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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtaagatcaatatgatctgcatatatgcacagcagaatgcaaatactctgttttctgattgtttgactggtaacacagGTGGAGAAACGATACTAATGTTATACTTGCTGATGAAATGGGTCTGGGAAAAACTATCCAATCTGTATCCATGCTTGGCTTCCTTCAT

Basic information

species Zea mays
transcript GRMZM2G141258_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G141258_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA02G45000.1 (Glycine max), 3'ss of exon 10
gtacgtaagatcaatatgatctgcatatatg-cacagcagaatgcaaatactctgttttctgattgtttgactggtaacacagGTGGAGAAACGATACTAATGTTATACTTGCTGATGAAATGGGTCTGGGAAAAACTATCCAATCTGTATCCATGCTTGGCTTCCTTCAT
          |    || ||||| |||| || ||  | | | |  || |  |  || |||| | | | ||  |||     ||| |||||||| ||||| ||||| ||  | |||||||||||||| || ||||||||| | || || ||||| |||||||| || || || 
---------gtatgcat-atctgtatatttgtcaaggtacattttaattttttggtgttctaaatctgtgtatgg-----cagTTGGAGAAATGATACAAATGTCATTTTAGCTGATGAAATGGGCCTTGGAAAAACTGTTCAGTCAGTATCGATGCTTGGTTTTCTACAG

upper sequence: GRMZM2G141258_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv06s0009g03750.t01 (Vitis vinifera), 3'ss of exon 10
-------------------gtacgtaagatcaatatgatctgcatatatgcacagcaga------atgcaaatactc---tgttttctgattg---tttgactggtaacacagGTGGAGAAACGATACTAATGTTATACTTGCTGATGAAATGGGTCTGGGAAAAACTATCCAATCTGTATCCATGCTTGGCTTCCTTCAT
                    |  | | ||||| | | | ||  | | ||| ||   | |      || | |||  |    | | | || ||     | |   |  ||  |||| |||||||| ||||||||||||||  | ||||||||||||||||| || |||||| | || || || || |||||||| ||  | || 
gtatgctggtttcttttgttttagaatgatcagtttaaactaaaaaaatgtactttaaatataatattctaattttagcatatatactaatcagcttctctttcatagaacagCTGGAGAAATGATACTAATGTTATTTTGGCTGATGAAATGGGTCTTGGCAAAACTGTGCAGTCAGTTTCTATGCTTGGGTTTTTGCAG

upper sequence: GRMZM2G141258_T01 (Zea mays), 3'ss of exon 10
lower sequence: PP1S317_10V6.1 (Physcomitrella patens), 3'ss of exon 11
-----------------gtacgtaagatcaatatgatctgcatatatgcacagcag-aatgcaaatact--ctgttttctgattgtttgactggtaacacagGTGGAGAAACGATACTAATGTTATACTTGCTGATGAAATGGGTCTGGGAAAAACTATCCAATCTGTATCCATGCTTGGCTTCCTTCAT
                   | ||    |  | ||    ||   ||| |      |   ||   | | |   |  ||| ||| |  || |  ||||   | || ||||||||||| || |||||||| ||||| |||||||||||||| || || ||  | || || || || |||||||| || ||||| 
gaggtatcgttgcgcaatcatgtcgtttagagattgagtgtggataggtctgatattgatattatttcgaaccttttgctgttgcttgggttggt--tatagTTGGAGAAACGACACCAATGTTATTCTTGCGGATGAAATGGGTCTTGGCAAGACGGTTCAGTCAGTGTCGATGCTTGGATTTCTTCAG

upper sequence: GRMZM2G141258_T01 (Zea mays), 3'ss of exon 10
lower sequence: PP1S93_123V6.1 (Physcomitrella patens), 3'ss of exon 11
----------------------------------------------------------------------------------------------gtacgtaagatcaatatgatctgcatatatgcacagcagaatgcaaatactctgtt---ttctgattgtt--tgactggtaacacagGTGGAGAAACGATACTAATGTTATACTTGCTGATGAAATGGGTCTGGGAAAAACTATCCAATCTGTATCCATGCTTGGCTTCCTTCAT
                                                                                              ||   | |  ||     |      |  || |   ||     |     || |||  |     ||  ||| |  |   |||    |||| ||||| ||||| || |||||||| ||||| |||||||||||||| || || ||  | || || || || |||||||| ||  | || 
gtatgcaccaaattgcagcgattttgtcaacgtcacagtggcatattcactgaggacaaatgttagtggatagaaatagtggtggcagtaacgagtcactgatgtcgccgagtgggtgagttaaggtaagtctggttttggtattctactgagcccttgttgctgttatgtgggtgaacagTTGGAGGAACGACACCAATGTTATCCTTGCAGATGAAATGGGTCTTGGCAAGACAGTTCAGTCAGTCTCGATGCTTGGATTTTTGCAG

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), 47 (downstream exon)
Score: 158

CTAGTTTGAGGAGGCTTGATGGTCAGCCAGAATGGCTAAAAGCTGGCAAGCTTCGTGATTATCAGCTGGAAGGACTAAACTTTCTCGTCAATGGgtacgtaaga ... ggtaacacagGTGGAGAAACGATACTAATGTTATACTTGCTGATGAAATGGGTCTGGGAAAAACTATCCAATCTGTATCCATGCTTGGCTTCCTTCAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 136

CTAGTTTGAGGAGGCTTGATGGTCAGCCAGAATGGCTAAAAGCTGGCAAGCTTCGTGATTATCAGCTGGAAGGACTAAACTTTCTCGTCAATGGgtacgtaaga ... ggtaacacagGTGGAGAAACGATACTAATGTTATACTTGCTGATGAAATGGGTCTGGGAAAAACTATCCAATCTGTATCCATGCTTGGCTTCCTTCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 127

CTAGTTTGAGGAGGCTTGATGGTCAGCCAGAATGGCTAAAAGCTGGCAAGCTTCGTGATTATCAGCTGGAAGGACTAAACTTTCTCGTCAATGGgtacgtaaga ... ggtaacacagGTGGAGAAACGATACTAATGTTATACTTGCTGATGAAATGGGTCTGGGAAAAACTATCCAATCTGTATCCATGCTTGGCTTCCTTCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 239

CTAGTTTGAGGAGGCTTGATGGTCAGCCAGAATGGCTAAAAGCTGGCAAGCTTCGTGATTATCAGCTGGAAGGACTAAACTTTCTCGTCAATGGgtacgtaaga ... ggtaacacagGTGGAGAAACGATACTAATGTTATACTTGCTGATGAAATGGGTCTGGGAAAAACTATCCAATCTGTATCCATGCTTGGCTTCCTTCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgcacagcagaatgcaaatactctgttttctgattgtttgactggtaacacagGTGGAGAAACGATACTAATGTTATACTTGCTGATGAAATGGGTCTGGGAAAAACTATCCAATCTGTATCCATGCTTGGCTTCCTTCAT
                                            tggtaac  putative branch site (score: 239)
                 aaatact  TA-rich tract