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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgtactgaaacagttctccaaaatccatttttgaataggattaatatagatggctcccaaactttttgtttgctgactctgaaccccttctattttcagTGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTG

Basic information

species Zea mays
transcript GRMZM5G846811_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G846811_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g02840.1 (Oryza sativa), 3'ss of exon 3
gtgtactgaaacagttctccaaaatccatttttgaataggattaatatagatggctccca---aactttttgtttgctgactctgaaccccttctattttcagTGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTG
 | |  ||| ||     |     |||  ||||       |||| |  |   | |   |||   |   |  |  ||| ||| ||| |||    |    ||||||||||||||||| |||||||||||||||||||||||||| || || || || || ||||||||||
ttatgttgatacttgattt---gatcatttttgtggctcgattcacttttttagtctccacttatggtacttcttgttgattctaaactttgttatatttcagTGGATACCTGAGCTGAAGCATTATGCACCTGGTGTGCCTATCATCCTTGTGGGAACAAAGCTTG

upper sequence: GRMZM5G846811_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA01G36880.1 (Glycine max), 3'ss of exon 4
-------------------------------------------------------------gtgtactgaaacagttctccaaaatccatttttgaata-----ggattaatatagatggctcccaaactttttgttt---------gctgactctgaacccc--------ttctattttcagTGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTG
                                                             |   | |  ||   ||||  |    |  |  |  |  |     |||| |   || |||      |||   ||  |||         |  ||   | ||   |        ||  ||||||||||||| || ||  ||||||||||||| |||||||| || |||||||| || || ||||||||||
gtacttcgtggcaatttattgtggtcatagtgttttgggtgtatttcttcttatttattttgataattataaggtttctgtatggcctgtaatgaaggatgtatggatcatgttatatgttaagaaaataattcatttataaaaaaagtcgatgataaattgcatgtgtggtttcattttcagTGGATTCCGGAGTTGAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTG

upper sequence: GRMZM5G846811_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA11G11510.1 (Glycine max), 3'ss of exon 3
gtgtactgaaacagttctccaaaatccatttttgaataggattaatatagatggctcccaaactttttgtt--tgctgactctgaaccccttct--------attttcagTGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTG
                                    || | ||   ||   |   |  |     ||||||   |    |||||| ||   || |        ||||||||||||| |||||  ||| ||||||||| |||||||| ||||||||||| || || ||||| ||||
-----------------------------------gtaagcttggcatttttctttttcttttgttttgtccctctctactctggactaattttttcccgtcattttcagTGGATTCCTGAGTTGAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTG

upper sequence: GRMZM5G846811_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA11G08380.1 (Glycine max), 3'ss of exon 4
----------------------------------------------------------------------------------gtgtactgaaacagttctccaaaat-ccatttttgaataggattaatatagatggctcccaaactttttgtttgctgactctgaaccccttctattttcagTGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTG
                                                                                   ||||  |||  |  | |  |  ||   || ||| || |  || |||  |  |   |   ||     |  |    ||  | |   |   ||   |||||||||||| || ||  |||||||||||||||||||||| || |||||||| || || ||||||||||
gtacttcgttgcaatttattgtggtcagagtgttttgggagaattcttatttcttttgagaatcatgaggtttctgtatggcctgtaacgaaggatgtatggatcatgttatattttaagaaaat-aattcatttatataaaaagtcgatgataaattgcatgt---ctggtttctttttcagTGGATTCCAGAGTTGAAGCATTATGCACCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTG

upper sequence: GRMZM5G846811_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA12G03660.1 (Glycine max), 3'ss of exon 3
gtgtactgaaacagttctccaaaatccatttttgaataggattaatatagatggctcccaaactttttgtttgctgactctgaaccccttctattttcagTGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTG
             ||   |     |   |||||   |    ||  | |   |  ||| | ||  |        || | | |    ||| ||  | | |||||||| |||||  ||| ||||||||| |||||||| ||||||||||| || || ||||| ||||
-------------gtaagcttgggt---tttttactttttttttttttttgtacctctctaatctg-----gactaattttc--tcccatccttgtccagTGGATTCCTGAGTTGAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTG

upper sequence: GRMZM5G846811_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G02580.2 (Glycine max), 3'ss of exon 3
--------------gtgtactgaaacagt--tctccaaaatccatttttgaataggattaatatag-atggctcccaaactttttgtttgctgactctgaaccccttctattttcagTGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTG
               |  | |   || ||  | |   ||||| |||| || |     | | |||   ||| ||    || || |||||      || |      |||||   |||||||||| |||||||| | ||||||||| |||||||| ||||| |||||||| || |||||| | |
gtttacttctttctctcaattaggacggtgatattttaaatcaatttctgcac----tcagtatgatatgactgattaagttattgtt------cttttggtttcttct---ttcagTGGATCCCTGAACTAAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAG

upper sequence: GRMZM5G846811_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G05160.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------------------------------------gtgtac-tgaaacagttctccaaaatccatttttgaataggattaatatagatggctcccaaactttttgtttgctgactctgaaccccttctattttcagTGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTG
                                                                                ||||  ||  |   |||   || |    |     | ||      || || ||   |   |||     || |     | | ||      ||  ||||||||||||| || ||  |||| ||||||||||||| ||| || |||||| | || |||||||||||||
gtactttttccactatagtccaaagtttaagttcctagtgttgctcaaatttagaatgcacttctacatgttacctttaatgtaaatgtgatgtttccataataattgtaaagaactatatcctatttatattaattaaaaa----gtgctaataaattgtgtgttattttcattttcagTGGATTCCAGAGTTGAAACATTATGCACCTGATGTTCCCATTATTTTGGTTGGGACAAAGCTTG

upper sequence: GRMZM5G846811_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA04G02530.3 (Glycine max), 3'ss of exon 3
gtgtactgaaacagttctccaaaatccatttttgaataggattaatatagatggctcccaaactttttgtttgctgactctgaaccc-------------cttctattttcagTGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTG
|| || |    | ||||   | ||| || ||  ||     |||| |  |   |  | |   ||||  | | |        ||||                 ||||  ||||||||||| |||||||| | ||||||||| |||||||| ||||| |||||||| || |||||| | |
gtttatttcttcggttca--agaattcaattaggatggtaattatttaaatcgatttcttcacttagtatatataactgatgaaattattgctcttttgatttcttctttcagTGGATCCCTGAACTAAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAG

upper sequence: GRMZM5G846811_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA04G02540.1 (Glycine max), 3'ss of exon 4
--------------gtgtactgaaacagttct--ccaaaatccatttttgaataggat-taatatagatggctcccaaactttttgtttgctgactctgaaccccttctattttcagTGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTG
               |  | |   |  ||| |   | ||||| |||| ||       | | |||||  ||  |    || || ||||||      | ||      ||||  ||||||||||| |||||||| | ||||||||| |||||||| ||||| |||||||| || |||||| | |
gttcatttctttcattcaattaggatggttatattctaaatcaatttctgcgctcagtatgatataactgatt----aagttattgttt-----ttttgg----tttcttctttcagTGGATCCCTGAACTAAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAG

upper sequence: GRMZM5G846811_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv18s0001g14670.t01 (Vitis vinifera), 3'ss of exon 3
-gtgt-actgaaacagttctccaaaatccatttttgaataggattaatatagatggctcccaaactttttgtttgctgactctgaaccccttctattttcagTGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTG
  ||  ||| |   |||   | |   | |||| ||        |  | ||  |  |    |  |    |||||| ||   | |||     ||  | ||||||||||| |||||||||| |||||||||||||||||| ||||| ||||| || || || |||||||
gttgccacttatttagtctcctatttttcattatttttccttgtctaaatttacagaatgctgataaattgttttcttcttttga-----tttcaatttcagTGGATTCCTGAACTGAGGCATTATGCACCTGGTGTTCCAATAATTCTTGTTGGAACCAAGCTTG

upper sequence: GRMZM5G846811_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv03s0038g02380.t01 (Vitis vinifera), 3'ss of exon 4
-------------------------gtgtactgaaacagttctccaaaatccatttttgaataggattaatatagatggctcccaaactttttgtttgctgactctgaaccccttctattttcagTGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTG
                          | |  |       ||||||    | ||   |    |  | ||||||| | | |||   ||| | ||| | ||||         |   ||| || |||||||||| |||||  ||| |||||||||||| ||||| ||||| ||||| || |||||||||||||
gtaagtttggcttctactatgagagatttttttccttttttctccctcctgcaacatgtcgtctggttaatatggtttgctgataaattctttatgtgct---------ctgtttccatattcagTGGATTCCTGAGTTGAGGCATTATGCACCCGGTGTTCCAATAATTCTTGTCGGGACAAAGCTTG

upper sequence: GRMZM5G846811_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 4
-----------gtgtactgaaacagttctccaaaatccatttttgaata--ggattaata----tagatggctcccaaactttttgtttgctgactctgaacccct----tctattttcagTGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTG
            || |   |||         |  |    ||  ||| ||  ||| ||  |    ||||||||     |   | |  |  |     | | ||    |    |  ||||||||||||| || ||| |||||||||||||||||||||| || ||  |||| || || || |||||||
gtgaggacttgatggatcaaaatgaagtgatagcactttttagtgagtaaaggaataccaattttagatggcaatttattatgtcctgggagattttttaatgtttcggcttcattttcagTGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTTGGCACTAAGCTTG

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|101394632|gb|EB819252.1|EB819252
EST:     TGGCTTTCTCACTGATCAGTAAGGCCAGCTATGAGAATGTTTCGAAGAAG                         TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTA
genomic: TGGCTTTCTCACTGATCAGTAAGGCCAGCTATGAGAATGTTTCGAAGAAGgcaaggctct ... ctattttcagTGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTA
EST: gi|166627044|gb|EG048328.1|EG048328
EST:     TAAGGCCAGCTATGAGAANGTTTCGAAGAAG                         TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTA
genomic: TAAGGCCAGCTATGAGAATGTTTCGAAGAAGgcaaggctct ... ctattttcagTGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTA
EST: gi|32911002|gb|CF015814.1|CF015814
EST:     TGGCTTTCTCACTGATCAGTAAGGCCAGCTATGAGAATGTTTCGAAGAAG                         TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTA
genomic: TGGCTTTCTCACTGATCAGTAAGGCCAGCTATGAGAATGTTTCGAAGAAGgcaaggctct ... ctattttcagTGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTA
EST: gi|116814412|gb|EC856959.1|EC856959
EST:     TGGCTTTCTCACTGATCAGTAAGGCCAGCTATGAGAATGTTTCGAAGAAG                         TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTA
genomic: TGGCTTTCTCACTGATCAGTAAGGCCAGCTATGAGAATGTTTCGAAGAAGgcaaggctct ... ctattttcagTGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTA
EST: gi|22545282|gb|BU097655.1|BU097655
EST:     TGGCTTTCTCACTGATCAGTAAGGCCAGCTATGAGAATGTTTCGAAGAAG                         TGGATACCCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGT
genomic: TGGCTTTCTCACTGATCAGTAAGGCCAGCTATGAGAATGTTTCGAAGAAGgcaaggctct ... ctattttcagTGGATACC-TGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGT
EST: gi|211082353|gb|FK946329.1|FK946329
EST:     TGGCTTTCTCACTGATCAGTAAGGCCAGCTATGAGAATGTTTCGAAGAAG                         TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTA
genomic: TGGCTTTCTCACTGATCAGTAAGGCCAGCTATGAGAATGTTTCGAAGAAGgcaaggctct ... ctattttcagTGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTA
EST: gi|21331007|gb|BQ486388.1|BQ486388
EST:     TGGCTTTCTCACTGATCAGTAAGGCCAGCTATGAGAATGTTTCGAAGAAG                         TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTA
genomic: TGGCTTTCTCACTGATCAGTAAGGCCAGCTATGAGAATGTTTCGAAGAAGgcaaggctct ... ctattttcagTGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTA

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), 49 (downstream exon)
Score: 290

TTACAACAGACTGAGACCACTGAGCTATCGTGGAGCTGATGTTTTTCTTCTGGCTTTCTCACTGATCAGTAAGGCCAGCTATGAGAATGTTTCGAAGAAGgcaaggctct ... ctattttcagTGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 128

TTACAACAGACTGAGACCACTGAGCTATCGTGGAGCTGATGTTTTTCTTCTGGCTTTCTCACTGATCAGTAAGGCCAGCTATGAGAATGTTTCGAAGAAGgcaaggctct ... ctattttcagTGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 209

TTACAACAGACTGAGACCACTGAGCTATCGTGGAGCTGATGTTTTTCTTCTGGCTTTCTCACTGATCAGTAAGGCCAGCTATGAGAATGTTTCGAAGAAGgcaaggctct ... ctattttcagTGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 595

TTACAACAGACTGAGACCACTGAGCTATCGTGGAGCTGATGTTTTTCTTCTGGCTTTCTCACTGATCAGTAAGGCCAGCTATGAGAATGTTTCGAAGAAGgcaaggctct ... ctattttcagTGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatagatggctcccaaactttttgtttgctgactctgaaccccttctattttcagTGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTG
                          tgctgac  putative branch site (score: 595)
                                       ccccttctattttc  putative PPT
              aaacttttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtactgaaacagttctccaaaatccatttttgaataggattaatatagatggctcccaaactttttgtttgctgactctgaaccccttctattttcagTGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTG

-tgtactg
- - - - - - - - - - - - - - - - - - - - - - - - - - -gctccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgaacc