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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataggcttctccgggttactgactttgaaccatactttattctattggtgctagaagattgataagtgcaaaagtagcatgaagattctgatgatcaatgtacctgtgctttgcagGCGCACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTGAACTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAA

Basic information

species Zea mays
transcript AC217401.3_FGT002
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC217401.3_FGT002 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g49610.1 (Oryza sativa), 3'ss of exon 9
gtataggcttctccgggttactgactttgaaccatactttattctattggtgctagaagattgataagtgcaaaagtagcatgaagattctgatgatcaatgtacctgtgctttgcagGCGCACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTGAACTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAA
||||||   | |||   || |  || || ||   || ||| ||  ||   ||||| ||||||   |||||      ||  | ||  ||     | | || || |  | |    |||||||  |||| | ||||||||| ||||| ||  | |||||||||||||  ||||||||| ||||||| |||||  |||||||||  ||||||||||| ||||
gtatagttgtttcctc-ttgcc-acattcaattttagtttctt--atcaatgctacaagattagcaagtgtggc--taagacgagaatctc--ttacca-tgcat-tatttcgtgcagGCAAACTCTAATTGGCTTTATATCGTTCCGACTGGCATGTATGGAGCTGTGAACTACATAAAGGAGAAGTATAATAATCCAACAATCATCATATCTGAAA
















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|32856217|gb|CD995898.1|CD995898
EST:     TTCAAAGGGATGGGGTGCAAATTGGACAGATG                         GCGCACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGGCGTG
genomic: TTCAAAGGAATGGCGTGCAAATTGGACAGATGgtataggctt ... tgctttgcagGCGCACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTG
EST: gi|32832647|gb|CD972325.1|CD972325
EST:     TTCAAAGGAATGGCGTGCAAATTGGACAGATG                         GCGCACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTG
genomic: TTCAAAGGAATGGCGTGCAAATTGGACAGATGgtataggctt ... tgctttgcagGCGCACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTG
EST: gi|67013218|gb|CO441967.1|CO441967
EST:     TTCAAAGGAATGGCGTGCAAATTGGACAGATG                         GCGCACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTG
genomic: TTCAAAGGAATGGCGTGCAAATTGGACAGATGgtataggctt ... tgctttgcagGCGCACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTG
EST: gi|78075435|gb|DV503869.1|DV503869
EST:     TTCAAAGGAATGGCGTGCAAATTGGACAGATG                         GCGCACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTG
genomic: TTCAAAGGAATGGCGTGCAAATTGGACAGATGgtataggctt ... tgctttgcagGCGCACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTG
EST: gi|78022826|gb|DV491213.1|DV491213
EST:     CAAATTGGACCGATG                         GCGCACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTG
genomic: CAAATTGGACAGATGgtataggctt ... tgctttgcagGCGCACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTG
EST: gi|60351674|gb|DN218647.1|DN218647
EST:     TTCAAAGGAATGGCGTGCAAATTGGACAGATG                         GCGCACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTG
genomic: TTCAAAGGAATGGCGTGCAAATTGGACAGATGgtataggctt ... tgctttgcagGCGCACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTG
EST: gi|149013746|gb|EE043205.2|EE043205
EST:     TTCAAAGGAATGGCGTGCAAATTGGACAGATG                         GCGCACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGT
genomic: TTCAAAGGAATGGCGTGCAAATTGGACAGATGgtataggctt ... tgctttgcagGCGCACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGT
EST: gi|60340042|gb|DN207015.1|DN207015
EST:     TTCAAAGGAATGGCGTGCAAATTGGACAGATG                         GCGCACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTG
genomic: TTCAAAGGAATGGCGTGCAAATTGGACAGATGgtataggctt ... tgctttgcagGCGCACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTG
EST: gi|60394083|gb|DN226953.1|DN226953
EST:     TTCAAAGGAATGGCGTGCAAATTGGACAGATG                         GCGCACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTG
genomic: TTCAAAGGAATGGCGTGCAAATTGGACAGATGgtataggctt ... tgctttgcagGCGCACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTG
EST: gi|149014536|gb|EE044170.2|EE044170
EST:     CAAATTGGACAGATG                         GCGCACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTG
genomic: CAAATTGGACAGATGgtataggctt ... tgctttgcagGCGCACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTG
EST: gi|40336432|gb|CK370502.1|CK370502
EST:     TTCAAAGGAATGGCGTGCAAATTGGACAGATG                         GCGCACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTG
genomic: TTCAAAGGAATGGCGTGCAAATTGGACAGATGgtataggctt ... tgctttgcagGCGCACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTG
EST: gi|37393320|gb|CF633922.1|CF633922
EST:     CAATATTACTTTCAAAGGAATGGCGTGCAAATTGGACAGATG                         GCGCACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTG
genomic: CAATATTACTTTCAAAGGAATGGCGTGCAAATTGGACAGATGgtataggctt ... tgctttgcagGCGCACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTG
EST: gi|32834810|gb|CD974488.1|CD974488
EST:     TTCAAAGGAATGGCGTGCAAATTGGACAGATG                         GCGCACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTG
genomic: TTCAAAGGAATGGCGTGCAAATTGGACAGATGgtataggctt ... tgctttgcagGCGCACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTG
EST: gi|20507721|gb|BQ279747.1|BQ279747
EST:     TTCAAAGGAATGGCGTGCAAATTGGACAGATG                         GCGCACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTG
genomic: TTCAAAGGAATGGCGTGCAAATTGGACAGATGgtataggctt ... tgctttgcagGCGCACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTG

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: 233

TTCAAAGGAATGGCGTGCAAATTGGACAGATGgtataggctt ... tgctttgcagGCGCACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTGAACTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 114

TTCAAAGGAATGGCGTGCAAATTGGACAGATGgtataggctt ... tgctttgcagGCGCACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTGAACTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 44

TTCAAAGGAATGGCGTGCAAATTGGACAGATGgtataggctt ... tgctttgcagGCGCACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTGAACTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 196

TTCAAAGGAATGGCGTGCAAATTGGACAGATGgtataggctt ... tgctttgcagGCGCACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTGAACTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataagtgcaaaagtagcatgaagattctgatgatcaatgtacctgtgctttgcagGCGCACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTGAACTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAA
                        ttctgat  putative branch site (score: 196)
        aaaagta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataggcttctccgggttactgactttgaaccatactttattctattggtgctagaagattgataagtgcaaaagtagcatgaagattctgatgatcaatgtacctgtgctttgcagGCGCACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTGAACTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA