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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagcctaagagggtcatagttattggcattgttgggttcattgtttacttgttttgttaaaaaatatgcatgtgcaaggtacatactgtgaaattcattggagctcttgattcatgtatcgtagctcttttgctgaatttccgctaggcgactaattctcagtatctgttccttcccaccttctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATGTCACCTGTAAGAACACTTGCTGGGAGGCTGGAAAGGTGGCAAGGGAGAAATTGAAGAAGAAAAT

Basic information

species Zea mays
transcript AC213600.3_FGT002
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC213600.3_FGT002 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g16970.1 (Oryza sativa), 3'ss of exon 3
gtaagagcctaagagggtcatagttattggcattgttgggttcattgtttacttgttttgttaaaaaatatgcatgtg-caaggtacatactgtgaaattcattggagctcttgattcatgtatcgtagctcttttgctgaatttccgctaggc----gactaattctcagtatctgttccttcccaccttctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATGTCACCTGTAAGAACACTTGCTGGGAGGCTGGAAAGGTGGCAAGGGAGAAATTGAAGAAGAAAAT
         ||||||| | ||| |   ||||  |  |  ||  ||  || |  |||      |  |||| | ||       |  |  |      || |||    || ||| ||| | | |  | | |||  |||  |  ||||| ||||||         ||||||  |  ||| ||||  |  |  |||  |||||||||| || ||||||||||| ||||| ||||||||||| || ||||| || |||||||||||||| || | ||||||||| ||||||||||| ||| |
--------gtaagaggattataatcggtggccattctctgt--atcattcaaatgtaaacacagtaaatgtacacaaaatcaattgtaaggctagagattag--ggtgcttttgttccgtaaa-catagtgcttgagg-gaattcccgctatatttttttctaattacccatatgtgtttgtcgctgcctcttagATTGCTGCGACGGGAGTGATGAGTATGATAGCAATGTCACTTGCAAGAATACGTGCTGGGAGGCTGGTAAAGCGGCAAGGGATAAATTGAAGAAAAAAGT
















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|15427042|gb|BI542864.1|BI542864
EST:     CCACACTCCAGTCACGATCTTCTCGTCACGAGTGAATGACGGCATTTGTG                         ATTGCTGTGATGGGAGTGATGAATATGACAGCAATGTCACCTGTAAGAACA
genomic: CCACACTCCAGTCACGATCTTCTCGTCACGAGTGAATGACGGCATTTGTGgtaagagcct ... caccttctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATGTCACCTGTAAGAACA
EST: gi|211470279|gb|FL336879.1|FL336879
EST:     CCACACTCCAGTCACGATCTTCTCGTCACGAGTGAATGACGGCATTTGTG                         ATTGCTGTGATGGGAGTGATGAATATGACAGCAATGTCACCTGTAAGAACA
genomic: CCACACTCCAGTCACGATCTTCTCGTCACGAGTGAATGACGGCATTTGTGgtaagagcct ... caccttctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATGTCACCTGTAAGAACA
EST: gi|211091911|gb|FL362893.1|FL362893
EST:     CCACACTCCAGTCACGATCTTCTCGTCACGAGTGAATGACGGCATTTGTG                         ATTGCTGTGATGGGAGTGATGAATATGACAGCAATGTCACCTGTAAGAACA
genomic: CCACACTCCAGTCACGATCTTCTCGTCACGAGTGAATGACGGCATTTGTGgtaagagcct ... caccttctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATGTCACCTGTAAGAACA
EST: gi|211133488|gb|FL236777.1|FL236777
EST:     CCACACTCCAGTCACGATCTTCTCGTCACGAGTGAATGACGGCATTTGTG                         ATTGCTGTGATGGGAGTGATGAATATGACAGCAATGTCACCTGTAAGAACA
genomic: CCACACTCCAGTCACGATCTTCTCGTCACGAGTGAATGACGGCATTTGTGgtaagagcct ... caccttctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATGTCACCTGTAAGAACA
EST: gi|211391684|gb|FL461159.1|FL461159
EST:     CCACACTCCAGTCACGATCTTCTCGTCACGAGTGAATGACGGCATTTGTG                         ATTGCTGTGATGGGAGTGATGAATATGACAGCAATGTCACCTGTAAGAACA
genomic: CCACACTCCAGTCACGATCTTCTCGTCACGAGTGAATGACGGCATTTGTGgtaagagcct ... caccttctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATGTCACCTGTAAGAACA
EST: gi|211531444|gb|FL327584.1|FL327584
EST:     CCACACTCCAGTCACGATCTTCTCGTCACGAGTGAATGACGGCATTTGTG                         ATTGCTGTGATGGGAGTGATGAATATGACAGCAATGTCACCTGTAAGAACA
genomic: CCACACTCCAGTCACGATCTTCTCGTCACGAGTGAATGACGGCATTTGTGgtaagagcct ... caccttctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATGTCACCTGTAAGAACA
EST: gi|32945773|gb|CF050592.1|CF050592
EST:     CCACACTCCAGTCACGATCTTCTCGTCACGAGTGAATGACGGCATTTGTG                         ATTGCTGTGATGGGAGTGATGAATATGAAAGCAATGTCACCTGTAAGAACA
genomic: CCACACTCCAGTCACGATCTTCTCGTCACGAGTGAATGACGGCATTTGTGgtaagagcct ... caccttctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATGTCACCTGTAAGAACA
EST: gi|211389058|gb|FL461157.1|FL461157
EST:     CCACACTCCAGTCACGATCTTCTCGTCACGAGTGAATGACGGCATTTGTG                         ATTGCTGTGATGGGAGTGATGAATATGACAGCAATGTCACCTGTAAGAACA
genomic: CCACACTCCAGTCACGATCTTCTCGTCACGAGTGAATGACGGCATTTGTGgtaagagcct ... caccttctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATGTCACCTGTAAGAACA
EST: gi|15499427|gb|BI595940.1|BI595940
EST:     CCACACTCCAGTCACGATCTTCTCGTCACGAGTGAATGACGGCATTTGTG                         ATTGCTGTGATGGGAGTGATGAATATGACAGCAATGTCACCTGTAAGAACA
genomic: CCACACTCCAGTCACGATCTTCTCGTCACGAGTGAATGACGGCATTTGTGgtaagagcct ... caccttctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATGTCACCTGTAAGAACA
EST: gi|60344264|gb|DN211237.1|DN211237
EST:     CCACACTCCAGTCACGATCTTCTCGTCACGAGTGAATGACGGCATTTGTG                         ATTGCTGTGATGGGAGTGATGAATATGACAGCAATGTCACCTGTAAGAACA
genomic: CCACACTCCAGTCACGATCTTCTCGTCACGAGTGAATGACGGCATTTGTGgtaagagcct ... caccttctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATGTCACCTGTAAGAACA
EST: gi|211237696|gb|FL353195.1|FL353195
EST:     CCACACTCCAGTCACGATCTTCTCGTCACGAGTGAATGACGGCATTTGTG                         ATTGCTGTGATGGGAGTGATGAATATGACAGCAATGTCACCTGTAAGAACA
genomic: CCACACTCCAGTCACGATCTTCTCGTCACGAGTGAATGACGGCATTTGTGgtaagagcct ... caccttctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATGTCACCTGTAAGAACA
EST: gi|211133487|gb|FL236776.1|FL236776
EST:     ACACTTCCAGTCACGATCTTCTCGTCACGAGTTGAATGACGGCATTTGTG                         ATTGCTGTGATGGGAGT
genomic: ACACT-CCAGTCACGATCTTCTCGTCACGAGT-GAATGACGGCATTTGTGgtaagagcct ... caccttctagATTGCTGTGATGGGAGT
EST: gi|211262935|gb|FL345535.1|FL345535
EST:     CCACACTCCAGTCACGATCTTCTCGTCACGAGTGAATGACGGCATTTGTG                         ATTGCTGTGATGGGAGTGATGAATATGACAGCAATGTCACCTGTAAGAACA
genomic: CCACACTCCAGTCACGATCTTCTCGTCACGAGTGAATGACGGCATTTGTGgtaagagcct ... caccttctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATGTCACCTGTAAGAACA

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: 217

GGACATCTGCATGCCCTGAGGCGAAATTCTACTGCAAGAATGCAGGCCACACTCCAGTCACGATCTTCTCGTCACGAGTGAATGACGGCATTTGTGgtaagagcct ... caccttctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATGTCACCTGTAAGAACACTTGCTGGGAGGCTGGAAAGGTGGCAAGGGAGAAATTGAAGAAGAAAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 231

GGACATCTGCATGCCCTGAGGCGAAATTCTACTGCAAGAATGCAGGCCACACTCCAGTCACGATCTTCTCGTCACGAGTGAATGACGGCATTTGTGgtaagagcct ... caccttctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATGTCACCTGTAAGAACACTTGCTGGGAGGCTGGAAAGGTGGCAAGGGAGAAATTGAAGAAGAAAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 225

GGACATCTGCATGCCCTGAGGCGAAATTCTACTGCAAGAATGCAGGCCACACTCCAGTCACGATCTTCTCGTCACGAGTGAATGACGGCATTTGTGgtaagagcct ... caccttctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATGTCACCTGTAAGAACACTTGCTGGGAGGCTGGAAAGGTGGCAAGGGAGAAATTGAAGAAGAAAAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 252

GGACATCTGCATGCCCTGAGGCGAAATTCTACTGCAAGAATGCAGGCCACACTCCAGTCACGATCTTCTCGTCACGAGTGAATGACGGCATTTGTGgtaagagcct ... caccttctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATGTCACCTGTAAGAACACTTGCTGGGAGGCTGGAAAGGTGGCAAGGGAGAAATTGAAGAAGAAAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgaatttccgctaggcgactaattctcagtatctgttccttcccaccttctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATGTCACCTGTAAGAACACTTGCTGGGAGGCTGGAAAGGTGGCAAGGGAGAAATTGAAGAAGAAAAT
                  gactaat  putative branch site (score: 252)
                               tatctgttccttccca  putative PPT
                   actaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagagcctaagagggtcatagttattggcattgttgggttcattgtttacttgttttgttaaaaaatatgcatgtgcaaggtacatactgtgaaattcattggagctcttgattcatgtatcgtagctcttttgctgaatttccgctaggcgactaattctcagtatctgttccttcccaccttctagATTGCTGTGATGGGAGTGATGAATATGACAGCAATGTCACCTGTAAGAACACTTGCTGGGAGGCTGGAAAGGTGGCAAGGGAGAAATTGAAGAAGAAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA