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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatgttcatggcccgtataccaatacaaatatatcatattgtcactaacaggatttctcctttccaccacctagGCAAATTGTTCTATCCCAGTTCTGTGTGTAGCCAGAAACGTTGCATGCAATGTTAGGGGTGGTTTCTTCAA

Basic information

species Zea mays
transcript GRMZM2G120373_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120373_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g42600.1 (Oryza sativa), 3'ss of exon 4
gtgatgttcatggcccgtataccaatacaaata-tatcatattg-tcactaacaggatttctcctttccaccacctagGCAAATTGTTCTATCCCAGTTCTGTGTGTAGCCAGAAACGTTGCATGCAATGTTAGGGGTGGTTTCTTCAA
|| | | |||||  ||  |||||||| |||||| |||| | ||| |     ||   |      | ||| ||     ||||||| ||||||||||||||||| ||||| ||||| || ||||||||||||||||| || || ||||| ||
gtaacggtcatgctcc--ataccaatgcaaatagtatcttcttgcttggacactaaagaatctccttcaactttacagGCAAACTGTTCTATCCCAGTTCTCTGTGTCGCCAGGAATGTTGCATGCAATGTTAGAGGGGGCTTCTTTAA

upper sequence: GRMZM2G120373_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA13G25010.1 (Glycine max), 3'ss of exon 4
----------------gtgatgttcatggcccg-----------tataccaatacaaatatatcatattgtcactaacagga-----tttctcctttccaccacctagGCAAATTGTTCTATCCCAGTTCTGTGTGTAGCCAGAAACGTTGCATGCAATGTTAGGGGTGGTTTCTTCAA
                ||   |||    ||||            |  |  ||| ||| | |  | | || ||||||| | ||     ||    || |    |   |||||||    | ||||||| ||||||||||| || ||||| ||||| ||||||||||||||||| ||||| ||
gtaaattttctttcttgtatagttggaagcccaatactttcaattggatgaatgcaattttgcccttttttcactaatatgaactgattaaatctgtttgtcttgtagGCAAGCAATACTATCCCTGTTCTGTGTGTTGCAAGAAATGTTGCTTGCAATGTTAGGGGTGGCTTCTTTAA

upper sequence: GRMZM2G120373_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA07G31430.1 (Glycine max), 3'ss of exon 4
----------------gtgatgttcatggcccg-----------tataccaatacaaatatatcatattgtcactaacaggatttct----cctttccaccacctagGCAAATTGTTCTATCCCAGTTCTGTGTGTAGCCAGAAACGTTGCATGCAATGTTAGGGGTGGTTTCTTCAA
                ||   |||    ||||            |  || |||  || | | || | || ||||||   | | |  |    ||| |    |   |||||||    | ||||||| || || ||||| || ||||| ||||| ||||||||||||||||| ||||| ||
gtaaattttctttcttgtatagttggaagcccaattctttcaattgcacgaatggaattttgtc-ttttttcactatatgaactgattaaacctgtttgtcttgtagGCAAGCAATACTATCCCTGTCCTATGTGTTGCAAGAAATGTTGCTTGCAATGTTAGGGGTGGCTTCTTTAA

upper sequence: GRMZM2G120373_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA13G31510.1 (Glycine max), 3'ss of exon 4
------------------gtgatgt--tcatggcccgtataccaatacaaatatatcatattgtcactaacaggatttctcctttccaccacctagGCAAATTGTTCTATCCCAGTTCTGTGTGTAGCCAGAAACGTTGCATGCAATGTTAGGGGTGGTTTCTTCAA
                   | ||||  |  |       |||  | | ||    |    || |||  || |   ||||   | | |  | |   |||||||    | |  ||||  |  ||||| | || ||||| ||||| ||||||||||||||||| ||||||||
gtaatttcacttacctatataatgtgatactaatatacataaaatttcattgtttctgtagtgtt-ctgaactgattaaacttgtttatcttgtagGCAAGCAATGCAGTCCCTTTCTTGTGTCTTGCAAGAAATGTTGCTTGCAATGTTAGGGGTGGCTTCTTCAA

upper sequence: GRMZM2G120373_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv00s0370g00040.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------------------gtgatgttcatggcccgtataccaatacaaatata-tcatattgtcactaacaggatttctcctttccaccacct----agGCAAATTGTTCTATCCCAGTTCTGTGTGTAGCCAGAAACGTTGCATGCAATGTTAGGGGTGGTTTCTTCAA
                                         |  |||| |        || |   |  | || ||  ||| |  |   | |   |   ||  | |  | |  | |    ||||||||  | ||||  | || |||||||| || ||||| |||||||||||||| || |||||||| |||||
gtatgcaccattgcacttggttatgcagttgaaagcttcaatactgttaaataataacatgctttttaagatttaaccatttctttgatgatgtgcactcatcataactcttcttttgaagGCAAATAATGCTATTTCCGTCCTGTGTGTTGCAAGAAATGTTGCATGCAATGTCAGAGGTGGTTTTTTCAA

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: 45 (upstream exon), 49 (downstream exon)
Score: 35

ATTAGTAATTGATGATCGCCTGAAAGTTTGGGATGAGAAGGATCAATTACGAGTTCATGTGGTTCCTGCATTTACTCCATATTATGCTCCTCAGGCGGAGgtgatgttca ... caccacctagGCAAATTGTTCTATCCCAGTTCTGTGTGTAGCCAGAAACGTTGCATGCAATGTTAGGGGTGGTTTCTTCAA


Block sizes: 39 (upstream exon), 45 (downstream exon)
Score: 16

ATTAGTAATTGATGATCGCCTGAAAGTTTGGGATGAGAAGGATCAATTACGAGTTCATGTGGTTCCTGCATTTACTCCATATTATGCTCCTCAGGCGGAGgtgatgttca ... caccacctagGCAAATTGTTCTATCCCAGTTCTGTGTGTAGCCAGAAACGTTGCATGCAATGTTAGGGGTGGTTTCTTCAA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 15

ATTAGTAATTGATGATCGCCTGAAAGTTTGGGATGAGAAGGATCAATTACGAGTTCATGTGGTTCCTGCATTTACTCCATATTATGCTCCTCAGGCGGAGgtgatgttca ... caccacctagGCAAATTGTTCTATCCCAGTTCTGTGTGTAGCCAGAAACGTTGCATGCAATGTTAGGGGTGGTTTCTTCAA


Block sizes: 46 (upstream exon), 43 (downstream exon)
Score: 31

ATTAGTAATTGATGATCGCCTGAAAGTTTGGGATGAGAAGGATCAATTACGAGTTCATGTGGTTCCTGCATTTACTCCATATTATGCTCCTCAGGCGGAGgtgatgttca ... caccacctagGCAAATTGTTCTATCCCAGTTCTGTGTGTAGCCAGAAACGTTGCATGCAATGTTAGGGGTGGTTTCTTCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaatacaaatatatcatattgtcactaacaggatttctcctttccaccacctagGCAAATTGTTCTATCCCAGTTCTGTGTGTAGCCAGAAACGTTGCATGCAATGTTAGGGGTGGTTTCTTCAA
                       cactaac  putative branch site (score: 31)
                                  tttctcctttccacca  putative PPT
     acaaatatatcatatt  TA-rich tract