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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAGAGCAAAGATGAAGGAGCAGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAGgtagtacttatgatgccattggaaattaactgacttgtggcttcatttttttcttgcataattgtgttgcttgtaaaggatataaccacatgacaccgactgttttgtatgagcag

Basic information

species Zea mays
transcript AC208327.4_FGT003
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC208327.4_FGT003 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os11g03990.1 (Oryza sativa), 5'ss of exon 12
GGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAGAGCAAAGATGAAGGAGCAGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAGgtagtacttatgatgccattggaaattaactgacttgtggcttcatttttttct-tgcataattgtgt-tgcttgtaaaggatataaccacatgacaccgactgttttgtatgagcag------------------------------------------------------
||||| |||||| || |||||||| |||||||| |||| ||||| || ||||| | || ||||||||||| ||||||||||||||||||| |||||||||| | | || | || ||| || ||||| | || | |||| ||| | || |||| | || | | ||| || | || |
GGAAAAAGATGCTGAAGAGGAGGCAGAGTTCAGGGCAAGGATGAGAGAACAGGCTGATGCCCCTGAAGATTTACCCCCACAACTTCTCTTTGTTCATCAGgtactgttaccacacttgttttatgtttacttcctctcattttcatatcattgtgtgcaccattccttgtgtaattaaaatacatgtttgtggacctcgagatgtatttcaaaagtacagacactgttactgagtgaaatcataaatgtgatgttgattgttttatgtgcag

upper sequence: AC208327.4_FGT003 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os12g03822.2 (Oryza sativa), 5'ss of exon 3
GGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAGAGCAAAGATGAAGGAGCAGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAGgtagtacttatgatgccattggaaattaactgacttgtggcttcatttttttct-tgcataattgtgt-tgcttgtaaaggatataaccacatgacaccgactgttttgtatgagcag------------------------------------------------------
||||| |||||| || |||||||| |||||||| |||| ||||| || ||||| | || ||||||||||| ||||||||||||||||||| |||||||||| | | || | || ||| || ||||| | || | | || ||| | || |||| | || | | ||| || | || |
GGAAAAAGATGCTGAAGAGGAGGCAGAGTTCAGGGCAAGGATGAGAGAACAGGCTGATGCCCCTGAAGATTTACCCCCACAACTTCTCTTTGTTCATCAGgtactgttaccacacttgttttatgtttacttcctctcattttcatatcattgtgttcaccattccttgtgtaattaaaatacatgtttgtggacctcgagatgtatttcaaaagtacagacactgttactgagtgaaatcataaatgtgatgttgattgttttatgtgcag

upper sequence: AC208327.4_FGT003 (Zea mays), 5'ss of exon 12
lower sequence: Vv11s0016g02270.t01 (Vitis vinifera), 5'ss of exon 11
GGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAGAGCAAAGATGAAGGAGCAGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAGgtagt---------acttatgatgccattggaa-attaa---ctgacttgtggctt-catttttttcttgcataattgtgttgcttgtaaaggatataaccacatgacaccgactgttttgtatgagcag
|||| ||||| ||| |||||||||||||||||||| ||| |||||||| | ||| || || |||||||| || |||||||||||||||| ||||||||| | | || | || |||||| | || || || | | || |||| |||||| |||| | | ||| | | |
AGAAAAAGATGAGGAAGAGGAGGCTGAGTTCAGAGCCCAGACAAAGGAGCAAGTAAATGCCCCCGAAGATTTACCACCACAACTTCTCTTTGTTCATCAGgttatttcctctcaaattctcttgttcttggaacaccaaaccctaacaattagttttcattcatttcttccatacactcatatttggtaccataaacag-------------------------------

