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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaataaggaatttatatagctagctcgtaaagtaccttacccaccttatatcctacaacctatcttgaaattttattggctgactttgtgaatgaaacggtgtcttacagTTATCTTGGAACATTTTGATCAAGTCGTTGGTGATTGCTTCATGGATTGTGTCAACTGTCTTATTGGTTTTGCAAATAACAAGTGCACTCCTCGGATTAG

Basic information

species Zea mays
transcript GRMZM2G335287_T01
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G335287_T01 (Zea mays), 3'ss of exon 22
lower sequence: LOC_Os07g37750.1 (Oryza sativa), 3'ss of exon 21
gtaaat---aaggaatttatatagctagctcgtaaagtaccttacccaccttatatcctacaacctatcttgaaattttattggctgactttgtgaatgaaacggtgtctt--acagTTATCTTGGAACATTTTGATCAAGTCGTTGGTGATTGCTTCATGGATTGTGTCAACTGTCTTATTGGTTTTGCAAATAACAAGTGCACTCCTCGGATTAG
|||| |   ||||||| || || ||||||     ||||   |  |  || || |  |  | |   ||  ||  | | | ||    |   ||| ||| | ||  | ||| ||   ||||||||||||| |||||||||||||| |||||||||||||||||||| || |||||||||||||||||||| |||||||| || ||||| ||||| |||||
gtaagtttaaaggaatata-attgctagcattagaagtgttt--cttactttct-ccaaaaatgttagattccattatcatca--ttgttttttgattaaatggatgtgtttggcagTTATCTTGGAGCATTTTGATCAAGTTGTTGGTGATTGCTTCATGGACTGCGTCAACTGTCTTATTGGTTTCGCAAATAATAAATGCACACCTCGAATTAG

upper sequence: GRMZM2G335287_T01 (Zea mays), 3'ss of exon 22
lower sequence: AT3G43300.1 (Arabidopsis thaliana), 3'ss of exon 23
gtaaataaggaatttatatagctagctcgtaaagtaccttacccaccttatatcctacaacctatcttgaaattttattggctgactttgtgaatgaaacggtgtcttacagTTATCTTGGAACATTTTGATCAAGTCGTTGGTGATTGCTTCATGGATTGTGTCAACTGTCTTATTGGTTTTGCAAATAACAAGTGCACTCCTCGGATTAG
|| |  ||  | |  ||  | |||   |        || |      || |  |    ||  || ||      ||||  |   ||  | ||| ||  |  || |   || |||||||  ||||||| ||||| || ||  | ||||| |||||||||||||||||||| ||||| ||  | ||||| ||||||||     |    ||||| ||
gtga-caaacagtccatcaaactattgcacttgtatccctgttttactcaattttctcactctttc-----gttttgataaatgtttgtgt-aaccactcgtttgtttgcagTTATTCTGGAACACTTTGACCAGGTGATAGGTGACTGCTTCATGGATTGTGTCAATTGTCTCATCAGGTTTGCCAATAACAAAGCTTCAGACCGGATAAG

upper sequence: GRMZM2G335287_T01 (Zea mays), 3'ss of exon 22
lower sequence: AT3G43300.2 (Arabidopsis thaliana), 3'ss of exon 23
gtaaataaggaatttatatagctagctcgtaaagtaccttacccaccttatatcctacaacct-atcttgaaattttattggctgactttgtgaatgaaacggtgtcttacagTTATCTTGGAACATTTTGATCAAGTCGTTGGTGATTGCTTCATGGATTGTGTCAACTGTCTTATTGGTTTTGCAAATAACAAGTGCACTCCTCGGATTAG-------------------------------------------------
                                       || ||   || ||  | |    || |   |    ||||  |   ||  | ||| ||  |  || |   || |||||||  ||||||| ||||| || ||  | ||||| |||||||||||||||||||| ||||| ||  | ||||| ||||||||     |    ||||| ||                                                 
--------------------------------------gtatccctgttttactcaattttctcactctttcgttttgataaatgtttgtgt-aaccactcgtttgtttgcagttattctggaacactttgaccaggtgataggtgactgcttcatggattgtgtcaattgtctcatcagGTTTGCCAATAACAAAGCTTCAGACCGGATAAGCCTGAAAGCTATTGCCCTTCTCAGAATATGTGAGGATCGGCTTGCAGAG

upper sequence: GRMZM2G335287_T01 (Zea mays), 3'ss of exon 22
lower sequence: Vv11s0016g00170.t01 (Vitis vinifera), 3'ss of exon 24
gtaaataaggaatttatatagctagctcgtaaagtacctt-acccaccttatatcctacaacctatcttgaaattttattggctgactttgtgaatgaaacggtgtcttacagTTATCTTGGAACATTTTGATCAAGTCGTTGGTGATTGCTTCATGGATTGTGTCAACTGTCTTATTGGTTTTGCAAATAACAAGTGCACTCCTCGGATTAG
||||   |  |    || |  ||   |  | | ||   || ||  |   |  ||  |     || | |||  ||||      ||||     | ||    | |     || ||||||||||||| || |||||||| || ||||| || ||||| ||||| |||||||||||||| ||||| ||| | ||||| ||  |  | | ||| || ||
gtaa--gaacatgccatttttcttctttcttatgtgtttttacttattctcaatgttttcttct-ttttgtcattt------ctgatacatttaacacgaagtatatttgcagTTATCTTGGAGCACTTTGATCAGGTAGTTGGAGACTGCTTTATGGACTGTGTCAACTGTCTCATTGGCTTTTCCAATAATAAAAGTTCCCATCGCATCAG

