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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acgtcgcgtgagcacgagatacgttcccttgttccatacctgttacatctgtttggtatctttattgatatgataaacaatttggtgaactgcatttcagTTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTTGACAAGAACAAGAACACCCCGTTGCATTACGCTGCTGGCTACGGCCGCA

Basic information

species Zea mays
transcript AC215244.3_FGT002
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC215244.3_FGT002 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os08g42690.1 (Oryza sativa), 3'ss of exon 6
-acgtcgcgtg-agcacgagatacgttcccttgttccatacctgttacatctgtttggtatctttattgatatgataaacaatttggtgaactgcatttcagTTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTTGACAAGAACAAGAACACCCCGTTGCATTACGCTGCTGGCTACGGCCGCA
 |  | |  ||  |   ||||    ||     |  |   | ||| | |   |  ||| |  ||   |    | |||      |             ||||||||||||||||||||  | |||||||| || |||||||||||||| ||| | ||||||||||||||||| ||| |||||||||| |||||||| ||    |
gatctagaatgtggtgtgagactttttttggggaactgcatctgctcc--ttacttgttcactgactaatcaggatttggggtcaaacttttattttttcagTTGAAGTGTGCCCAAGTACTTCTTGAGGCGGGTGCTGCAGTGGATGCTTTGGACAAGAACAAGAACACTCCGCTGCATTACGCCGCTGGCTATGGTATGA

upper sequence: AC215244.3_FGT002 (Zea mays), 3'ss of exon 6
lower sequence: EFJ08399 (Selaginella moellendorffii), 3'ss of exon 6
acgtcgcgtgagcacgagatacgttcccttgttccatacctgttacatctgtttggtatctttattgatatgataaacaatttggtgaactgcatttcagTTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTTGACAAGAACAAGAACACCCCGTTGCATTACGCTGCTGGCTACGGCCGCA
                                     | |   || ||    ||| | || |  |  |        ||   |  || | || | || |||||||| || ||  |    ||||| || ||||| ||    |||||| |  | ||||||||||| ||||| || ||||||||||||| |||||||||||| |
----------------------------------gtaagcaaatagattgagttgatttcctcctccac------gactcatctgtcatct-ctttccagTTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTGGACAAGAACAACAACACTCCATTGCATTACGCTGGTGGCTACGGCCGGA
















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|60398619|gb|DN231435.1|DN231435
EST:     AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAG                         TTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT
genomic: AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAGgtatgcagat ... tgcatttcagTTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT
EST: gi|211020509|gb|FL077073.1|FL077073
EST:     AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAG                         TTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT
genomic: AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAGgtatgcagat ... tgcatttcagTTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT
EST: gi|78026189|gb|DV494576.1|DV494576
EST:     AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAG                         TTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT
genomic: AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAGgtatgcagat ... tgcatttcagTTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT
EST: gi|211020513|gb|FL077077.1|FL077077
EST:     AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAG                         TTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT
genomic: AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAGgtatgcagat ... tgcatttcagTTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT
EST: gi|60352130|gb|DN219103.1|DN219103
EST:     AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAG                         TTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT
genomic: AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAGgtatgcagat ... tgcatttcagTTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT
EST: gi|148960886|gb|EE011567.2|EE011567
EST:     AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAG                         TTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT
genomic: AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAGgtatgcagat ... tgcatttcagTTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT
EST: gi|211384432|gb|FL031620.1|FL031620
EST:     AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAG                         TTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCNGTGGACGCTCTT
genomic: AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAGgtatgcagat ... tgcatttcagTTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT
EST: gi|60399909|gb|DN232719.1|DN232719
EST:     AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAG                         TTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT
genomic: AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAGgtatgcagat ... tgcatttcagTTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT
EST: gi|71428232|gb|DR809282.1|DR809282
EST:     AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAG                         TTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT
genomic: AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAGgtatgcagat ... tgcatttcagTTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT
EST: gi|20336929|gb|BQ172559.1|BQ172559
EST:     AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAG                         TTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT
genomic: AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAGgtatgcagat ... tgcatttcagTTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT
EST: gi|60401135|gb|DN233942.1|DN233942
EST:     AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAG                         TTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT
genomic: AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAGgtatgcagat ... tgcatttcagTTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT
EST: gi|211144128|gb|FL475582.1|FL475582
EST:     AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAG                         TTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT
genomic: AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAGgtatgcagat ... tgcatttcagTTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT
EST: gi|14245348|gb|BG873930.1|BG873930
EST:     AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAG                         TTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT
genomic: AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAGgtatgcagat ... tgcatttcagTTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT
EST: gi|148986783|gb|EE030579.2|EE030579
EST:     AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAG                         TTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT
genomic: AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAGgtatgcagat ... tgcatttcagTTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT
EST: gi|60355986|gb|DN222959.1|DN222959
EST:     AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAG                         TTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT
genomic: AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAGgtatgcagat ... tgcatttcagTTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT
EST: gi|110958273|gb|EE178325.1|EE178325
EST:     AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAG                         TTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT
genomic: AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAGgtatgcagat ... tgcatttcagTTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT
EST: gi|60341985|gb|DN208958.1|DN208958
EST:     AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAG                         TTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT
genomic: AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAGgtatgcagat ... tgcatttcagTTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT
EST: gi|149096548|gb|EE182297.2|EE182297
EST:     AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAG                         TTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT
genomic: AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAGgtatgcagat ... tgcatttcagTTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT
EST: gi|78115068|gb|DV533456.1|DV533456
EST:     AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAG                         TTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT
genomic: AAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAGgtatgcagat ... tgcatttcagTTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTT

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: 278

GGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAGgtatgcagat ... tgcatttcagTTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTTGACAAGAACAAGAACACCCCGTTGCATTACGCTGCTGGCTACGGCCGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 636

GGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAGgtatgcagat ... tgcatttcagTTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTTGACAAGAACAAGAACACCCCGTTGCATTACGCTGCTGGCTACGGCCGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 580

GGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAGgtatgcagat ... tgcatttcagTTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTTGACAAGAACAAGAACACCCCGTTGCATTACGCTGCTGGCTACGGCCGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 368

GGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAGgtatgcagat ... tgcatttcagTTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTTGACAAGAACAAGAACACCCCGTTGCATTACGCTGCTGGCTACGGCCGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catctgtttggtatctttattgatatgataaacaatttggtgaactgcatttcagTTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTTGACAAGAACAAGAACACCCCGTTGCATTACGCTGCTGGCTACGGCCGCA
                 tattgat  putative branch site (score: 368)
           tatctttattgatatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acgtcgcgtgagcacgagatacgttcccttgttccatacctgttacatctgtttggtatctttattgatatgataaacaatttggtgaactgcatttcagTTGAAGTGTGCCCAGATCCTTCTTGAAGCTGGTGCTGCAGTGGACGCTCTTGACAAGAACAAGAACACCCCGTTGCATTACGCTGCTGGCTACGGCCGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - -gcacgag
- - - - - - - - - - - - - - - - -ccatacc
- - - - - - - - - - - - - - - - - - - - - - - -tctgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaacaat