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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagattctcatacatattacataaacgttttatctgggcttgataaatattttcctttctacagAATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAA

Basic information

species Zea mays
transcript GRMZM2G148323_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 10
---------------------------------------------------------------------------------------gtagattctcatacatattacataaacgttttatctgggcttgataaatattttcctttctacagAATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAA
                                                                                       | | | |  | |   |   | | ||    || | |||   ||||||||| ||||| |||| |||||| ||| |||| || || |||||||||||||||||||||||||||||||| || |||||||| || || |||||||||||||| || |||||||||||||
gtagcatcttggacagaattattgatgcattttaggcctgtttggaacagtggaatgtcagcatgttgaggaattgcaccatttaatgcaaaattcc-tgtgttccaaacaagtccttaaactgaatttgataaatcttttcttttccacagAACGAGTGCTACTTTACACTACGGGACTTAAAACGGTGTAAACTCTCAGGGAATATATTCAACATCCTATTCAATCTCAACAAATTTATGGCATTTGAAA

upper sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA10G32500.1 (Glycine max), 3'ss of exon 10
--------------------------gtagattctcatacatattacataaacgttttatctgggcttgataaat----attttcctt--tctacagAATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAA
                           | ||||||  ||| | ||          |        |  |   || |    | | ||||   | | ||||||||| | ||| | ||  |||| ||  | ||| |  | ||||| || |||||  | ||||||||||||||||||||||||||||| || || || || |
gtttttctttgttcttgttcttgcgtcttgattcttttacttgtttttgttttactcctctgcagtatagcaagtggtaactgtcctacgtttgcagAATGAGGGATATATCACAATACGAGATGTTAAAGGCAGCAAACTTTCTGGAAATGTTTTCAATATTCTTTTCAATCTCAACAAGTTTATTGCTTTCGAGA

upper sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA20G35090.1 (Glycine max), 3'ss of exon 10
--------------------------gtagattctcatacatattacataaacgttttatctgggcttgataaat----attttcctt--tctacagAATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAA
                           | ||||||  ||| | ||       | ||        |  |   || |    | | ||||   | | ||||||||| | ||| | ||  |||| ||  | ||| |  ||||||| || |||||  | ||||||||||||||||||||||||||||| ||  | || || |
gtttttctttgttcttgttcttgcgtcttgattcttttacttgtttttgtttcattcctctgcagtatagcaagtggtaactgtcctacgtttgcagAATGAGGGATATATCACATTACGAGATGTTAAAGGCAGTAAACTTTCTGGAAATGTTTTCAATATTCTTTTCAATCTCAACAAGTTTATTACTTTCGAGA

upper sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 10
---------------------------------gtagattctcatacatattacataaacgttttatctgggctt--gataaatattttcctttctacagAATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAA
                                 ||   | || || | |  |     |   || | |||    ||   ||  | ||| | |  ||| ||| | ||||||||| ||||||| || ||| | ||| |  |||||||||||||||   | |||||||| || |||||||| || ||||||||||| |||||||
ttgtcctttttccatccttttggttgatattatgtcattacttatcctttatctgagatatttatttcttaattttaaattcaaattcttcactctgcagGAAGAGAGCTATATAACTCTGCGTGACCTGAAAGGTGGTAAACTCTCAGGAAGTGTTTTCAATATCCTGTTCAATCTGAATAAGTTCATGGCCTTTGAAA

upper sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 10
---------------------------------gtagattctcatacat-attacataaacgttttatctgggcttga-taaatattttcctttctacagAATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAA
                                 |    | || || | | ||   | | |  | || | |    |||| |  | ||| |  | ||| ||| ||||||||||| ||||||| || ||| | ||| |  |||||||||||||||   | |||||||| || |||||||| || ||||||||||| |||||||
ttgtccgttttccatctttttggttgatattatgccattacttatcctttatctgagatatttattttttaattttgaattcaaattcttttctctgcagGATGAGAGCTATATAACTCTGCGTGACCTGAAAGGTGGTAAACTCTCAGGAAGTGTTTTCAATATCCTGTTCAATCTGAATAAGTTCATGGCCTTTGAAA

upper sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT1G03960.2 (Arabidopsis thaliana), 3'ss of exon 10
--------------------------------gtagattctcatacatattacataa---acgttttatctg---ggcttgataaatatttt---cctttctacagAATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAA
                                 |   || ||  |  | ||   | |   |   ||||| ||   ||  | ||  ||||  |     |   | ||||| |||| || | | || || | |||  | ||| | |  ||||| |||| |||| | |||||||| || ||||| || || |||||||||||||||||||
gttagttactttacaaaccagaacatggttgtttgatttttccgagcttttttgttatttatcatttatttgactggaatcatctatatggtggatgtccttgcagAAGGAGAACTGTATCACCCTCCAGGATCTGAAAGGATCGAAACTTTCAGCAAACGTTTTCAATATACTCTTCAACCTTAATAAGTTCATGGCATTTGAAA

upper sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv07s0005g03730.t01 (Vitis vinifera), 3'ss of exon 11
-------------------gtagattctcatacatattacataaac--gttttatctgggcttgataaatattttcctttctacagAATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAA
                     ||||  ||   | | ||  |  |    |   || ||    || |        ||  |   | ||||  ||    ||| | || ||||| ||||| ||  | || ||||| || |||||  | |||||||||||||||||||| || ||||||||||| |||||||
gtcacggcttttttcgtacccagatcatctcccgtgttctagtagttagcaataactcattttcagggcatgatttttgcttgcagAGGGAAGAATATATCACCCTACGTGACTTGAAGGGATGCAAACTTTCTGGAAATGTTTTCAATATTCTTTTCAATCTTAATAAGTTCATGGCTTTTGAAA

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|23199690|gb|BU582255.1|BU582255
EST:     TATGATTGGACCAGAG                         AATGAGAGCTATTTAACTCTACGGGACTTAAAACGG-GTAAACTCTCAGGA
genomic: TATGATTGGACCAGAGgtagattctc ... ctttctacagAATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGA
EST: gi|87156079|gb|DY400868.1|DY400868
EST:     TGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAT                         AATGAGAGCTATTTAATTCTACAGGACTT
genomic: TGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctc ... ctttctacagAATGAGAGCTATTTAACTCTACGGGACTT
EST: gi|83279222|gb|DV943230.1|DV943230
EST:     TATGCCAGATGATTGATATGATTGGACCAGAG                         AATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGA
genomic: TATGCCAGATGATTGATATGATTGGACCAGAGgtagattctc ... ctttctacagAATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGA
EST: gi|23199745|gb|BU582310.1|BU582310
EST:     TGCTTTTTCTGGACATATTATGCCAGATGATTGCTATGATTGGACCAGAG                         AATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGA
genomic: TGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctc ... ctttctacagAATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGA
EST: gi|211505069|gb|FK974737.1|FK974737
EST:     TGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAG                         AATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGA
genomic: TGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctc ... ctttctacagAATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGA
EST: gi|26560172|gb|CA832407.1|CA832407
EST:     TGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAG                         AATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGA
genomic: TGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctc ... ctttctacagAATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGA

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: 48 (upstream exon), 48 (downstream exon)
Score: 323

TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctc ... ctttctacagAATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 224

TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctc ... ctttctacagAATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 211

TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctc ... ctttctacagAATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 247

TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctc ... ctttctacagAATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atacatattacataaacgttttatctgggcttgataaatattttcctttctacagAATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAA
                            gcttgat  putative branch site (score: 247)
                                      tattttcctttctac  putative PPT
                                 ataaatattttccttt  TA-rich tract