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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattaactgaacctgatattgtgtcacttagttgtttttacagctttgagcatgatagttaggcacaaaatctttttggtttcagttttacatgtgccagcgcactataacttctctctctttctgcagGTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAG

Basic information

species Zea mays
transcript GRMZM2G110185_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA19G45140.1 (Glycine max), 3'ss of exon 3
gtatattaactgaacctgatattgtgtcacttagttgtttttacagctttgagcatgatagttaggcacaaaatctttttggtttcagttttacatgtgccagcgcactataacttctctctctttctgcagGTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAG
                                        | | |  ||||   ||  | ||      | || |  ||||      | | |||   |||          || |   || | | |||   ||||||||||| || |||||||| ||||  || ||| | || ||||||||||||||||| ||||| || || |||||||||
---------------------------------------gtcatatttttgtagattttggt------cgaagtgctttt------aatattatgggtgttgcta----atgatgactgtgtattta-acagGTAGCAAGGTGCACAAAGATCATAAATCCAAATTCAGAAGATGCCAAATATGTTATCAATGTGAAGCAGATTGCAAAG

upper sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G05220.2 (Glycine max), 3'ss of exon 3
gtatattaactgaacctgatattgtgtcacttagttgtttttacagctttgagcatgatagttaggcacaaaatctttttggtttcagttttacatgtgccagcgcactataacttctctctctttctgcagGTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAG
                                               | |  |  | ||     || |     |||   || ||| |  ||| || |     ||  |||||   |  |      ||   ||||| ||||| || ||||||||||||| ||| ||| | || |||||||| |||||||| ||||| || || |||||||||
------------------------------------------gtgattatttgttttatttagtggaatttgttctaagtgttttaatatttgca-ggatttgctaactatggttattta----ttgaacagGTGGCAAGGTGCACAAAGATTATAAACCCAAATTCTGAAGATGCCAAGTATGTTATCAATGTGAAGCAGATTGCAAAG

upper sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 3
gtatattaactgaacctgatattgtgtcacttagttgtttttacagctttgagcatgatagttaggcacaaaatctttttggtttcagttttacatgtgccagcgcactataacttctctctctttctgcagGTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAG
                                             | |||   | ||||  || |    | ||  |||   || | | | | |  | |  |   | |   |  ||  | |      ||  |||| |||||||| |||||||| || ||||| ||| | || |||||||||||||| |||||||| |||||||||||||||
------------------------------------------gtggtttt--tcttgat--tttgttgaacaacatttactgtcttaatataatgtatatc--tgaagagtggctggttttggaaact--agGTGGCAAGATGCACAAAGATAATTAGCCCCAATTCTGAGGATGCCAAATATGTGATAAATGTTAAACAAATTGCAAAG

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|149015235|gb|EE045022.2|EE045022
EST:     GGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAA                         GTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATAT
genomic: GGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAAgtatattaac ... ctttctgcagGTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATAT
EST: gi|149015481|gb|EE045355.2|EE045355
EST:     GGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAA                         GTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATAT
genomic: GGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAAgtatattaac ... ctttctgcagGTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATAT
EST: gi|18964384|gb|BM660974.1|BM660974
EST:     GGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAA                         GTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATAT
genomic: GGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAAgtatattaac ... ctttctgcagGTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATAT
EST: gi|101395193|gb|EB819526.1|EB819526
EST:     GGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAA                         GTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATAT
genomic: GGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAAgtatattaac ... ctttctgcagGTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATAT
EST: gi|149087114|gb|EE176653.2|EE176653
EST:     GGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAA                         GTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATAT
genomic: GGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAAgtatattaac ... ctttctgcagGTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATAT
EST: gi|211399660|gb|FL004434.1|FL004434
EST:     GGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAA                         GTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATAT
genomic: GGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAAgtatattaac ... ctttctgcagGTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATAT
EST: gi|211283515|gb|FL004410.1|FL004410
EST:     GGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAA                         GTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATAT
genomic: GGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAAgtatattaac ... ctttctgcagGTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATAT
EST: gi|30087195|gb|CB885403.1|CB885403
EST:     GGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAA                         GTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATAT
genomic: GGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAAgtatattaac ... ctttctgcagGTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATAT
EST: gi|19437016|gb|BM953426.1|BM953426
EST:     GGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAA                         GTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATAT
genomic: GGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAAgtatattaac ... ctttctgcagGTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATAT
EST: gi|211035074|gb|FL073374.1|FL073374
EST:     GGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAA                         GTAGCAAGGATGTACAAA
genomic: GGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAAgtatattaac ... ctttctgcagGTAGCAAG-ATGTACAAA
EST: gi|78085799|gb|DV514192.1|DV514192
EST:     GGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAA                         GTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATAT
genomic: GGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAAgtatattaac ... ctttctgcagGTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATAT
EST: gi|211010592|gb|FL355819.1|FL355819
EST:     GGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAA                         GTMGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATAT
genomic: GGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAAgtatattaac ... ctttctgcagGTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATAT
EST: gi|28930845|gb|CB334206.1|CB334206
EST:     GGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAA                         GTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATAT
genomic: GGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAAgtatattaac ... ctttctgcagGTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATAT
EST: gi|211283518|gb|FL004413.1|FL004413
EST:     GGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAA                         GTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATAT
genomic: GGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAAgtatattaac ... ctttctgcagGTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATAT

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 36 (downstream exon)
Score: 25

GGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAAgtatattaac ... ctttctgcagGTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAG


Block sizes: 49 (upstream exon), 25 (downstream exon)
Score: 32

GGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAAgtatattaac ... ctttctgcagGTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 89

GGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAAgtatattaac ... ctttctgcagGTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggtttcagttttacatgtgccagcgcactataacttctctctctttctgcagGTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAG
                              ctataac  putative branch site (score: 89)
                              ctataacttctctctc  CT-rich tract
           ttttacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatattaactgaacctgatattgtgtcacttagttgtttttacagctttgagcatgatagttaggcacaaaatctttttggtttcagttttacatgtgccagcgcactataacttctctctctttctgcagGTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG