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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTGGATGATGAATGCCCGGAAGATTTCATCAAGGGTTTGATTCTCTCTGTTCGTTCTCTGCTTCCTGTTGAGCCACTAGTTGATGAATGCGAGAAGAGgtttgaattctttattcctggggtctgcaaagtgacaagtttcacattccctttttaagtggatcacatctgtttgaatatgtgtatcag

Basic information

species Zea mays
transcript GRMZM2G057576_T02
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057576_T01 (Zea mays), 5'ss of exon 21
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 22
TTCTGGATGATGAATGCCCGGAAGATTTCATCAAGGGTTTGATTCTCTCTGTTCGTTCTCTGCTTCCTGTTGAGCCACTAGTTGATGAATGCGAGAAGAGgtttgaattctttat----tcctggggtctgcaaagtgacaagtttcacattccctt---tttaagtggat-cacatctgtttgaatatgtgtatcag---------------------
| || |||||||| ||||| ||||||||||| |||||||||||||| ||||| |||||||| |||||||||||||||||||||||||||||||||||||||| ||| ||||||||    || ||   ||  ||    |   |    ||  | | | |      ||    || |   | |||||   |     | |||                      
TACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCCTTCCTGTTGAGCCACTAGTTGATGAATGCGAGAAGAGgtatga-ttctttatattatcttgtattccacagccagcttaagggcatgtgcacatgcacacaaacatatgcttttttgtttcgttgctgatctcatcttttatatttcttttttcag

upper sequence: GRMZM2G057576_T01 (Zea mays), 5'ss of exon 21
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 22
TTCTGGATGATGAATGCCCGGAAGATTTCATCAAGGGTTTGATTCTCTCTGTTCGTTCTCTGCTTCCTGTTGAGCCACTAGTTGATGAATGCGAGAAGAGgtttgaattctttat----tcctggggtctgcaaagtgacaagtttcacattccctt---tttaagtggat-cacatctgtttgaatatgtgtatcag---------------------
| || |||||||| ||||| ||||||||||| |||||||||||||| ||||| |||||||| |||||||||||||||||||||||||||||||||||||||| ||| ||||||||    || ||   ||  |||   ||  |    ||  | | |        ||    || |   | |||||   |       |||                      
TACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCCTTCCTGTTGAGCCACTAGTTGATGAATGCGAGAAGAGgtatga-ttctttatattatcttgtattccacaaccagattaagggcatgtgcacacgcacacaaacatatgcttttttgttttgttgctgacctcatcttttatatttcttttttcag

upper sequence: GRMZM2G057576_T01 (Zea mays), 5'ss of exon 21
lower sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 22
TTCTGGATGATGAATGCCCGGAAGATTTCATCAAGGGTTTGATTCTCTCTGTTCGTTCTCTGCTTCCTGTTGAGCCACTAGTTGATGAATGCGAGAAGAGgtttg--aattctttattcctggggtctgcaaagtgacaagtttcacattccctttttaagtggatcacatctgtttgaatatgtgtatcag
|  | |||||||||||||| || |||||||| || ||| | ||||| || ||||||||||| ||||| ||||||||  ||||||| ||||| |||||||||| ||  | || |||   ||  |  ||  |||| |  ||  ||     ||| | ||| |  |      |                       
TGTTAGATGATGAATGCCCTGAGGATTTCATTAAAGGTCTTATTCTTTCAGTTCGTTCTCTTCTTCCAGTTGAGCCTTTAGTTGAAGAATGTGAGAAGAGgtgtgcaagttttttccaccctgcatccccaaattaccatattattttttctcatttcactttctatgcgcag-------------------

upper sequence: GRMZM2G057576_T01 (Zea mays), 5'ss of exon 21
lower sequence: GLYMA14G06340.1 (Glycine max), 5'ss of exon 22
TTCTGGATGATGAATGCCCGGAAGATTTCATCAAGGGTTTGATTCTCTCTGTTCGTTCTCTGCTTCCTGTTGAGCCACTAGTTGATGAATGCGAGAAGAGgtttgaattctttattcctggggtctgcaaagtgacaagtttcacattccctttttaagtggatc-acatctgtttgaatatgtgtatcag
| || |||||||||||| | |||||||| ||||| || ||||| || |||||||||||  | || || || ||||| || || || ||||| ||||||||||      | |||   | | |   ||      |      || ||   |   || |||  |    |    ||| ||||| ||||        
TGCTAGATGATGAATGCGCAGAAGATTTTATCAAAGGCTTGATCCTTTCTGTTCGTTCATTACTGCCAGTGGAGCCCCTTGTGGAGGAATGTGAGAAGAGgt----ggtgttttccctttgatcctatgtgttattgctttgcattcttgtttcttattttatcctgtgtctttttga-tatgcag-----

upper sequence: GRMZM2G057576_T01 (Zea mays), 5'ss of exon 21
lower sequence: GLYMA11G06720.1 (Glycine max), 5'ss of exon 22
TTCTGGATGATGAATGCCCGGAAGATTTCATCAAGGGTTTGATTCTCTCTGTTCGTTCTCTGCTTCCTGTTGAGCCACTAGTTGATGAATGCGAGAAGAGgtttg--aattctttattcctggggtctgcaaagtgacaagtttcacattccctttttaagtggatcacatctgtttgaatatgtgtatcag
|  | |||||||||||||| |||||||| ||||| ||| | || || || ||||| ||||| || || ||||||||  ||||||| ||||| || ||||||| ||  | || | | |   |   |  |    |||  |   |   |  |||  || | | ||   |    | ||  |               
TGTTAGATGATGAATGCCCTGAAGATTTTATCAAAGGTCTTATACTTTCAGTTCGCTCTCTCCTGCCAGTTGAGCCTTTAGTTGAAGAATGTGAAAAGAGgtgtgctagttttctctctattttgcatctccagtatcgt-tgctatgttcatttctcatgttctttttttatgcatag-------------

upper sequence: GRMZM2G057576_T01 (Zea mays), 5'ss of exon 21
lower sequence: GLYMA14G06340.2 (Glycine max), 5'ss of exon 22
TTCTGGATGATGAATGCCCGGAAGATTTCATCAAGGGTTTGATTCTCTCTGTTCGTTCTCTGCTTCCTGTTGAGCCACTAGTTGATGAATGCGAGAAGAGgtttgaattctttattcctggggtctgcaaagtgacaagtttcacattccctttttaagtggatc-acatctgtttgaatatgtgtatcag
   | |||||||||||| | |||||||| ||||| || ||||| || |||||||||||  | || || || ||||| || || || ||||| ||||||||||      | |||   | | |   ||      |      || ||   |   || |||  |    |    ||| ||||| ||||        
---TAGATGATGAATGCGCAGAAGATTTTATCAAAGGCTTGATCCTTTCTGTTCGTTCATTACTGCCAGTGGAGCCCCTTGTGGAGGAATGTGAGAAGAGGT----Ggtgttttccctttgatcctatgtgttattgctttgcattcttgtttcttattttatcctgtgtctttttga-tatgcag-----

upper sequence: GRMZM2G057576_T01 (Zea mays), 5'ss of exon 21
lower sequence: GLYMA11G35460.1 (Glycine max), 5'ss of exon 21
TTCTGGATGATGAATGCCCGGAAGATTTCATCAAGGGTTTGATTCTCTCTGTTCGTTCTCTGCTTCCTGTTGAGCCACTAGTTGATGAATGCGAGAAGAGgtttgaattctttattcctggggtctgcaaagtgacaagt-ttcacattccctttttaagtggatcacatctgtttgaatatgtgtatcag
|| | |||||||||||||| |||||||| ||||| || ||||||||||||||||||||  | || || || ||||| || || || || || || |||||||    | | | | |||       || ||         ||  ||||||| |   ||    ||    || | | || | ||           
TTTTAGATGATGAATGCCCAGAAGATTTTATCAAAGGCTTGATTCTCTCTGTTCGTTCCTTACTGCCAGTGGAGCCTCTTGTGGAGGAGTGTGAAAAGAGgt----agtatctgttctctaatccttcattactttttgtgctcacatttctgattattctgtggtacttttcttggtatgcag-------

