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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtattacgactagttctagacactatgtaatttgtaccattgttgcttctagcgaaccatgtttatgttctgtcgtggataactatgctccatatttaatggtgatgtttgtttccctcttatttgcagGTACATTGATAGTGCTGGCTTAAGTGGTCCTATACCATCATCATTTTCGAAACTTACACGATTGAAAACATT

Basic information

species Zea mays
transcript GRMZM2G126858_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126858_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os04g52600.1 (Oryza sativa), 3'ss of exon 6
gtacgtattacgactagttctagacactatgtaatttgtaccattgttgcttctagcgaaccatgtttatgttctgtcgtggataactatgctccatatttaatggtgatgtttgtttccctcttatttgcagGTACATTGATAGTGCTGGCTTAAGTGGTCCTATACCATCATCATTTTCGAAACTTACACGATTGAAAACATT
           |     ||||||     |  |  ||| |    || ||| | ||| | ||||||  | ||      || ||||  |||  |||| || |||  || |  |      ||  |||| | ||||||||||||||| ||||||||||||||||||||  |||||||||||||||| || |||||| || || |||||||
-----------gtacgtttctagttgggacttcgtttttcttttttttggt-ctacctaaccattctgat------tcttggactactcagctcaatgtttgctgctact-----cttatctctcaattgcagGTACATTGACAGTGCTGGCTTAAGTGGTCCACTACCATCATCATTTTCCAAGCTTACAAGAATGCAAACATT

upper sequence: GRMZM2G126858_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os04g52614.1 (Oryza sativa), 3'ss of exon 6
gtacgtattacgactagttctagacactatgtaatttgtaccattgttgcttctagcgaaccatgtttatgttctgtcgtggataactatgctccatatttaatggtgatgtttgtttccctcttatttgcagGTACATTGATAGTGCTGGCTTAAGTGGTCCTATACCATCATCATTTTCGAAACTTACACGATTGAAAACATT
                || |    |  ||||  |||    |  || |||||| | ||  ||||   |      |  |  ||  |   |   ||  | | | ||||       |||  |  |||||| ||| ||||||||||| ||||||||||||||||||||  ||||||||||||| || || |||||| || || ||| |||
----------------gtgcgtttctatatgggatt----ctgtt-ttgctttttgcttaccaaagtaccaaaccattctgttttcttggact--aaactaaatg-------ttgggtttctcttaattgtagGTACATTGACAGTGCTGGCTTAAGTGGTCCGTTACCATCATCATTGTCCAAGCTTACAAGAATGCAAATATT

upper sequence: GRMZM2G126858_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os04g52630.1 (Oryza sativa), 3'ss of exon 5
gtacgtattacgactagttctagacactatgtaatttgtaccattgttgcttctagcgaaccatgtttatgttctgtcgtggataactatgctccatatttaatggtgatgtttgtttccctcttatttgcagGTACATTGATAGTGCTGGCTTAAGTGGTCCTATACCATCATCATTTTCGAAACTTACACGATTGAAAACATT
                    |||    |||  ||    |  |||  || ||| || | || |||  |||| ||||    |||    ||  |||| || |||     || | ||||| ||||||  | ||| ||||||||||| ||||||||||||||||||    |||||||||||||||| || ||||||  | || ||| |||
-------------------gtaggt-ttattcaagactt--catcttttcttttaccaaaacat--ttattttct----tgggcttctcagctcaatttttc----tgctatttgtatccctc--aattgtagGTACATTGACAGTGCTGGCTTAAGTGGTGAGCTACCATCATCATTTTCCAAGCTTACAAAAGTGGAAAAATT

upper sequence: GRMZM2G126858_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os04g52640.3 (Oryza sativa), 3'ss of exon 6
gtacgtattacgactagttctagacactatgtaatttgtaccattgttgcttctagcgaaccatgtttatgttctgtcgtggataactatgctccatatttaatggtgatgtttgtttccctcttatttgcagGTACATTGATAGTGCTGGCTTAAGTGGTCCTATACCATCATCATTTTCGAAACTTACACGATTGAAAACATT
                ||      ||  |  ||||||||  | |||||  || |      | | |   |  || | |  ||    ||||| |  | || |   |  || | ||||| || |||  | |||||||| |||||| |||||||||||||||||     ||||||||||||| || || |||||| || |||||| |||
----------------gtgtgtttcaacaaataatttgtcactttgttctttttt-----ctacgaagacattttattttgttggactattcagcctaatgtgttctgctatttgtatctctc--aattgcagGTTCATTGACAGTGCTGGCTTAAGTGGAGAGCTACCATCATCATTATCCAAGCTTACAAGAATGAAAATATT

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), 44 (downstream exon)
Score: 76

GAGTTTAGGCACGAACAATTTAACTGGCTCCCTTCCTTCTGAATTGGGTAACCTGGTTAAACTAGAGCATATgtacgtatta ... ttatttgcagGTACATTGATAGTGCTGGCTTAAGTGGTCCTATACCATCATCATTTTCGAAACTTACACGATTGAAAACATT


Block sizes: 39 (upstream exon), 44 (downstream exon)
Score: 29

GAGTTTAGGCACGAACAATTTAACTGGCTCCCTTCCTTCTGAATTGGGTAACCTGGTTAAACTAGAGCATATgtacgtatta ... ttatttgcagGTACATTGATAGTGCTGGCTTAAGTGGTCCTATACCATCATCATTTTCGAAACTTACACGATTGAAAACATT


Block sizes: 46 (upstream exon), 44 (downstream exon)
Score: 42

GAGTTTAGGCACGAACAATTTAACTGGCTCCCTTCCTTCTGAATTGGGTAACCTGGTTAAACTAGAGCATATgtacgtatta ... ttatttgcagGTACATTGATAGTGCTGGCTTAAGTGGTCCTATACCATCATCATTTTCGAAACTTACACGATTGAAAACATT


Block sizes: 45 (upstream exon), 45 (downstream exon)
Score: 32

GAGTTTAGGCACGAACAATTTAACTGGCTCCCTTCCTTCTGAATTGGGTAACCTGGTTAAACTAGAGCATATgtacgtatta ... ttatttgcagGTACATTGATAGTGCTGGCTTAAGTGGTCCTATACCATCATCATTTTCGAAACTTACACGATTGAAAACATT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggataactatgctccatatttaatggtgatgtttgtttccctcttatttgcagGTACATTGATAGTGCTGGCTTAAGTGGTCCTATACCATCATCATTTTCGAAACTTACACGATTGAAAACATT
                                 tttgtttccctcttat  CT-rich tract
                 atatttaat  TA-rich tract