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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAGgtactctccttgcacattgtactattataagttttattctcttcacactagaagcaaggtatattcttatcaggaacttttggtgactggcacgtttttt...

Basic information

species Zea mays
transcript GRMZM5G863152_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G863152_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os07g18720.1 (Oryza sativa), 5'ss of exon 3
ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAGgtac---tctccttgcacattgtactattataagttttattctcttcacac-tagaagcaaggtatattcttatcaggaacttttggtgactggcacgtttttt-
||||||||||||||||||| |||||||||||||| |||| ||||||||    || |   ||   ||  |||||   |||| | ||  ||||| || | |||| |||   ||      | | |   |||| || |||      |   || 
ATTAAAAGCAAGAAGAGGCAAAAGGATGTTGCACAGGAACCAAGgtacgaaccttcaatcatgctgctctattg-gagttctttttccttcatacctggaagtaagaactaaca--gttatg--ttttttgttactcatttatggatta
















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|211223994|gb|FL296362.1|FL296362
EST:     ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG                         TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAATGGG
genomic: ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAGgtactctcct ... tttgatgtagTGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAATGGG
EST: gi|211135925|gb|FL188995.1|FL188995
EST:     ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG                         TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAATG
genomic: ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAGgtactctcct ... tttgatgtagTGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAATG
EST: gi|211226060|gb|FL296376.1|FL296376
EST:     ATTAAAGAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG                         TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAATGGGTGCCAGA
genomic: ATTAAA-AGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAGgtactctcct ... tttgatgtagTGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAATGGGTGCCAGA
EST: gi|71305070|gb|DR788672.1|DR788672
EST:     ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG                         TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT
genomic: ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAGgtactctcct ... tttgatgtagTGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT
EST: gi|211226055|gb|FL296371.1|FL296371
EST:     ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG                         TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT
genomic: ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAGgtactctcct ... tttgatgtagTGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT
EST: gi|211223997|gb|FL296365.1|FL296365
EST:     ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG                         TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT
genomic: ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAGgtactctcct ... tttgatgtagTGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT
EST: gi|76920373|gb|DV168136.1|DV168136
EST:     ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG                         TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT
genomic: ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAGgtactctcct ... tttgatgtagTGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT
EST: gi|211226059|gb|FL296375.1|FL296375
EST:     ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG                         TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT
genomic: ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAGgtactctcct ... tttgatgtagTGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT
EST: gi|211226058|gb|FL296374.1|FL296374
EST:     ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG                         TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT
genomic: ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAGgtactctcct ... tttgatgtagTGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT
EST: gi|211224000|gb|FL296368.1|FL296368
EST:     ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG                         TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT
genomic: ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAGgtactctcct ... tttgatgtagTGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT
EST: gi|71432424|gb|DR813474.1|DR813474
EST:     ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG                         TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT
genomic: ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAGgtactctcct ... tttgatgtagTGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT
EST: gi|211223995|gb|FL296363.1|FL296363
EST:     ATTAAAAGCAAGAAGAGGCGAAAGGATCGTTGCACTGGAATCAAG                         TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT
genomic: ATTAAAAGCAAGAAGAGGCGAAAGGAT-GTTGCACTGGAATCAAGgtactctcct ... tttgatgtagTGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT
EST: gi|211226057|gb|FL296373.1|FL296373
EST:     ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG                         TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT
genomic: ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAGgtactctcct ... tttgatgtagTGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT
EST: gi|166551775|gb|EG294357.1|EG294357
EST:     GTTGCACTGGAATCAAG                         TGAGGTAATATCTGGAAATCCAAGGAACAGGGTACCAAT
genomic: GTTGCACTGGAATCAAGgtactctcct ... tttgatgtagTGAGGTAATATCTGGAAATCCAAGGAACAGGG-ACCAAT
EST: gi|78081578|gb|DV509990.1|DV509990
EST:     ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG                         TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT
genomic: ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAGgtactctcct ... tttgatgtagTGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT
EST: gi|211223993|gb|FL296361.1|FL296361
EST:     ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG                         TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT
genomic: ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAGgtactctcct ... tttgatgtagTGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT

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), 38 (downstream exon)
Score: 138

ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAGgtactctcct ... tttgatgtagTGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT


Block sizes: 46 (upstream exon), 38 (downstream exon)
Score: 200

ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAGgtactctcct ... tttgatgtagTGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT


Block sizes: 44 (upstream exon), 38 (downstream exon)
Score: 91

ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAGgtactctcct ... tttgatgtagTGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT


Block sizes: 44 (upstream exon), 38 (downstream exon)
Score: 125

ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAGgtactctcct ... tttgatgtagTGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAGgtactctccttgcacattgtactattataagttttattctcttcacactagaagcaaggtatattcttatcaggaacttttggtgactggcacgtttttt

- -  AAGCAA
- - - AGCAAG
- - -  GCAAGA
- - - -  AAGAAG
- - - - - - AAGAGG
- - - - - - - - - - - AGGATG