upper sequence: GRMZM2G057576_T01 (Zea mays), 5'ss of exon 21
lower sequence: GLYMA18G02960.1 (Glycine max), 5'ss of exon 21
TTCTGGATGATGAATGCCCGGAAGATTTCATCAAGGGTTTGATTCTCTCTGTTCGTTCTCTGCTTCCTGTTGAGCCACTAGTTGATGAATGCGAGAAGAGgtttgaattctttattcctggggtctgcaaagtgacaagtttcacattccctttttaagtggatcacatctgtttgaatatgtgtatcag
|| | ||||||||||| || |||||||| ||||| || ||||||||||||||||||||  | || || || ||||| || || || || || ||||||||||    | | | | |||       || ||          |||     || | |||    |   ||     |  |||   |||        
TTTTAGATGATGAATGTCCAGAAGATTTTATCAAAGGCTTGATTCTCTCTGTTCGTTCCTTACTGCCAGTGGAGCCCCTTGTGGAGGAGTGTGAGAAGAGgt----agtatcttttctctaatcctacat-----ttctttttgtgctcgcatttctgattattccgtggtacttgg-catgcag-----

upper sequence: GRMZM2G057576_T01 (Zea mays), 5'ss of exon 21
lower sequence: GLYMA14G37510.1 (Glycine max), 5'ss of exon 20
TTCTGGATGATGAATGCCCGGAAGATTTCATCAAGGGTTTGATTCTCTCTGTTCGTTCTCTGCTTCCTGTTGAGCCACTAGTTGATGAATGCGAGAAGAGgtttg--aattctttattcctggggtctgcaaagtgacaagtttcacattccctttttaagtggatcacatctgtttgaatatgtgtatcag
|  | |||||||||||||| ||||||||||| || ||| | || || || ||||||||||| ||||| ||||||||  ||||||| ||||| |||||||||| ||  | || |||   ||  |  ||  |||| |  ||  ||    |||   ||| | | || |     | ||                  
TATTAGATGATGAATGCCCTGAAGATTTCATTAAAGGTCTTATACTTTCAGTTCGTTCTCTTCTTCCAGTTGAGCCTTTAGTTGAAGAATGTGAGAAGAGgtgtgcaagttttttccaccctgcatccccaaattaccatatt----attt--tttctcattgcactttctatgcgcag-------------

upper sequence: GRMZM2G057576_T01 (Zea mays), 5'ss of exon 21
lower sequence: GLYMA01G38580.1 (Glycine max), 5'ss of exon 22
TTCTGGATGATGAATGCCCGGAAGATTTCATCAAGGGTTTGATTCTCTCTGTTCGTTCTCTGCTTCCTGTTGAGCCACTAGTTGATGAATGCGAGAAGAGgtttgaattctttattcctggggtctgcaaagtgacaagtttcacattccctttttaagtggatcacatctgtttgaatatgtgtatcag
|  | |||||||||||||| |||||||| || || ||| | || || || ||||||||||| || || ||||||||  ||||||| ||||| ||||||||||  |   ||| | |  ||    ||| ||   | |    |  ||  |||  ||| | | |  ||    | ||  |               
TGTTAGATGATGAATGCCCTGAAGATTTTATTAAAGGTCTTATACTTTCAGTTCGTTCTCTCCTGCCAGTTGAGCCTTTAGTTGAAGAATGTGAGAAGAGgtgcg---tctctctatctttcatctccactatcat---tgccatgttca-tttctcatttaattttttatgcatag-------------

upper sequence: GRMZM2G057576_T01 (Zea mays), 5'ss of exon 21
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 22
TTCTGGATGATGAATGCCCGGAAGATTTCATCAAGGGTTTGATTCTCTCTGTTCGTTCTCTGCTTCCTGTTGAGCCACTAGTTGATGAATGCGAGAAGAGgtttgaattctttattcctggggtctgcaaagtgacaagtttcacattccctttttaagtggatcacatctgtttgaatatgtgtatcag
| || |||||||||||||| |||||||| || || ||  | |||||||||||||||||  ||||||||||||| ||||| || || ||||| ||||||||||      | ||  |      ||| |||   ||    | ||     |      ||   |    ||  || |||||     | |  |    
TGCTTGATGATGAATGCCCTGAAGATTTTATAAAAGGCCTCATTCTCTCTGTTCGTTCATTGCTTCCTGTTGAACCACTTGTCGAGGAATGTGAGAAGAGgtgaatccttttggtcatcctggtttgc---gttcataattatgtctgtttagttctggaaactctaatatgtttctgctttttcag---

upper sequence: GRMZM2G057576_T01 (Zea mays), 5'ss of exon 21
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 22
TTCTGGATGATGAATGCCCGGAAGATTTCATCAAGGGTTTGATTCTCTCTGTTCGTTCTCTGCTTCCTGTTGAGCCACTAGTTGATGAATGCGAGAAGAGgtttgaattctttattcctggggtctgcaaagtgacaagtttcacattccctttttaagtggatcacatctgtttgaatatgtgtatcag
|||| |||||||||||||| ||||||||||| || ||| | ||||| || ||||| ||||| |||||||||||||| || || || ||||| ||||| ||||      | ||||    ||     |    | | | |  ||| |      ||| ||   |   |   |||  ||||  | |   |  |||
TTCTAGATGATGAATGCCCTGAAGATTTCATTAAAGGTCTCATTCTTTCAGTTCGGTCTCTTCTTCCTGTTGAGCCCCTCGTGGAGGAATGTGAGAAAAGgtgcattgtttttacctgtgtaccgtttccattaatatttttaa----ttcttattgctttcgttttatcattttgtgttttgtttgcag

upper sequence: GRMZM2G057576_T01 (Zea mays), 5'ss of exon 21
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 22
TTCTGGATGATGAATGCCCGGAAGATTTCATCAAGGGTTTGATTCTCTCTGTTCGTTCTCTGCTTCCTGTTGAGCCACTAGTTGATGAATGCGAGAAGAGgtttgaattctttattcctggggtctgcaaagtgacaagtttcacattccctttttaagtggatcacatctg-tttgaatatgtgtatcag
| || ||||||||||| || ||||||||||| || ||| | ||||| ||||| || || ||||||||||||||||| || || |||||||| |||||||||  |||    | | | |||    | |||   ||  |  |||   || |  |||||||  |  ||  | | || |||| || ||  | ||||
TGCTAGATGATGAATGTCCAGAAGATTTCATTAAAGGTCTAATTCTTTCTGTCCGGTCGCTGCTTCCTGTTGAGCCCCTTGTGGATGAATGTGAGAAGAGg--tga----tgtgtccctaccatatgccctgtt-cgggtt---cactttctttttacttcaattgcttatgctttgcatgtggttttcag

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), 49 (downstream exon)
Score: 161

TTCTGGATGATGAATGCCCGGAAGATTTCATCAAGGGTTTGATTCTCTCTGTTCGTTCTCTGCTTCCTGTTGAGCCACTAGTTGATGAATGCGAGAAGAGgtttgaattc ... tgtgtatcagGAACCGCCTACGGTTGCTTACTCAATTCTTGGAGCATCTAGTGAGTGAAGGTAGCCAAGATGTGCATGTCCACAATGCTCTTGGGAAAATCATCATCGAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 121

TTCTGGATGATGAATGCCCGGAAGATTTCATCAAGGGTTTGATTCTCTCTGTTCGTTCTCTGCTTCCTGTTGAGCCACTAGTTGATGAATGCGAGAAGAGgtttgaattc ... tgtgtatcagGAACCGCCTACGGTTGCTTACTCAATTCTTGGAGCATCTAGTGAGTGAAGGTAGCCAAGATGTGCATGTCCACAATGCTCTTGGGAAAATCATCATCGAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 96

TTCTGGATGATGAATGCCCGGAAGATTTCATCAAGGGTTTGATTCTCTCTGTTCGTTCTCTGCTTCCTGTTGAGCCACTAGTTGATGAATGCGAGAAGAGgtttgaattc ... tgtgtatcagGAACCGCCTACGGTTGCTTACTCAATTCTTGGAGCATCTAGTGAGTGAAGGTAGCCAAGATGTGCATGTCCACAATGCTCTTGGGAAAATCATCATCGAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 151

TTCTGGATGATGAATGCCCGGAAGATTTCATCAAGGGTTTGATTCTCTCTGTTCGTTCTCTGCTTCCTGTTGAGCCACTAGTTGATGAATGCGAGAAGAGgtttgaattc ... tgtgtatcagGAACCGCCTACGGTTGCTTACTCAATTCTTGGAGCATCTAGTGAGTGAAGGTAGCCAAGATGTGCATGTCCACAATGCTCTTGGGAAAATCATCATCGAC