTAACCTTACTTACAGAAGGTGTTAAAGTTAGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 915

GGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAGgtaactgaat ... ttgtgaccagGAATCTCTCGACAACATTAACCTATTCTCGATCATTACAGTCATGTCATTCTTCCTGTTGGCCCCAGTAACCTTACTTACAGAAGGTGTTAAAGTTAGTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAGgtaactgaattactattaaattttcttgggtaatgaaagcaatcagctaattgatctgtttagtcccagtttttaataggtatgttcgtatatgccttctatgttgattgtatgcctaaccctctttctttccatcccttgtgaccag

- - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA