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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtacacattaacaacacctgggtgttcaaaaaagatcttgagggtttatttgatctattgatgattctaacactattagatgtttgaatggttgcctctccagGACAGGAATTTAAATCAGCTGGCGTCATCTGAATCATCTAGTTCTGGTACGAGGAATTATGTTCCAGGAAGCAGTGATCCTCATAGCAGTGGTTTGCGGC

Basic information

species Zea mays
transcript GRMZM2G107867_T04
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107867_T04 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g17980.2 (Oryza sativa), 3'ss of exon 8
gttagtacacattaacaacacctgggtgttcaaaaaagatcttgagggtttatttgatctattgatgattctaacactattagatgtttgaatggttgcctctccagGACAGGAATTTAAATCAGCTGGCGTCATCTGAATCATCTAGTTCTGGTACGAGGAATTATGTTCCAGGAAGCAGTGATCCTCATAGCAGTGGTTTGCGGC
|||||| || ||| ||| || ||   |||   | | |  |    | |   | ||| ||  | ||     ||| |||               ||||||    |   |||| |||||||| ||||   | || ||||| |||||| | |||||   ||| ||| ||||| |||||||||||||||||||||||  |||||||||||| |
gttagttcaaatttacagcatctt--tgtctgacataatttgcaaag---tgtttaattaactg-----tctgacat-------------gatggtt----cattagGAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATACAAGGCATTATCTTCCAGGAAGCAGTGATCCTCATGCCAGTGGTTTGCGCC

upper sequence: GRMZM2G107867_T04 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os08g37800.1 (Oryza sativa), 3'ss of exon 8
gttagtacacattaacaacacctgggtgttcaaaaaagatcttgagggtttatttgatctattgatgattctaacactattagatgtttgaatggttgcctctccagGACAGGAATTTAAATCAGCTGGCGTCATCTGAATCATCTAGTTCTGGTACGAGGAATTATGTTCCAGGAAGCAGTGATCCTCATAGCAGTGGTTTGCGGC
|||||| || ||| ||| ||  |   |||   | | |  |    |     | ||| ||  | ||     ||| ||  ||                  |  ||   |||| |||||| | ||||   | || ||||| |||||| | |||||   ||| ||| ||||| | |||||||||||||||||||||  |||||||||||| |
gttagttcaaatttacaccatttt--tgtctgacataatttgcaaaa---tgtttaattaactg-----tctgaccttac-----------------ggttcattagGAGAGGAATCTTAATCGCTTTGCTTCATCAGAATCAGCAAGTTCAAATACAAGGCATTATCTCCCAGGAAGCAGTGATCCTCATGCCAGTGGTTTGCGCC
















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|18661445|gb|BM501401.1|BM501401
EST:     GGTTTAGAGCAACTAGTGGCTATCTTGGGGCAGATTATCAAGAATCAATG                         GACAGGAATTTAAATCAGCTGGCGTCATCTGAATCATCTAGTTCTGGTACG
genomic: GGTTTAGAGCAACTAGTGGCTATCTTGGGGCAGATTATCAAGAATCAATGgttagtacac ... gcctctccagGACAGGAATTTAAATCAGCTGGCGTCATCTGAATCATCTAGTTCTGGTACG
EST: gi|6031419|gb|AW076321.1|AW076321
EST:     AGAGCAACTAGTGGCTATCTTGGGGCAGATTATCAAGAATCAATG                         GACAGGAATTTAAATCAGCTGGCGTCATCTGAATCATCTAGTTCTGGTACG
genomic: AGAGCAACTAGTGGCTATCTTGGGGCAGATTATCAAGAATCAATGgttagtacac ... gcctctccagGACAGGAATTTAAATCAGCTGGCGTCATCTGAATCATCTAGTTCTGGTACG
EST: gi|211186172|gb|FL452293.1|FL452293
EST:     GGTTTAGAGCAACTAGTGGCTATCTTGGGGCAGATTATCAAGAATCAATG                         GACAGGAATTTAAATCAGCTGGCGTCATCTGAATCATCTAGTTCTGGTACG
genomic: GGTTTAGAGCAACTAGTGGCTATCTTGGGGCAGATTATCAAGAATCAATGgttagtacac ... gcctctccagGACAGGAATTTAAATCAGCTGGCGTCATCTGAATCATCTAGTTCTGGTACG
EST: gi|60341419|gb|DN208392.1|DN208392
EST:     GGTTTAGAGCAACTAGTGGCTATCTTGGGGCAGATTATCAAGAATCAATG                         GACAGGAATTTAAATCAGCTGGCGTCATCTGAATCATCTAGTTCTGGTACG
genomic: GGTTTAGAGCAACTAGTGGCTATCTTGGGGCAGATTATCAAGAATCAATGgttagtacac ... gcctctccagGACAGGAATTTAAATCAGCTGGCGTCATCTGAATCATCTAGTTCTGGTACG
EST: gi|91872727|gb|EB402684.1|EB402684
EST:     GGTTTAGAGCAACTAGTGGCTATCTTGGGGCAGATTATCAAGAATCAATG                         GACAGGAATTTAAATCAGCTGGCGTCATCTGAATCATCTAGTTCTGGTACG
genomic: GGTTTAGAGCAACTAGTGGCTATCTTGGGGCAGATTATCAAGAATCAATGgttagtacac ... gcctctccagGACAGGAATTTAAATCAGCTGGCGTCATCTGAATCATCTAGTTCTGGTACG
EST: gi|6056642|gb|AW091047.1|AW091047
EST:     AGAGCAACTAGTGGCTATCTTGGGGCAGATTATCAAGAATCAATG                         GACAGGAATTTAAATCAGCTGGCGTCATCTGAATCATCTAGTTCTGGTACG
genomic: AGAGCAACTAGTGGCTATCTTGGGGCAGATTATCAAGAATCAATGgttagtacac ... gcctctccagGACAGGAATTTAAATCAGCTGGCGTCATCTGAATCATCTAGTTCTGGTACG
EST: gi|32930411|gb|CF035223.1|CF035223
EST:     GGTTTAGAGCAACTAGTGGCTATCTTGGGGCAGATTATCAAGAATCAATG                         GACAGGAATTTAAATCAGCTGGCGTCATCTGAATCATCTAGTTCTGGTA
genomic: GGTTTAGAGCAACTAGTGGCTATCTTGGGGCAGATTATCAAGAATCAATGgttagtacac ... gcctctccagGACAGGAATTTAAATCAGCTGGCGTCATCTGAATCATCTAGTTCTGGTA
EST: gi|211210980|gb|FL114022.1|FL114022
EST:     GGTTTAGAGCAACTAGTGGCTATCTTGGGGCAGATTATCAAGAATCAATG                         GACAGGAATTTAAATCAGCTGGCGTCATCTGAATCATCTAGTTCTGGTACG
genomic: GGTTTAGAGCAACTAGTGGCTATCTTGGGGCAGATTATCAAGAATCAATGgttagtacac ... gcctctccagGACAGGAATTTAAATCAGCTGGCGTCATCTGAATCATCTAGTTCTGGTACG
EST: gi|211186173|gb|FL452294.1|FL452294
EST:     GGTTTAGAGCAACTAGTGGCTATCTTGGGGCAGATTATCAAGAATCAATG                         GACAGGAATTTAAATCAGCTGGCGTCATCTGAATCATCTAGTTCTGGTACG
genomic: GGTTTAGAGCAACTAGTGGCTATCTTGGGGCAGATTATCAAGAATCAATGgttagtacac ... gcctctccagGACAGGAATTTAAATCAGCTGGCGTCATCTGAATCATCTAGTTCTGGTACG
EST: gi|60398350|gb|DN231166.1|DN231166
EST:     GGTTTAGAGCAACTAGTGGCTATCTTGGGGCAGATTATCAAGAATCAATG                         GACAGGAATTTAAATCAGCTGGCGTCATCTGAATCATCTAGTTCTGGTACG
genomic: GGTTTAGAGCAACTAGTGGCTATCTTGGGGCAGATTATCAAGAATCAATGgttagtacac ... gcctctccagGACAGGAATTTAAATCAGCTGGCGTCATCTGAATCATCTAGTTCTGGTACG
EST: gi|71762342|gb|DR960279.1|DR960279
EST:     GGTTTAGAGCAACTAGTGGCTATCTTGGGGCAGATTATCAAGAATCAATG                         GACAGGAATTTAAATCAGCTGGCGTCATCTGAATCATCTAGTTCTGGTACG
genomic: GGTTTAGAGCAACTAGTGGCTATCTTGGGGCAGATTATCAAGAATCAATGgttagtacac ... gcctctccagGACAGGAATTTAAATCAGCTGGCGTCATCTGAATCATCTAGTTCTGGTACG
EST: gi|211440538|gb|FL230375.1|FL230375
EST:     GTTTAGAGCAACTAGTGGCTATCTTGGGGGCAGATTATCAAGAATCANTG                         GACAGGAATTTAAATCAGCTGGCGTCATCTGAAATCATCTAGTTCTGGGTA
genomic: GTTTAGAGCAACTAGTGGCTATCTTGGGG-CAGATTATCAAGAATCAATGgttagtacac ... gcctctccagGACAGGAATTTAAATCAGCTGGCGTCATCTGAA-TCATCTAGTTCTGG-TA
EST: gi|211208425|gb|FL114020.1|FL114020
EST:     TAGAGCAACTAGTGGCTATCTTGGGGCAGATTATCAAGAATCAATG                         GACAGGAATTTAAATCAGCTGGCGTCATCTGAATCATCTAGTTCTGGTACG
genomic: TAGAGCAACTAGTGGCTATCTTGGGGCAGATTATCAAGAATCAATGgttagtacac ... gcctctccagGACAGGAATTTAAATCAGCTGGCGTCATCTGAATCATCTAGTTCTGGTACG

