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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agctacatattactattgcataaatcactctcgttattagtcaatggactactttagattatgaaaataattggatttgtaatttctatttaccctacagGACGGACAATGCAATTAAAAATCACTGGAACAGTTCAGTGAAGAAAAAGGTCGATTCGTACATATCTTCTGGTTTACTTTCACAAGTCCCATGCCTCTCT

Basic information

species Zea mays
transcript GRMZM2G470307_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G470307_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g13570.1 (Oryza sativa), 3'ss of exon 6
agctacatattactattgcataaatcactctcgttatta-gtcaatg-gactactttagattatgaaaataattggatttgtaat-ttctatttacccta-cagGACGGACAATGCAATTAAAAATCACTGGAACAGTTCAGTGAAGAAAAAGGTCGATTCGTACATATCTTCTGGTTTACTTTCACAAGTCCCATGCCTCTCT
   || || | |||  |||  || | || || |||||||    |||  | |   ||| || ||   |||| |||| |  |||||  |||||||| || || |||||||||||||||||||||||||||||||||||||||||| ||||| || ||||| || ||||| || || ||||||||| | |||||| | || ||| ||
---tatatgt-acttctgctcaattaacgcttgttattataaaaatatgccctttttggactactgaaatgattgaacctgtaacattctatttcccttatcagGACGGACAATGCAATTAAAAATCACTGGAACAGTTCAGTAAAGAAGAAAGTCGACTCATACATGTCATCAGGTTTACTTACCCAAGTCTCGTGTCTCCCT

upper sequence: GRMZM2G470307_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g12860.1 (Oryza sativa), 3'ss of exon 6
agctacatattactattgcataaatcactctcgtta--ttagtcaatgga--ctactttagattatgaaaataattggatttgtaat-ttctatttacccta-cagGACGGACAATGCAATTAAAAATCACTGGAACAGTTCAGTGAAGAAAAAGGTCGATTCGTACATATCTTCTGGTTTACTTTCACAAGTCCCATGCCTCTCT
       || |  | |   || |||   ||| ||||  ||  | ||   |  ||  |||||| |||  || | |||| |||| |||  |||| ||| ||||| ||||||||||||| |||||||||||||||||||||||||||| ||||| || ||| |||| ||||| || || ||||||||| | |||||  | || ||| ||
------gtacttttgtgcaattaattcttcttgttaatttttttaaaaaaacctcttttagactattgaagtcattgaatttttaaaattctgtttcccctatcagGACGGACAATTCAATTAAAAATCACTGGAACAGTTCAGTAAAGAAGAAAGTCAATTCATACATGTCATCAGGTTTACTTACCCAAGTTTCGTGTCTCCCT

upper sequence: GRMZM2G470307_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA17G26240.1 (Glycine max), 3'ss of exon 7
-----------agctacatattactattgcataaatcactctcgttattagtcaatggactactttagattatgaaaataattggatttgtaatttctatttaccctacagGACGGACAATGCAATTAAAAATCACTGGAACAGTTCAGTGAAGAAAAAGGTCGATTCGTACATATCTTCTGGTTTACTTTCACAAGTCCCATGCCTCTCT
            | |     |   | || ||   |  | | | |||  |  | ||| | ||   | |  || ||| |        | ||||   || | || |    ||||||| |||||||| ||||||||||||||||||||||| || || || ||  | ||||| ||  |  | || ||  | ||| | ||  |   ||   |  ||
aattatagcatcggtgtgcctgtttttttcaagtacaattttagttcattcttaatcgtctgtgtaaagttgtgacat-------acttgtg-cttttgttgaa---acagGACAGACAATGCTATTAAAAATCACTGGAACAGTTCTGTCAAAAAGAAATTGGATTCTTATTTGGCATCAGGCCTGCTTACTCAGTTTGAATCTGTTCCT

upper sequence: GRMZM2G470307_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA14G21490.1 (Glycine max), 3'ss of exon 3
agctacatattactattgcataaatcactctcgttattagtcaatggactactttagattatgaaaataa--ttg-gatttgtaatttctatttaccctacagGACGGACAATGCAATTAAAAATCACTGGAACAGTTCAGTGAAGAAAAAGGTCGATTCGTACATATCTTCTGGTTTACTTTCACAAGTCCCATGCCTCTCT
|  |  |||  |  | |||         |||| |    | |   | |   | | |  ||  |     |||  ||| ||  |   | | || ||      ||||||| |||||||| ||||||||||||||||||||||| || || || ||  | ||||| ||  |  | || ||| | ||| | ||  ||  ||   |  ||
aatt--atagcatcagtgcgcctggttttctcatgtgcaattt-tagttcattcttaatcgtctctgtaaagttgtgacgtactagtgcttttgttgaaacagGACAGACAATGCTATTAAAAATCACTGGAACAGTTCTGTCAAAAAGAAATTGGATTCTTATTTGGCATCAGGTCTGCTTACTCAGTTCGAATCTATACCT

upper sequence: GRMZM2G470307_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT5G11510.1 (Arabidopsis thaliana), 3'ss of exon 7
----agctacatattactattgcataaatcactct-cgttattagtcaat------ggactactttagattatgaaaataattggatttgtaatttctatttaccctacagGACGGACAATGCAATTAAAAATCACTGGAACAGTTCAGTGAAGAAAAAGGTCGATTCGTACATATCTTCTGGTTTACTTTCACAAGTCCCATGCCTCTCT-
       |   ||||  ||||  | ||||||   | | |  ||| |||||      ||  | |||    || |   |  |||    |||     | |||| |   | ||||| |||| |||| |||||||||||||||| |||||||||| ||||| ||  | ||||| ||||| || |||||  |  ||  |  ||| ||| |||   |  
gtactcatttctattgttatttgaaaaatcatcgtacatatttattcaatcttaaaggtattcttctatttgttctagcaatatagttt---tctgctatgttatcaacagGTCGGATAATGGAATTAAAAATCACTGGCACAGTTCAGTCAAGAAGAAACTTGATTCCTACATGTCGTCTGGCCT-TTTGGATCAGTACCAAGCCATGCCT

upper sequence: GRMZM2G470307_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv11s0016g03750.t01 (Vitis vinifera), 3'ss of exon 6
agctacatattactattgcataaatcactctcgttattagtcaatggactactttagattatgaaaataatt----ggatttgtaatttctatttaccctacagGACGGACAATGCAATTAAAAATCACTGGAACAGTTCAGTGAAGAAAAAGGTCGATTCGTACATATCTTCTGGTTTACTTTCACAAGTCCCATGCCTCTCT
    |   | ||  |||||  |  |  |  ||   | | |  |||   ||   |  ||   | |  ||||||      || | |   ||||  ||  ||  |||||| ||||||||||| ||||||||||||||||| ||||| || || ||| | || || ||  |  | || ||||||||| ||||  ||| | |  | |||
---aagtgaatataattgc-cattttcccatcagaactcggaaatatcctttctacgaaattaagcataatttctgaaatgtctgtgttcttgttttccatcagGACAGACAATGCAATAAAAAATCACTGGAACAGCTCAGTAAAAAAGAAGTTGGAATCTTATTTGGCATCAGGTTTACTTGCACAGTTCCAAAGTTTGTCT

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), 49 (downstream exon)
Score: 163

ACAAGGAGGCATGGACGCAAGAAGAGGAGATTACTCTTATTCATGCTCATAGGATGTATGGAAATAAATGGGCCGAACTTACGAAATTTTTACCTGGAAGgtaaccacat ... taccctacagGACGGACAATGCAATTAAAAATCACTGGAACAGTTCAGTGAAGAAAAAGGTCGATTCGTACATATCTTCTGGTTTACTTTCACAAGTCCCATGCCTCTCT


Block sizes: 29 (upstream exon), 26 (downstream exon)
Score: 7

ACAAGGAGGCATGGACGCAAGAAGAGGAGATTACTCTTATTCATGCTCATAGGATGTATGGAAATAAATGGGCCGAACTTACGAAATTTTTACCTGGAAGgtaaccacat ... taccctacagGACGGACAATGCAATTAAAAATCACTGGAACAGTTCAGTGAAGAAAAAGGTCGATTCGTACATATCTTCTGGTTTACTTTCACAAGTCCCATGCCTCTCT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 18

ACAAGGAGGCATGGACGCAAGAAGAGGAGATTACTCTTATTCATGCTCATAGGATGTATGGAAATAAATGGGCCGAACTTACGAAATTTTTACCTGGAAGgtaaccacat ... taccctacagGACGGACAATGCAATTAAAAATCACTGGAACAGTTCAGTGAAGAAAAAGGTCGATTCGTACATATCTTCTGGTTTACTTTCACAAGTCCCATGCCTCTCT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 11

ACAAGGAGGCATGGACGCAAGAAGAGGAGATTACTCTTATTCATGCTCATAGGATGTATGGAAATAAATGGGCCGAACTTACGAAATTTTTACCTGGAAGgtaaccacat ... taccctacagGACGGACAATGCAATTAAAAATCACTGGAACAGTTCAGTGAAGAAAAAGGTCGATTCGTACATATCTTCTGGTTTACTTTCACAAGTCCCATGCCTCTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggactactttagattatgaaaataattggatttgtaatttctatttaccctacagGACGGACAATGCAATTAAAAATCACTGGAACAGTTCAGTGAAGAAAAAGGTCGATTCGTACATATCTTCTGGTTTACTTTCACAAGTCCCATGCCTCTCT
                                     tttctatttaccct  CT-rich tract
            attatgaaaataattg  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agctacatattactattgcataaatcactctcgttattagtcaatggactactttagattatgaaaataattggatttgtaatttctatttaccctacagGACGGACAATGCAATTAAAAATCACTGGAACAGTTCAGTGAAGAAAAAGGTCGATTCGTACATATCTTCTGGTTTACTTTCACAAGTCCCATGCCTCTCT

agctaca
- - - - - - - attgcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa