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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgttatgcaaccgattcatgtatgtttgtagcatctatgttttccaaacttccaattgcactctgaacaattcttttaagaagttgctctgtgtgtttaatagacagtcagtttgacactgatcttgccacatgaatttgtaccactgtcaaaagccacatgtgcgatcaatagtgttgctacttttttcacagACAGCAAAAATCAATCAAGGGAACACTGCTTTGAAGCGAGTGGTTGAGTCTATTGCTAATGGTGATTCCCATGTTCCATTCAGGGACAGCAAACTCACAA

Basic information

species Zea mays
transcript GRMZM2G408308_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G408308_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g56540.1 (Oryza sativa), 3'ss of exon 3
gtgtgttatgcaaccgattcatgtatgtttgtagcatctatgttttccaaacttccaattgcactctgaacaattcttttaagaagttgctctgtgtgtttaatagacagtcagtttgacactgatcttgccacatgaatttgtaccactgtcaaaagccacatgtgcgatcaatagtgttgctacttttttcacagACAGCAAAAATCAATCAAGGGAACACTGCTTTGAAGCGAGTGGTTGAGTCTATTGCTAATGGTGATTCCCATGTTCCATTCAGGGACAGCAAACTCACAA
                                                                                       |||   |  |   || |||  | |   |||    |  ||  ||  |  ||         |  |  || |||   ||| |    |  | | | ||  |||| ||   |||||| ||||| || || ||||||||||| |||||||| |||||||||||||| |||||||||||||| ||||||||||||||  | |||||||| |||||||
---------------------------------------------------------------------------------------tgcaaagattagctactag-tactttttttcctgcaaattatgttatgtgt-------tcgataacagaagtt-catattttgtttacattattattactgttga-acagACTGCAAAGATTAACCAAGGGAACACGGCTTTGAAACGAGTGGTTGAGTCCATTGCTAATGGTGACTCCCATGTTCCATTTCGAGACAGCAAGCTCACAA

upper sequence: GRMZM2G408308_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G32610.1 (Glycine max), 3'ss of exon 4
gtgtgttatgcaaccgattcatgtatgtttgtagcatctatgttttccaaacttccaattgcactctgaacaattcttttaagaagttgctctgtgtgtttaatagacagtcagtttgacact--gatcttgccacatgaatttgtaccactgtcaaaagccacatgtgcgatcaatagtgttgctacttttttcacagACAGCAAAAATCAATCAAGGGAACACTGCTTTGAAGCGAGTGGTTGAGTCTATTGCTAATGGTGATTCCCATGTTCCATTCAGGGACAGCAAACTCACAA
                                                                                                            | |   |||  || |  ||| || |    |  | |  | |   | ||    |     | | |  | || |   ||            | |||| ||||||||||||||||| || |  ||| ||||| ||||||| ||||| ||||| ||||| ||||| ||||| || ||||||||||||||||| || |
----------------------------------------------------------------------------------------------------------gtaatttttttaccattttgatttttcttttttgaatcatgcagttctctgctgattattatactgttaacaaaattat----------atagACTGCAAAAATCAATCAAGGAAATATAGCTCTGAAGAGAGTGGTGGAGTCCATTGCAAATGGCGATTCACATGTGCCTTTCAGGGACAGCAAACTTACCA

upper sequence: GRMZM2G408308_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA20G34970.1 (Glycine max), 3'ss of exon 3
gtgtgttatgcaaccgattcatgtatgtttgtagcatctatgttttccaaacttccaattgcactctgaacaattcttttaagaagttgctctgtgtgtttaatagacagtcagtttgacactgatcttgccacatgaatttgtaccactgtcaaaagccacatgtgcgatcaatagtgttgctacttttttcacagACAGCAAAAATCAATCAAGGGAACACTGCTTTGAAGCGAGTGGTTGAGTCTATTGCTAATGGTGATTCCCATGTTCCATTCAGGGACAGCAAACTCACAA
                                                                                                    |||      | || |||||      | ||    |||| | || | |  |||  |  ||     | | |  |||||    ||            | |||| ||||||||||||||||| || |  ||  ||||| ||||||| ||||| ||||| ||||| ||||| ||||| || || |||||||||||||| || |
---------------------------------------------------------------------------------------------------gtaactttttgccaatttgatttcattttttaatcatgtagttct-ctgctg--attagtatactatactgtcaatgaaatt------------atagACTGCAAAAATCAATCAAGGAAATATAGCGCTGAAGAGAGTGGTGGAGTCCATTGCAAATGGCGATTCACATGTGCCTTTTAGGGACAGCAAACTTACCA

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: 442

GGATGTCCCATCTGTGGGAGGAAGATTAATGCTTGTGGACATGGCTGGATCTGAAAACATAGAAGCTGCAGGACAAACAGGATTTGAAGCCAAAATGCAGgtgtgttatg ... tttttcacagACAGCAAAAATCAATCAAGGGAACACTGCTTTGAAGCGAGTGGTTGAGTCTATTGCTAATGGTGATTCCCATGTTCCATTCAGGGACAGCAAACTCACAA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 50

GGATGTCCCATCTGTGGGAGGAAGATTAATGCTTGTGGACATGGCTGGATCTGAAAACATAGAAGCTGCAGGACAAACAGGATTTGAAGCCAAAATGCAGgtgtgttatg ... tttttcacagACAGCAAAAATCAATCAAGGGAACACTGCTTTGAAGCGAGTGGTTGAGTCTATTGCTAATGGTGATTCCCATGTTCCATTCAGGGACAGCAAACTCACAA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 39

GGATGTCCCATCTGTGGGAGGAAGATTAATGCTTGTGGACATGGCTGGATCTGAAAACATAGAAGCTGCAGGACAAACAGGATTTGAAGCCAAAATGCAGgtgtgttatg ... tttttcacagACAGCAAAAATCAATCAAGGGAACACTGCTTTGAAGCGAGTGGTTGAGTCTATTGCTAATGGTGATTCCCATGTTCCATTCAGGGACAGCAAACTCACAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 25

GGATGTCCCATCTGTGGGAGGAAGATTAATGCTTGTGGACATGGCTGGATCTGAAAACATAGAAGCTGCAGGACAAACAGGATTTGAAGCCAAAATGCAGgtgtgttatg ... tttttcacagACAGCAAAAATCAATCAAGGGAACACTGCTTTGAAGCGAGTGGTTGAGTCTATTGCTAATGGTGATTCCCATGTTCCATTCAGGGACAGCAAACTCACAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaccactgtcaaaagccacatgtgcgatcaatagtgttgctacttttttcacagACAGCAAAAATCAATCAAGGGAACACTGCTTTGAAGCGAGTGGTTGAGTCTATTGCTAATGGTGATTCCCATGTTCCATTCAGGGACAGCAAACTCACAA
                                     ttgctacttttttc  CT-rich tract
                                         tactttttt  TA-rich tract