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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctttggacatgaaaattgtttgtaatgtggtcttttggctgattgtttgggagtactaatttgaattaactctatttgtttctcttgtgacaagttcagGAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTGACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAA

Basic information

species Zea mays
transcript GRMZM2G080930_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G080930_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g54770.1 (Oryza sativa), 3'ss of exon 1
cctttggacatgaaaat----tgtttgtaatgtggtcttttggctgattgtttgggagtactaatttgaattaactctatttgtttctcttgtgacaagttcagGAATT-GTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTGACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAA
  ||  |   ||||  |      ||| |  | ||||| | | ||   |  | | | | ||    |  | |  | || || ||| |||  || | ||   |||||| ||| |||| | ||||||||| |||||||||||||||||||| | || |||||||| |||||||| ||||||||||| || |||||||||||||||||| 
gtttatggtctgaaggtgtaacatttatcttttggtcctcttgc-attcatgtagaaatatatttagggaagagctataattggttcctttcttac---ttcagGGATTTGTTCACGATGGCCCGCTTGTATGTTGGCAACTTGGATCCCCGAGTGACTTCCGGGGAACTTGAAGATGAGTTTCGTGTGTTTGGAGTTCTGCGA-

upper sequence: GRMZM2G080930_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA17G29080.2 (Glycine max), 3'ss of exon 1
-----------cctttggacatgaaaattgtttgtaatgtggtcttttggctgattgtttgggagtac-taatttgaattaactctatttgtttctcttgtgacaagttcagGAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTGACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAA
            ||| | ||   ||||   | | | |       ||||   |     ||||  | | |    ||| |||| | |  ||||| ||   ||        ||| | ||         ||| | |||||||||||||| |||||||||||||| || ||     | || |||||||| || ||||| || || |||||| | ||  
tttgaaatcattcttcgaaccctaaaaacatctttcaccga---ttttcattttccctttgcaaattcaccgtttaaatttaattaatttgcttgattttcagGTTCTTCTGAAAA-------GATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAGTCACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCG--

upper sequence: GRMZM2G080930_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA14G17930.4 (Glycine max), 3'ss of exon 1
-----------------------------------------------------------------------------------------cctttggacatgaaaattgtttgtaatgtggtcttttggctgattgtttgggagtac-taatttgaattaactctatttgtttctcttgtgacaagttcagGAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTGACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAA
                                                                                          ||| | ||   ||||   | |||         |||| | |     ||||  ||| |    ||| |||| | |  ||||  ||   ||        ||| | ||         ||| | |||||||||||||| |||||||||||||| || ||     | || |||||||| || |||||||| || |||||| | ||  
gttcagatctctcttctcagtttccgattttcctttttacttcgctttcaaccccctccttttcaatttccccaatcttttgaaatctttcttcgaaccctaaaaacatctgtccccga---ttttcgtttcccctttgcaagttcaccgtttaaatttaattaattttcttaattttcagGTTCTTCTGAAAA-------GATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAGTCACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCG--

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|211113501|gb|FL364717.1|FL364717
EST:     CGGGCGGGAGCTTGGACGTGCTACTCTGCTCTCATCTCGTTTCCGCGCAG                         GAATTGTTCACAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTG
genomic: CGGGCGGGAGCTTGGACGTGCTACGCTGCTCTCATCTCGTTTCCGCGCAGgtaatcccaa ... acaagttcagGAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTG
EST: gi|211105696|gb|FL316276.1|FL316276
EST:     CGGGCGGGAGCTTGGACGTGCTACGCTGCTCTCATCTCGTTTCCGCGCAG                         GAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTG
genomic: CGGGCGGGAGCTTGGACGTGCTACGCTGCTCTCATCTCGTTTCCGCGCAGgtaatcccaa ... acaagttcagGAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTG
EST: gi|211260063|gb|FL327809.1|FL327809
EST:     CGGGCGGGAGCTTGGACGTGCTACTCTGCTCTCATCTCGTTTCCGCGCAG                         GAATTGTTCACAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTG
genomic: CGGGCGGGAGCTTGGACGTGCTACGCTGCTCTCATCTCGTTTCCGCGCAGgtaatcccaa ... acaagttcagGAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTG
EST: gi|211310251|gb|FL338861.1|FL338861
EST:     CGGGCGGGAGCTTGGACGTGCTACGCTGCTCTCATCTCGTTTCCGCGCAG                         GAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTG
genomic: CGGGCGGGAGCTTGGACGTGCTACGCTGCTCTCATCTCGTTTCCGCGCAGgtaatcccaa ... acaagttcagGAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTG
EST: gi|18964300|gb|BM660926.1|BM660926
EST:     GGCGGGAGCTTGGACCGGGCCTCCGCTGCTCTCATCTCGTTTCCGCGCAG                         GAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTG
genomic: GGCGGGAGCTTGGA-CGTG-CTACGCTGCTCTCATCTCGTTTCCGCGCAGgtaatcccaa ... acaagttcagGAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTG
EST: gi|211158830|gb|FL334283.1|FL334283
EST:     CGGGCGGGAGCTTGGACGTGCTACGCTGCTCTCATCTCGTTTCCGCGCAG                         GAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTG
genomic: CGGGCGGGAGCTTGGACGTGCTACGCTGCTCTCATCTCGTTTCCGCGCAGgtaatcccaa ... acaagttcagGAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTG
EST: gi|211072623|gb|FL332514.1|FL332514
EST:     CGGGCGGGAGCTTGGACGTGCTACGCTGCTCTCATCTCGTTTCCGCGCAG                         GAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTG
genomic: CGGGCGGGAGCTTGGACGTGCTACGCTGCTCTCATCTCGTTTCCGCGCAGgtaatcccaa ... acaagttcagGAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTG
EST: gi|211205317|gb|FL316783.1|FL316783
EST:     CGGGCGGGAGCTTGGACGTGCTACGCTGCTCTCATCTCGTTTCCGCGCAG                         GAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTG
genomic: CGGGCGGGAGCTTGGACGTGCTACGCTGCTCTCATCTCGTTTCCGCGCAGgtaatcccaa ... acaagttcagGAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTG
EST: gi|211375406|gb|FL332329.1|FL332329
EST:     CGGGCGGGAGCTTGGACGTGCTACTCTGCTCTC-TCTCGTTTCCGCGCAG                         GAATTGTTCACAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTG
genomic: CGGGCGGGAGCTTGGACGTGCTACGCTGCTCTCATCTCGTTTCCGCGCAGgtaatcccaa ... acaagttcagGAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTG
EST: gi|211215612|gb|FL316847.1|FL316847
EST:     CGGGCGGGAGCTTGGACGTGCTACTCTGCTCTCATCTCGTTTCCGCGCAG                         GAATTGTTCACAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTG
genomic: CGGGCGGGAGCTTGGACGTGCTACGCTGCTCTCATCTCGTTTCCGCGCAGgtaatcccaa ... acaagttcagGAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTG
EST: gi|211138186|gb|FL349860.1|FL349860
EST:     CGGGCGGGAGCTTGGACGTGCTACTCTGCTCTCATCTCGTTTCCGCGCAG                         GAATTGTTCACAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTG
genomic: CGGGCGGGAGCTTGGACGTGCTACGCTGCTCTCATCTCGTTTCCGCGCAGgtaatcccaa ... acaagttcagGAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTG
EST: gi|211274557|gb|FL349470.1|FL349470
EST:     GGGGCGGGAGCTTGGACGTGCTACGCTGCTCTCATCTCGTTTCCGCGCAG                         GAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTG
genomic: -GGGCGGGAGCTTGGACGTGCTACGCTGCTCTCATCTCGTTTCCGCGCAGgtaatcccaa ... acaagttcagGAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTG
EST: gi|211432430|gb|FL327491.1|FL327491
EST:     CGGGCGGGAGCTTGGACGTGCTACGCTGCTCTCATCTCGTTTCCGCGCAG                         GAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTG
genomic: CGGGCGGGAGCTTGGACGTGCTACGCTGCTCTCATCTCGTTTCCGCGCAGgtaatcccaa ... acaagttcagGAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTG
EST: gi|211416748|gb|FL321413.1|FL321413
EST:     CGGGCGGGAGCTTGGACGTGCTACGCTGCTCTCATCTCGTTTCCGCGCAG                         GAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTG
genomic: CGGGCGGGAGCTTGGACGTGCTACGCTGCTCTCATCTCGTTTCCGCGCAGgtaatcccaa ... acaagttcagGAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTG
EST: gi|211470387|gb|FL342153.1|FL342153
EST:     CGGGCGGGAGCTTGGACGTGCTACGCTGCTCTCATCTCGTTTCCGCGCAG                         GAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTG
genomic: CGGGCGGGAGCTTGGACGTGCTACGCTGCTCTCATCTCGTTTCCGCGCAGgtaatcccaa ... acaagttcagGAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTG
EST: gi|211047373|gb|FL359874.1|FL359874
EST:     CGGGCGGGAGCTTGGACGTGCTACGCTGCTCTCATCTCGTTTCCGCGCAG                         GAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTG
genomic: CGGGCGGGAGCTTGGACGTGCTACGCTGCTCTCATCTCGTTTCCGCGCAGgtaatcccaa ... acaagttcagGAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTG
EST: gi|211091140|gb|FL328973.1|FL328973
EST:     CGGGCGGGAGCTTGGACGTGCTACGCTGCTCTCATCTCGTTTCCGCGCAG                         GAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTG
genomic: CGGGCGGGAGCTTGGACGTGCTACGCTGCTCTCATCTCGTTTCCGCGCAGgtaatcccaa ... acaagttcagGAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTG

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: 46 (upstream exon), 49 (downstream exon)
Score: 27

TCTGCCCTACTCCTCTTCCGCCGCCTCCAACACCGCAGACGCAGCTGCCGCGGGCGGGAGCTTGGACGTGCTACGCTGCTCTCATCTCGTTTCCGCGCAGgtaatcccaa ... acaagttcagGAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTGACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 12

TCTGCCCTACTCCTCTTCCGCCGCCTCCAACACCGCAGACGCAGCTGCCGCGGGCGGGAGCTTGGACGTGCTACGCTGCTCTCATCTCGTTTCCGCGCAGgtaatcccaa ... acaagttcagGAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTGACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAA


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 19

TCTGCCCTACTCCTCTTCCGCCGCCTCCAACACCGCAGACGCAGCTGCCGCGGGCGGGAGCTTGGACGTGCTACGCTGCTCTCATCTCGTTTCCGCGCAGgtaatcccaa ... acaagttcagGAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTGACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAA


Block sizes: 47 (upstream exon), 25 (downstream exon)
Score: 12

TCTGCCCTACTCCTCTTCCGCCGCCTCCAACACCGCAGACGCAGCTGCCGCGGGCGGGAGCTTGGACGTGCTACGCTGCTCTCATCTCGTTTCCGCGCAGgtaatcccaa ... acaagttcagGAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTGACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgggagtactaatttgaattaactctatttgtttctcttgtgacaagttcagGAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTGACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAA
            taatttgaattaactc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctttggacatgaaaattgtttgtaatgtggtcttttggctgattgtttgggagtactaatttgaattaactctatttgtttctcttgtgacaagttcagGAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTGACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - catgaaa
- - - - - - - - -tgtttgt
- - - - - - - - - - - - - - - - - - - -ctgattg