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|20337018|gb|BQ172648.1|BQ172648
EST:     AGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAG                         GGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATG
genomic: AGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAGgtagtactta ... gtatgagcagGGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATG
EST: gi|78544326|gb|DV621824.1|DV621824
EST:     AGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAG                         GGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATG
genomic: AGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAGgtagtactta ... gtatgagcagGGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATG
EST: gi|32935721|gb|CF040533.1|CF040533
EST:     AGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAG                         GGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATG
genomic: AGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAGgtagtactta ... gtatgagcagGGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATG
EST: gi|37378418|gb|CF625898.1|CF625898
EST:     AGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAG                         GGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATG
genomic: AGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAGgtagtactta ... gtatgagcagGGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATG
EST: gi|33467486|gb|CF244535.1|CF244535
EST:     AGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAG                         GGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATG
genomic: AGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAGgtagtactta ... gtatgagcagGGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATG
EST: gi|33096363|gb|CF056357.1|CF056357
EST:     AGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAG                         GGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATG
genomic: AGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAGgtagtactta ... gtatgagcagGGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATG
EST: gi|78545045|gb|DV622543.1|DV622543
EST:     AGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAG                         GGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATG
genomic: AGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAGgtagtactta ... gtatgagcagGGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATG
EST: gi|37379638|gb|CF626567.1|CF626567
EST:     AGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGTTCATCAG                         GGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATG
genomic: AGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAGgtagtactta ... gtatgagcagGGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATG
EST: gi|74242019|gb|DT649933.1|DT649933
EST:     AGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAG                         GGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATG
genomic: AGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAGgtagtactta ... gtatgagcagGGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATG
EST: gi|19769450|gb|BQ034171.1|BQ034171
EST:     AGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAG                         GGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATG
genomic: AGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAGgtagtactta ... gtatgagcagGGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATG
EST: gi|211412498|gb|FL461990.1|FL461990
EST:     AGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAG                         GGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATG
genomic: AGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAGgtagtactta ... gtatgagcagGGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATG
EST: gi|19769952|gb|BQ034673.1|BQ034673
EST:     AGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAG                         GGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATG
genomic: AGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAGgtagtactta ... gtatgagcagGGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATG
EST: gi|50339077|gb|CO534203.1|CO534203
EST:     AGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAG                         GGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATG
genomic: AGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAGgtagtactta ... gtatgagcagGGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATG
EST: gi|211466441|gb|FL172132.1|FL172132
EST:     AGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAG                         GGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATG
genomic: AGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAGgtagtactta ... gtatgagcagGGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATG
EST: gi|21088827|gb|BQ401140.1|BQ401140
EST:     AGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAG                         GGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATG
genomic: AGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAGgtagtactta ... gtatgagcagGGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATG
EST: gi|37380594|gb|CF627120.1|CF627120
EST:     GGCAAACGCA-CTGAAGATTTTGCCCCCACAACTTCTCTTTGCTCATCAG                         GGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATG
genomic: GGCAAACGCACCTGAAGA-TTTGCCCCCACAACTTCTCTTTGCTCATCAGgtagtactta ... gtatgagcagGGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATG
EST: gi|211355147|gb|FL476248.1|FL476248
EST:     AGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAG                         GGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATG
genomic: AGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAGgtagtactta ... gtatgagcagGGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATG
EST: gi|32866680|gb|CF006362.1|CF006362
EST:     AGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAG                         GGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATG
genomic: AGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAGgtagtactta ... gtatgagcagGGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATG

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), 48 (downstream exon)
Score: 230

GGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAGAGCAAAGATGAAGGAGCAGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAGgtagtactta ... gtatgagcagGGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATGATCATATCAACGGCAATTGATGGCTTCAACGTGTTGATGCCTAGCAACA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 122

GGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAGAGCAAAGATGAAGGAGCAGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAGgtagtactta ... gtatgagcagGGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATGATCATATCAACGGCAATTGATGGCTTCAACGTGTTGATGCCTAGCAACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 217

GGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAGAGCAAAGATGAAGGAGCAGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAGgtagtactta ... gtatgagcagGGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATGATCATATCAACGGCAATTGATGGCTTCAACGTGTTGATGCCTAGCAACA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 111

GGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAGAGCAAAGATGAAGGAGCAGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAGgtagtactta ... gtatgagcagGGCCAGAGAGACTTGAAAGAACTGCACTGGCACCCACAGATACCGTCGATGATCATATCAACGGCAATTGATGGCTTCAACGTGTTGATGCCTAGCAACA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAGAGCAAAGATGAAGGAGCAGGCAAACGCACCTGAAGATTTGCCCCCACAACTTCTCTTTGCTCATCAGgtagtacttatgatgccattggaaattaactgacttgtggcttcatttttttcttgcataattgtgttgcttgtaaaggatataaccacatgacaccgactgttttgtatgagcag

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