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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaaggataagttgctccagcaattatgaaattactttgcactttgcagtcagcaatctgttatatgatttctaatggtcagtttttatgttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG

Basic information

species Zea mays
transcript GRMZM2G057329_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057329_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g59700.1 (Oryza sativa), 3'ss of exon 2
tcaaggataagttgctccagcaattatgaaattactttgcactttgcagtcagcaatctgttatat--gatttctaatggtc--agtttttatgttg-attgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG
    |  || ||   |   ||||   ||      ||||   |     | | |   | || | | ||    | |  |||  |   || ||      || ||||||| |||   | ||| ||||| || |||||||| || || |||||| |||||||||||||||||||||||||||| |||||||   |||||
----gattatgtgatttaggcaaaagtgcgcaagctttcacccacatattgaatta-ctatcacatccattgttcaatcatagaagcttcatcactggattgcagGAAATCAGGTTTACCACAGGGATATAAGGGTTGTCAGTTCCATCGAGTGATCAAAGATTTCATGATTCAGGGAGGTGACTATATGAAG

upper sequence: GRMZM2G057329_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv13s0084g00620.t01 (Vitis vinifera), 3'ss of exon 1
-tcaaggataagttgctccagcaattatgaaattactttgcactttgcagtcagcaatctgttatatgatttctaatggtcagtttttatgttgatt-gcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG
 |      |   ||    |  || | ||    ||| ||| ||   || | |      ||| ||   |  ||  || | |     |   ||  ||||| ||||||||  ||  || ||    ||||| ||||| ||||| ||||| || || |||||||||||||||||||||| |||||| ||  | |||
gtttttattcttttctaacttcactcattttcttatttt-caggatg-atttccttttctttttctttcttcttatttgatgaatacaataatgatttgcagAAAAGCTGGATTACCTGTTGGTTACAAGGGATGCCAGTTCCACAGGGTCATCAAAGATTTCATGATTCAGGCTGGTGATTTTGTCAAG
















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|211112964|gb|FL394568.1|FL394568
EST:     GGCAGTTCTGCACTGGGGAGCATAG                         AAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
genomic: GGCAGTTCTGCACTGGGGAGCATAGgtaagaaact ... ttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
EST: gi|211494317|gb|FL423862.1|FL423862
EST:     GGCAGTTCTGCACTGGGGAGCATAG                         AAAAAATGCTTTGCCACAAGGTYATAAGGGCTGCCAATTCCATAGAGTGAT
genomic: GGCAGTTCTGCACTGGGGAGCATAGgtaagaaact ... ttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
EST: gi|19058149|gb|BM736816.1|BM736816
EST:     GGCAGTTCTGCACTGGGGAGCATAG                         AAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
genomic: GGCAGTTCTGCACTGGGGAGCATAGgtaagaaact ... ttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
EST: gi|211023124|gb|FL428614.1|FL428614
EST:     GGCAGTTCTGCACTGGGGAGCATAG                         AAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
genomic: GGCAGTTCTGCACTGGGGAGCATAGgtaagaaact ... ttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
EST: gi|19057931|gb|BM736598.1|BM736598
EST:     GGCAGTTCTGCACTGGGGAGCATAG                         AAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
genomic: GGCAGTTCTGCACTGGGGAGCATAGgtaagaaact ... ttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
EST: gi|19058424|gb|BM737091.1|BM737091
EST:     CGGCAGTTCTGCACTGGGGAGCATAG                         AAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
genomic: CGGCAGTTCTGCACTGGGGAGCATAGgtaagaaact ... ttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
EST: gi|211494316|gb|FL423861.1|FL423861
EST:     GGCAGTTCTGCACTGGGGAGCATAG                         AAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
genomic: GGCAGTTCTGCACTGGGGAGCATAGgtaagaaact ... ttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
EST: gi|87153432|gb|DY398221.1|DY398221
EST:     GGCAGTTCTGCACTGGGGAGCATAG                         AAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
genomic: GGCAGTTCTGCACTGGGGAGCATAGgtaagaaact ... ttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
EST: gi|211452160|gb|FL396759.1|FL396759
EST:     GGCAGTTCTGCACTGGGGAGCATAG                         AAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
genomic: GGCAGTTCTGCACTGGGGAGCATAGgtaagaaact ... ttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
EST: gi|211129147|gb|FL382949.1|FL382949
EST:     GGCAGTTCTGCACTGGGGAGCATAG                         AAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
genomic: GGCAGTTCTGCACTGGGGAGCATAGgtaagaaact ... ttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
EST: gi|60349165|gb|DN216138.1|DN216138
EST:     GGCAGTTCTGCACTGGGGAGCATAG                         AAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
genomic: GGCAGTTCTGCACTGGGGAGCATAGgtaagaaact ... ttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
EST: gi|60349812|gb|DN216785.1|DN216785
EST:     GGCAGTTCTGCACTGGGGAGCATAG                         AAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
genomic: GGCAGTTCTGCACTGGGGAGCATAGgtaagaaact ... ttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
EST: gi|60394638|gb|DN227508.1|DN227508
EST:     GGCAGTTCTGCACTGGGGAGCATAG                         AAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
genomic: GGCAGTTCTGCACTGGGGAGCATAGgtaagaaact ... ttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
EST: gi|24766439|gb|CA401593.1|CA401593
EST:     GCACTGGGGAGCATAG                         AAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
genomic: GCACTGGGGAGCATAGgtaagaaact ... ttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
EST: gi|211360429|gb|FL377716.1|FL377716
EST:     GGCAGTTCTGCACTGGGGAGCATAG                         AAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
genomic: GGCAGTTCTGCACTGGGGAGCATAGgtaagaaact ... ttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
EST: gi|211357849|gb|FL385252.1|FL385252
EST:     GGCAGTTCTGCACTGGGGAGCATAG                         AAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
genomic: GGCAGTTCTGCACTGGGGAGCATAGgtaagaaact ... ttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
EST: gi|87152302|gb|DY397091.1|DY397091
EST:     GGCAGTTCTGCACTGGGGAGCATAG                         AAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
genomic: GGCAGTTCTGCACTGGGGAGCATAGgtaagaaact ... ttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
EST: gi|211073855|gb|FL392646.1|FL392646
EST:     GGCAGTTCTGCACTGGGGAGCATAG                         AAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
genomic: GGCAGTTCTGCACTGGGGAGCATAGgtaagaaact ... ttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
EST: gi|211027097|gb|FL381991.1|FL381991
EST:     GGCAGTTCTGCACTGGGGAGCATAG                         AAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
genomic: GGCAGTTCTGCACTGGGGAGCATAGgtaagaaact ... ttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
EST: gi|211365914|gb|FL387069.1|FL387069
EST:     GGCAGTTCTGCACTGGGGAGCATNN                         NNNNNNTGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
genomic: GGCAGTTCTGCACTGGGGAGCATAGgtaagaaact ... ttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
EST: gi|211099687|gb|FL379428.1|FL379428
EST:     GGCAGTTCTGCACTGGGGAGCATAG                         AAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
genomic: GGCAGTTCTGCACTGGGGAGCATAGgtaagaaact ... ttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
EST: gi|22490292|gb|BU050215.1|BU050215
EST:     GGCAGTTCTGCACTGGGGAGCATAG                         AAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
genomic: GGCAGTTCTGCACTGGGGAGCATAGgtaagaaact ... ttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
EST: gi|211206179|gb|FL469079.1|FL469079
EST:     GGCAGTTCTGCACTGGGGAGCATAG                         AAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
genomic: GGCAGTTCTGCACTGGGGAGCATAGgtaagaaact ... ttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
EST: gi|211048939|gb|FL421705.1|FL421705
EST:     GGCAGTTCTGCACTGGGGAGCATAG                         AAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
genomic: GGCAGTTCTGCACTGGGGAGCATAGgtaagaaact ... ttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
EST: gi|8577336|gb|BE129973.1|BE129973
EST:     GGCAGTTCTGCACTGGGGAGCATAG                         AAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
genomic: GGCAGTTCTGCACTGGGGAGCATAGgtaagaaact ... ttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
EST: gi|211433999|gb|FL392548.1|FL392548
EST:     GGCAGTTCTGCACTGGGGAGCATAG                         AAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
genomic: GGCAGTTCTGCACTGGGGAGCATAGgtaagaaact ... ttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
EST: gi|211254561|gb|FL409666.1|FL409666
EST:     GGCAGTTCTGCACTGGGGAGCATAG                         AAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
genomic: GGCAGTTCTGCACTGGGGAGCATAGgtaagaaact ... ttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
EST: gi|78179385|gb|DV549758.1|DV549758
EST:     GGCAGTTCTGCACTGGGGAGCATAG                         AAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
genomic: GGCAGTTCTGCACTGGGGAGCATAGgtaagaaact ... ttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
EST: gi|60398036|gb|DN230852.1|DN230852
EST:     GGCAGTTCTGCACTGGGGAGCATAG                         AAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
genomic: GGCAGTTCTGCACTGGGGAGCATAGgtaagaaact ... ttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
EST: gi|211523932|gb|FL381031.1|FL381031
EST:     GGCAGTTCTGCACTGGGGAGCATAG                         AAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
genomic: GGCAGTTCTGCACTGGGGAGCATAGgtaagaaact ... ttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
EST: gi|211042680|gb|FL406379.1|FL406379
EST:     GGCAGTTCTGCACTGGGGAGCATAG                         AAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT
genomic: GGCAGTTCTGCACTGGGGAGCATAGgtaagaaact ... ttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGAT

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: 24 (upstream exon), 49 (downstream exon)
Score: 170

GCAGTTCTGCACTGGGGAGCATAGgtaagaaact ... ttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG


Block sizes: 24 (upstream exon), 49 (downstream exon)
Score: 101

GCAGTTCTGCACTGGGGAGCATAGgtaagaaact ... ttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG


Block sizes: 24 (upstream exon), 49 (downstream exon)
Score: 137

GCAGTTCTGCACTGGGGAGCATAGgtaagaaact ... ttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG


Block sizes: 24 (upstream exon), 49 (downstream exon)
Score: 91

GCAGTTCTGCACTGGGGAGCATAGgtaagaaact ... ttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcagtcagcaatctgttatatgatttctaatggtcagtttttatgttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG
               ttatatgatttctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaaggataagttgctccagcaattatgaaattactttgcactttgcagtcagcaatctgttatatgatttctaatggtcagtttttatgttgattgcagAAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - -gctccag
- - - - - - - - - - - - - - - - - ctttgca