upper sequence: GRMZM2G335287_T01 (Zea mays), 3'ss of exon 22
lower sequence: EFJ32651 (Selaginella moellendorffii), 3'ss of exon 22
gtaaataaggaatttatatagctagctcgtaaagtaccttacccaccttatatcctacaacctatcttgaaattttattggctgactttgtgaatgaaacggtgtcttacagTTATCTTGGAACATTTTGATCAAGTCGTTGGTGATTGCTTCATGGATTGTGTCAACTGTCTTATTGGTTTTGCAAATAACAAGTGCACTCCTCGGATTAG
                                                       ||       |||| | ||||| |   |     | |    |       | |    ||||| |  | ||  |||||||||||||||  || || |||||||||||||| |||||||||||||| | |||||| || |||||    |   |||| || ||
------------------------------------------------------gtaggcgggttcttcacattttctcaccacctctagccggtt------ttttccgcagTTGTGCTTGAGAATTTTGATCAAGTCGCAGGAGACTGCTTCATGGATTGCGTCAACTGTCTTATGGCTTTTGCGAACAACAAAACTAGCTCTCGAATAAG

upper sequence: GRMZM2G335287_T01 (Zea mays), 3'ss of exon 22
lower sequence: EFJ20775 (Selaginella moellendorffii), 3'ss of exon 21
gtaaataaggaatttatatagctagctcgtaaagtaccttacccaccttatatcctacaacctatcttgaaattttattggctgactttgtgaatgaaacggtgtcttacagTTATCTTGGAACATTTTGATCAAGTCGTTGGTGATTGCTTCATGGATTGTGTCAACTGTCTTATTGGTTTTGCAAATAACAAGTGCACTCCTCGGATTAG
                                                       ||       |||| | ||||| |   |     | |    |       |||    ||||| |  | ||  |||||||||||||||  || || ||||| |||||||| |||||||||||||| | |||||| || |||||    |   |||| || ||
------------------------------------------------------gtaggcgggttcttcacattttctcaccacctctagccggtt------tgttccgcagTTGTGCTTGAGAATTTTGATCAAGTCGCAGGAGACTGCTTTATGGATTGCGTCAACTGTCTTATGGCTTTTGCGAACAACAAAACTAGCTCTCGAATAAG

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: 47 (upstream exon), 49 (downstream exon)
Score: 178

ATAAAGTCAGGGTGGCGTTGTGTATTCATGATATTTACTGCAGCGGCTGATGACGAGGATGAATCAATTGTTGAGAGTGCTTTTGAAAATGTAGAACAAGgtaaataagg ... tgtcttacagTTATCTTGGAACATTTTGATCAAGTCGTTGGTGATTGCTTCATGGATTGTGTCAACTGTCTTATTGGTTTTGCAAATAACAAGTGCACTCCTCGGATTAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 118

ATAAAGTCAGGGTGGCGTTGTGTATTCATGATATTTACTGCAGCGGCTGATGACGAGGATGAATCAATTGTTGAGAGTGCTTTTGAAAATGTAGAACAAGgtaaataagg ... tgtcttacagTTATCTTGGAACATTTTGATCAAGTCGTTGGTGATTGCTTCATGGATTGTGTCAACTGTCTTATTGGTTTTGCAAATAACAAGTGCACTCCTCGGATTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 105

ATAAAGTCAGGGTGGCGTTGTGTATTCATGATATTTACTGCAGCGGCTGATGACGAGGATGAATCAATTGTTGAGAGTGCTTTTGAAAATGTAGAACAAGgtaaataagg ... tgtcttacagTTATCTTGGAACATTTTGATCAAGTCGTTGGTGATTGCTTCATGGATTGTGTCAACTGTCTTATTGGTTTTGCAAATAACAAGTGCACTCCTCGGATTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 161

ATAAAGTCAGGGTGGCGTTGTGTATTCATGATATTTACTGCAGCGGCTGATGACGAGGATGAATCAATTGTTGAGAGTGCTTTTGAAAATGTAGAACAAGgtaaataagg ... tgtcttacagTTATCTTGGAACATTTTGATCAAGTCGTTGGTGATTGCTTCATGGATTGTGTCAACTGTCTTATTGGTTTTGCAAATAACAAGTGCACTCCTCGGATTAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caacctatcttgaaattttattggctgactttgtgaatgaaacggtgtcttacagTTATCTTGGAACATTTTGATCAAGTCGTTGGTGATTGCTTCATGGATTGTGTCAACTGTCTTATTGGTTTTGCAAATAACAAGTGCACTCCTCGGATTAG
                      ggctgac  putative branch site (score: 161)
     tatcttgaaattttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaataaggaatttatatagctagctcgtaaagtaccttacccaccttatatcctacaacctatcttgaaattttattggctgactttgtgaatgaaacggtgtcttacagTTATCTTGGAACATTTTGATCAAGTCGTTGGTGATTGCTTCATGGATTGTGTCAACTGTCTTATTGGTTTTGCAAATAACAAGTGCACTCCTCGGATTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC