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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgaatatgcgtcaagaaggctatactttacttgtttttgatgatcaggttatgatattgaattgatgatctcttcagGTATTTGAGAAGCTTGGGCCAAGCCTATATGACTTTCTGCGAAAGAATAGCTACCGTTCATTTCCTATTGACCTTGTCCGAGAATTTGCCAGACAAATAT

Basic information

species Zea mays
transcript GRMZM2G386991_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G386991_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g62080.1 (Oryza sativa), 3'ss of exon 7
gtaagtgaatatgcgtcaagaaggctatactttacttgtttttgatgatcaggttatgatattgaattgatgatctcttcagGTATTTGAGAAGCTTGGGCCAAGCCTATATGACTTTCTGCGAAAGAATAGCTACCGTTCATTTCCTATTGACCTTGTCCGAGAATTTGCCAGACAAATAT
||||||  || ||| |||||||||||    || |  |||||| |||| ||||  | | ||||||||||  | |  |  |||||||||||||| ||| || |||||| |||||||||| || ||||||||||| || ||| ||||||| || |||||||| || |||||||||||||||||||
gtaagtacatgtgcatcaagaaggcttcctttca--tgttttggatggtcagaatttaatattgaattactaactttgtcagGTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGTTATCGTGCATTTCCGATCGACCTTGTTCGGGAATTTGCCAGACAAATAT

upper sequence: GRMZM2G386991_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA19G35800.1 (Glycine max), 3'ss of exon 3
--------------gtaagtg-aatatgcgtcaa--gaaggctatactttacttgtttttgatgatcaggttatgatattgaattga-tgatctcttcagGTATTTGAGAAGCTTGGGCCAAGCCTATATGACTTTCTGCGAAAGAATAGCTACCGTTCATTTCCTATTGACCTTGTCCGAGAATTTGCCAGACAAATAT
               ||  || ||| ||  | ||   | |  | | | ||| |  |    | |||  |  || ||  || || || | || | ||  |||||||||||||||||||| |||||| |||| || ||||| || || || |  || ||||| ||  | ||||| ||||| || || |||| ||||||| | |
gtaagtatttattgatatttgtaatttgattaaatgaaggaatgtgcatta-tcatgcgagttgaaaaacttgtgg-atggatttaaatggtttcaacagGTATTTGAGAAGCTTGGACCAAGCTTATACGATTTTCTCCGCAAAAACAATTATCGTTCTTTATCAATTGATCTTGTTCGGGAGTTTGGCAGACAACTTT

upper sequence: GRMZM2G386991_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA03G33100.1 (Glycine max), 3'ss of exon 5
-----------------------------gtaagtga-atatgcgtcaagaaggctatactttacttgtttttga--tgatcaggttatgatattgaattga-tgatctcttcagGTATTTGAGAAGCTTGGGCCAAGCCTATATGACTTTCTGCGAAAGAATAGCTACCGTTCATTTCCTATTGACCTTGTCCGAGAATTTGCCAGACAAATAT
                              ||| ||| |     ||| |       || ||| | |  | | |||  | |  |  ||  |  || || || | || | ||  |||||||||||||||||||| |||||| ||||||| ||||| || || || ||||| ||||| ||||||||||| ||||| || || |||| ||||||| | |
gtaagtatttattgatatttgtaatttaattaaatgacaggaatgtctattcaatcatgcttaaatattctgtgagttaaaaaacttgcgg-atggatttaaatggtttcaacagGTATTTGAGAAGCTTGGACCAAGCTTATATGATTTTCTCCGCAAAAACAGCTATCGTTCTTTTCCTATTGATCTTGTTCGGGAGTTTGGCAGACAACTTT

upper sequence: GRMZM2G386991_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT3G53570.4 (Arabidopsis thaliana), 3'ss of exon 7
------------------------------gtaagtgaatatgcg---tcaagaaggctatactttacttgtttttgatgatcaggt-tatgatattgaattgatgatctcttcagGTATTTGAGAAGCTTGGGCCAAGCCTATATGACTTTCTGCGAAAGAATAGCTACCGTTCATTTCCTATTGACCTTGTCCGAGAATTTGCCAGACAAATAT
                                | | ||| ||||    ||   | | | | |  |||  ||  ||  | || |  |   |||   || |||    | | ||  |||||||||||||||||||| |||||| ||||||| ||||| || || || ||||||||||||||||| ||||| ||||| || ||  ||| ||||||| | |
gtaagtgctgttacctttatttgacaagtttgaggggaaaatgcaatttcttcacgcccaaatgttatgtgagttaaaagaacttgcgcatgggtttaaat----ggtttcaacagGTATTTGAGAAGCTTGGACCAAGCTTATATGATTTTCTCCGCAAAAACAGCTACCGTTCATTTCCCATTGATCTTGTTCGGGAGCTTGGCAGACAACTTT

upper sequence: GRMZM2G386991_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv08s0040g02640.t01 (Vitis vinifera), 3'ss of exon 5
--------------------gtaagtgaatatgcgtcaagaag--------gctatactttacttg--tttttgatga--tcaggttatgatattgaatt--gatgatctcttcagGTATTTGAGAAGCTTGGGCCAAGCCTATATGACTTTCTGCGAAAGAATAGCTACCGTTCATTTCCTATTGACCTTGTCCGAGAATTTGCCAGACAAATAT
                    || | |  ||     | |||  |        | | |  | | | |   | ||   |||  | |     ||    || |||   ||| | |   ||||| |||||||||||||| |||||| |||| || ||||| || || || ||||||||||| ||||||||||| ||||| || ||  ||| ||||||| | |
gtaagtatttattggtacttgtgatttgattcatttgaaggggcaatccatgttgttttgtgcctaaatattctgtgagttaaaaacttgcggatggatttaaatggtttgagcagGTCTTTGAGAAGCTTGGACCAAGCTTATACGATTTTCTCCGCAAAAACAGCTACCGTTCTTTTCCTATTGATCTTGTTCGGGAGCTTGGCAGACAACTTT

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|32866970|gb|CF006652.1|CF006652
EST:     TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATTTGTATA                         GTATTTGAGAAGCTTGGGCCAAGCCTATATGACTTTCTGCGAAAGAATAGC
genomic: TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATTTGTATAgtaagtgaat ... atctcttcagGTATTTGAGAAGCTTGGGCCAAGCCTATATGACTTTCTGCGAAAGAATAGC
EST: gi|149089547|gb|EE178794.2|EE178794
EST:     TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATTTGTATA                         GTATTTGAGAAGCTTGGGCCAAGCCTATATGACTTTCTGCGAAAGAATAGC
genomic: TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATTTGTATAgtaagtgaat ... atctcttcagGTATTTGAGAAGCTTGGGCCAAGCCTATATGACTTTCTGCGAAAGAATAGC
EST: gi|6095292|gb|AW119959.1|AW119959
EST:     TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATTTGTATA                         GTATTTGAGAAGCTTGGGCCAAGCCTATATGACTTTCTGCGAAAGAATAGC
genomic: TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATTTGTATAgtaagtgaat ... atctcttcagGTATTTGAGAAGCTTGGGCCAAGCCTATATGACTTTCTGCGAAAGAATAGC
EST: gi|6695913|gb|AW289021.1|AW289021
EST:     TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATTTGTATA                         GTATTTGAGAAGCTTGGGCCAAGCCTATATGACTTTCTGCGAAAGAATAGC
genomic: TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATTTGTATAgtaagtgaat ... atctcttcagGTATTTGAGAAGCTTGGGCCAAGCCTATATGACTTTCTGCGAAAGAATAGC

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: 46 (upstream exon), 48 (downstream exon)
Score: 228

TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATTTGTATAgtaagtgaat ... atctcttcagGTATTTGAGAAGCTTGGGCCAAGCCTATATGACTTTCTGCGAAAGAATAGCTACCGTTCATTTCCTATTGACCTTGTCCGAGAATTTGCCAGACAAATAT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 174

TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATTTGTATAgtaagtgaat ... atctcttcagGTATTTGAGAAGCTTGGGCCAAGCCTATATGACTTTCTGCGAAAGAATAGCTACCGTTCATTTCCTATTGACCTTGTCCGAGAATTTGCCAGACAAATAT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 204

TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATTTGTATAgtaagtgaat ... atctcttcagGTATTTGAGAAGCTTGGGCCAAGCCTATATGACTTTCTGCGAAAGAATAGCTACCGTTCATTTCCTATTGACCTTGTCCGAGAATTTGCCAGACAAATAT


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 213

TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATTTGTATAgtaagtgaat ... atctcttcagGTATTTGAGAAGCTTGGGCCAAGCCTATATGACTTTCTGCGAAAGAATAGCTACCGTTCATTTCCTATTGACCTTGTCCGAGAATTTGCCAGACAAATAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactttacttgtttttgatgatcaggttatgatattgaattgatgatctcttcagGTATTTGAGAAGCTTGGGCCAAGCCTATATGACTTTCTGCGAAAGAATAGCTACCGTTCATTTCCTATTGACCTTGTCCGAGAATTTGCCAGACAAATAT
                                     aattgat  putative branch site (score: 213)
                                              tctcttc  putative PPT
                          ttatgatattgaatt  TA-rich tract