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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAAGGAACCAATAGAACATCAAGGCTTCAAATAACAACGAACAAAAAAGGAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttatatcattttattggtctttatattgaaaaccccagttaaagcctagaaaaaaatgtatagaatatgaatactgaacctctgagtattaagca...

Basic information

species Zea mays
transcript GRMZM2G006130_T06
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006130_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os11g03730.2 (Oryza sativa), 5'ss of exon 6
TAAAGGAACCAATAGAACATCAAGGCTTCAAATAACAACGAACAAAAAAGGAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttatatcattttattggtctttat-attgaaaaccccagttaaagcctagaaaaaaatgtatagaatatgaatactgaacctctgagtattaagca-----------------------------------------------
| ||||||| |||||||| |||||||||||||||||||| ||||| || |||||||| ||| ||||||||||||| |||||||||| |||||| ||||||| |  ||||||  | || |    ||| || | || |||    |    | |||  |       | |      |||| ||| || |          |||||                                                 
TCAAGGAACAAATAGAACCTCAAGGCTTCAAATAACAACTAACAAGAAGGGAGTTGTATGGTTTGATCAAGTATCGCTCATGCCTGCAGACACTTACAAGgtacattatattttgttgtcaaacttcattactggaaaaggaaaacgatgccatgggctttttatgctatctatgtatagtgtatgataacactttaagtcttcatgggctttttcaagtgcttccaacatttcttttacacatacag

upper sequence: GRMZM2G006130_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os12g03470.5 (Oryza sativa), 5'ss of exon 6
TAAAGGAACCAATAGAACATCAAGGCTTCAAATAACAACGAACAAAAAAGGAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttatatcattttattggtctttat-attgaaaaccccagttaaagcctagaaaaaaatgtatagaatatgaatactgaacctctgagta-ttaagca-----------------------------------------------
||||||||| |||||||| |||||||||||||||||||| | ||| || |||||||| ||| |||||||||| || |||||| ||| |||||| ||||||| |  ||||||  | ||||    |||  | | || |||    |    |   | |   |    |  ||   || |  |||  |    |   |  | ||||                                                  
TAAAGGAACAAATAGAACCTCAAGGCTTCAAATAACAACTACCAAGAAGGGAGTTGTATGGTTTGATCAAGTCTCTCTCATGTCTGCAGACACTTACAAGgtacattatattttgttatcaaacttcgttactggaaaaggaaaacgatatc-atggactttttcatgctatctctatatagtgtatgataccacttaaatcttcatgggctttttctactgcttccaacatttcttttacacattcag
