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: 71

GCAACTGTTGCATATTATTTACTATTGGACAATCGGTTTAGAGCAACTAGTGGCTATCTTGGGGCAGATTATCAAGAATCAATGgttagtacac ... gcctctccagGACAGGAATTTAAATCAGCTGGCGTCATCTGAATCATCTAGTTCTGGTACGAGGAATTATGTTCCAGGAAGCAGTGATCCTCATAGCAGTGGTTTGCGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 194

GCAACTGTTGCATATTATTTACTATTGGACAATCGGTTTAGAGCAACTAGTGGCTATCTTGGGGCAGATTATCAAGAATCAATGgttagtacac ... gcctctccagGACAGGAATTTAAATCAGCTGGCGTCATCTGAATCATCTAGTTCTGGTACGAGGAATTATGTTCCAGGAAGCAGTGATCCTCATAGCAGTGGTTTGCGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 243

GCAACTGTTGCATATTATTTACTATTGGACAATCGGTTTAGAGCAACTAGTGGCTATCTTGGGGCAGATTATCAAGAATCAATGgttagtacac ... gcctctccagGACAGGAATTTAAATCAGCTGGCGTCATCTGAATCATCTAGTTCTGGTACGAGGAATTATGTTCCAGGAAGCAGTGATCCTCATAGCAGTGGTTTGCGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 131

GCAACTGTTGCATATTATTTACTATTGGACAATCGGTTTAGAGCAACTAGTGGCTATCTTGGGGCAGATTATCAAGAATCAATGgttagtacac ... gcctctccagGACAGGAATTTAAATCAGCTGGCGTCATCTGAATCATCTAGTTCTGGTACGAGGAATTATGTTCCAGGAAGCAGTGATCCTCATAGCAGTGGTTTGCGGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgatctattgatgattctaacactattagatgtttgaatggttgcctctccagGACAGGAATTTAAATCAGCTGGCGTCATCTGAATCATCTAGTTCTGGTACGAGGAATTATGTTCCAGGAAGCAGTGATCCTCATAGCAGTGGTTTGCGGC
                ttctaac  putative branch site (score: 131)
                                           ttgcctctcc  putative PPT
                         tattagat  TA-rich tract