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|211353134|gb|FL044611.1|FL044611
EST:     GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAG                         GGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
genomic: GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttata ... gcacacacagGGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
EST: gi|211350735|gb|FL044608.1|FL044608
EST:     GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAG                         GGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
genomic: GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttata ... gcacacacagGGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
EST: gi|211350729|gb|FL044602.1|FL044602
EST:     GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAG                         GGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
genomic: GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttata ... gcacacacagGGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
EST: gi|32924412|gb|CF029224.1|CF029224
EST:     GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAG                         GGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
genomic: GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttata ... gcacacacagGGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
EST: gi|32924555|gb|CF029367.1|CF029367
EST:     GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAG                         GGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
genomic: GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttata ... gcacacacagGGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
EST: gi|32924548|gb|CF029360.1|CF029360
EST:     GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAG                         GGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
genomic: GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttata ... gcacacacagGGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
EST: gi|211350733|gb|FL044606.1|FL044606
EST:     GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAG                         GGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
genomic: GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttata ... gcacacacagGGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
EST: gi|211221447|gb|FL389601.1|FL389601
EST:     GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAG                         GGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
genomic: GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttata ... gcacacacagGGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
EST: gi|211350724|gb|FL044597.1|FL044597
EST:     GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAG                         GGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
genomic: GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttata ... gcacacacagGGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
EST: gi|211350722|gb|FL044595.1|FL044595
EST:     GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAG                         GGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
genomic: GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttata ... gcacacacagGGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
EST: gi|211350723|gb|FL044596.1|FL044596
EST:     GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAG                         GGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
genomic: GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttata ... gcacacacagGGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
EST: gi|211353135|gb|FL044612.1|FL044612
EST:     GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAG                         GGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
genomic: GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttata ... gcacacacagGGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
EST: gi|32924263|gb|CF029075.1|CF029075
EST:     GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAG                         GGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACC
genomic: GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttata ... gcacacacagGGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACC
EST: gi|8367922|gb|BE050867.1|BE050867
EST:     GAGTTGTATGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAG                         GGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
genomic: GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttata ... gcacacacagGGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
EST: gi|211350730|gb|FL044603.1|FL044603
EST:     GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAG                         GGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
genomic: GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttata ... gcacacacagGGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
EST: gi|211353132|gb|FL044609.1|FL044609
EST:     GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAG                         GGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
genomic: GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttata ... gcacacacagGGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
EST: gi|18963147|gb|BM660266.1|BM660266
EST:     ATCACTCATGCCTGAAGACACATACAAG                         GGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
genomic: ATCACTCATGCCTGAAGACACATACAAGgcatgttata ... gcacacacagGGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
EST: gi|18661865|gb|BM501621.1|BM501621
EST:     ATCAAGTATCACTCATGCCTGAAGACACATACAAG                         GGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
genomic: ATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttata ... gcacacacagGGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
EST: gi|211350725|gb|FL044598.1|FL044598
EST:     GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAG                         GGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
genomic: GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttata ... gcacacacagGGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
EST: gi|211350728|gb|FL044601.1|FL044601
EST:     GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAG                         GGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
genomic: GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttata ... gcacacacagGGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
EST: gi|211150003|gb|FL374637.1|FL374637
EST:     GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAG                         GGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
genomic: GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttata ... gcacacacagGGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
EST: gi|211079656|gb|FL402147.1|FL402147
EST:     GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAANACACATACAAG                         GGACATGGTTTCCGCACANAACTTATATCCATGCTTTTGGATTTGAAACCA
genomic: GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttata ... gcacacacagGGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
EST: gi|211350734|gb|FL044607.1|FL044607
EST:     GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAG                         GGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
genomic: GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttata ... gcacacacagGGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
EST: gi|91051534|gb|EB161952.1|EB161952
EST:     GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAG                         GGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
genomic: GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttata ... gcacacacagGGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
EST: gi|211350732|gb|FL044605.1|FL044605
EST:     GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAG                         GGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
genomic: GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttata ... gcacacacagGGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
EST: gi|211350727|gb|FL044600.1|FL044600
EST:     GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAG                         GGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
genomic: GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttata ... gcacacacagGGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
EST: gi|149100793|gb|EE186887.2|EE186887
EST:     GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAG                         GGACATGGTTTCCGCACAGACCTTATATCCATGCTTTTGG
genomic: GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttata ... gcacacacagGGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGG
EST: gi|211350731|gb|FL044604.1|FL044604
EST:     GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAG                         GGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
genomic: GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttata ... gcacacacagGGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
EST: gi|211353136|gb|FL044613.1|FL044613
EST:     GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAG                         GGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
genomic: GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttata ... gcacacacagGGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
EST: gi|32924256|gb|CF029068.1|CF029068
EST:     GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAG                         GGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA
genomic: GAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttata ... gcacacacagGGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCA

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), 49 (downstream exon)
Score: 314

TAAAGGAACCAATAGAACATCAAGGCTTCAAATAACAACGAACAAAAAAGGAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttata ... gcacacacagGGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1130

TAAAGGAACCAATAGAACATCAAGGCTTCAAATAACAACGAACAAAAAAGGAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttata ... gcacacacagGGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 807

TAAAGGAACCAATAGAACATCAAGGCTTCAAATAACAACGAACAAAAAAGGAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttata ... gcacacacagGGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 504

TAAAGGAACCAATAGAACATCAAGGCTTCAAATAACAACGAACAAAAAAGGAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttata ... gcacacacagGGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAAAGGAACCAATAGAACATCAAGGCTTCAAATAACAACGAACAAAAAAGGAGTTGTTTGGCTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgcatgttatatcattttattggtctttatattgaaaaccccagttaaagcctagaaaaaaatgtatagaatatgaatactgaacctctgagtattaagca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA