Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAGTTTGTGCACCCAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagccttaactatttttatttcagtattactattactgctgcagatgtttattattcatggcattgacgtttccag

Basic information

species Zea mays
transcript GRMZM2G010823_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G010823_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g21950.1 (Oryza sativa), 5'ss of exon 4
TAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAGTTTGTGCACCCAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagccttaactattttt---------atttcagtattactattactgctgcagatgtttattattcatggcattgacgtttccag
||||||  ||||||| |||||||| ||||| || ||||||||||| ||||| ||||| |||||||| || ||||| || ||||||||||||||||||||||||||  || |||||||||         |||| | | |  |  ||||   ||| |||||| || ||| |||    |||| ||| |||
TAGGGCCGCTGAGATTCTTGGACATAAGCGTGGCGAGAAGTTTGTACACCCTAATGATCATGTGAACAGATCACAGTCCTCAAATGATACATTTCCCACTgtaagatttcactatttttttggccgtcattttaatgt-gcatttacctttgctgatgtt-atgatttatgttgctgacattttcag

upper sequence: GRMZM2G010823_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA10G02040.1 (Glycine max), 5'ss of exon 4
TAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAGTTTGTGCACCCAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagcct----taactatttttatttcagtattactattactgctgcagatgtttattattcatggcattgacgtttccag--------------------------------------------------------------------------------------------
  | ||| | ||||| ||||| || |||||||||| |||||| |||||||||||||||||||| ||||| || || ||||| ||||||||||| || || ||||||||    ||| ||| | ||||||   | |  | ||  || || |     ||  |||   ||    ||   || |                                                                                               
CCGAGCAGCAGAGATTCTTGGCCATAAGCGCGGTGGGAAGTTCGTGCACCCAAATGACCATGTCAATAGATCGCAGTCTTCTAATGATACATTCCCAACCgtaagcctcttgtaattatatatatttc--caattttttttttgttgaattgtcttgctatctgtg-tggtgcaattcctgataaactgtttcttatactttgtttacccactgttctggtcttgtttaaagtattgatttctttttaatctgtaattgtttacttctttccag

upper sequence: GRMZM2G010823_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA02G01920.1 (Glycine max), 5'ss of exon 4
TAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAGTTTGTGCACCCAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagcct----taactatttttatttcagtattactattactgctgcagatgttt-attattcatggcattgacgtttccag-----------------------------------------------------------------------------------------
  | ||| | ||||| ||| | || ||||| |||| |||||| |||||||||||||||||||| ||||| ||||| ||||||||||||||||| || |||||||||||    ||| ||| | |||| | || ||  | ||  || || | |||| |    ||   ||   |  |  | |  |                                                                                          
CCGAGCAGCAGAGATTCTTTGGCATAAGCGGGGTGGGAAGTTAGTGCACCCAAATGACCATGTCAATAGATCACAGTCTTCAAATGATACATTCCCAACTgtaagcctcttgtaattatatatattcccgttttttt-ttgttgttg-atatgtctcgccatctgtgtagtgcaactcttgatagactttcttaaactttgtttatccactgtacagctcttgtttaaagtattgatttctttttaatctatatttgtttacttctttccag

upper sequence: GRMZM2G010823_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA02G01930.2 (Glycine max), 5'ss of exon 4
TAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAGTTTGTGCACCCAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagccttaactatttttatttcagtattactattactgctgcagatgtttattattcatggcattgacgtttccag--------------------------------------------------------------------
  | ||| | ||||| ||||| || ||||| |||||||||||||||||||||||||||||||| ||||| ||||| ||||| ||||||||||| || |||||||||||    || |  ||| |   |   |   ||| || || |   ||| | | |  ||||  |  ||  |||| |                                                                    
CCGAGCAGCAGAGATTCTTGGCCATAAGCGTGGTGAGAAGTTTGTGCACCCAAATGACCATGTCAATAGATCACAGTCTTCTAATGATACATTCCCAACTgtaagcctcttgtaatgatatgt---tcccaaatttattgttgaattggttcactgtcaatggtgt--acaattcctgatgaattgttttcctactgtgttacctggtatacaatttttaatctatatttgtttacttctttccag

upper sequence: GRMZM2G010823_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT5G50950.3 (Arabidopsis thaliana), 5'ss of exon 3
TAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAGTTTGTGCACCCAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagccttaact---atttttatt--tcagtattactattactgc-tgca-gatgtttatt-----attcatggcattgacgtttccag------------------------------------------------------------------------------
||| ||| ||||||| ||||| ||||| || ||||| ||  ||||||||||||||||||||||||| || ||||||||||| ||||| || ||||| ||||||||| |||  |   ||| | |||  ||| ||  | || |  ||| |||   | ||| |||       | | ||  ||   ||  ||                                                                                
TAGAGCAGCTGAGATTCTTGGTCACAAACGTGGTGAAAAAATTGTGCACCCAAATGACCATGTGAACAGATCACAATCTTCTAATGACACTTTTCCAACTgtaagctttagtttgcattctcattagtcattaccaataattttgcatgcttaacgttcattcaattgcttacggtgttcgtgtaaccgattgcttttatttcctatatgtatgctcactgctctgtcaagtactacttgacggtcgtataattttggttttgtatag

upper sequence: GRMZM2G010823_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT2G47510.2 (Arabidopsis thaliana), 5'ss of exon 5
TAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAGTTTGTGCACCCAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagccttaactatttttatttcagtattactattactgctgcagatgtttattattcatggcattgacgtttccag-------------------------------------------------------------------
||| ||| ||||||| ||||| | ||| || |||||||| | |||||||||||||||||||||||| || ||||||||||| || || || ||||| || |||||| ||    ||||  ||| |||   ||| | ||||  |  | ||| ||    ||  |   |||    ||||                                                                      
TAGAGCAGCTGAGATTCTTGGTCGCAAACGTGGTGAGAAATGTGTGCACCCAAATGACCATGTGAACAGATCACAATCTTCTAACGACACTTTTCCTACCgtaagcttt---catttgcattccagc--taccaatact-ttttacatgctttaagtttttaaaatttttctttcttatatgttggctcacttccctttcaacttctaattgacggtcttttttttttttttggcttttgtctag

upper sequence: GRMZM2G010823_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv14s0060g01700.t01 (Vitis vinifera), 5'ss of exon 2
TAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAGTTTGTGCACCCAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagccttaactatttttatttcagtattactattactgctgcagatgtttattattcatggcattgacgtttccag------------------------
||| ||| ||||||| ||||| ||||| || ||||| ||||| |||||||||||||| ||||| || || |||||||| |||||||| |||||||| || |||||   |   | |  | ||   | | |||  | | | |        ||   |  ||| |   | |      | ||                         
TAGAGCAGCTGAGATTCTTGGCCACAAACGGGGTGAAAAGTTCGTGCACCCAAATGATCATGTCAACAGATCACAATCATCAAATGACACATTTCCGACAgtaagtgcttggtgtcct-atgggaattttagaacttcagaaatgtgagtgggtctttc-taatactagtaaattcaactactgtaccttttaaagatatag

upper sequence: GRMZM2G010823_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv07s0005g00880.t01 (Vitis vinifera), 5'ss of exon 5
TAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAGTTTGTGCACCCAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagcctt---aactatttttatt-tcagtattactattactg-ctgc--agatgtttattattcatggcattgacgtttccag-----------------------------------------------
||| ||| ||||||| ||||| ||  |||| ||||| || | |||||| |||||||||||||| || || ||||||||||| ||||||||||| || ||||||||||||   ||| |   |     | | | |||  || |||  || |  | |||  | | |  |||  |||||  |     |                                                
TAGAGCAGCTGAGATTCTTGGCCATCAGCGTGGTGAAAAATATGTGCATCCAAATGACCATGTTAACAGATCACAATCTTCTAATGATACATTCCCTACTgtaagccttttgaacaagaatagccatgatttttaagataactatctacttaaatggct-tgacccatttcattgttgaaatgatgattttttactggtttttattgaattctatgtttgttgtttgtccag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|148999094|gb|EE030327.2|EE030327
EST:     CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACT                         GTAATGCATATAGCGACGGCCGTTGAGATACATTCGAGGTTTATCCCAAGT
genomic: CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagcctta ... acgtttccagGTAATGCATATAGCGACGGCCGTTGAGATACATTCGAGGTTTATCCCAAGT
EST: gi|211324568|gb|FL223785.1|FL223785
EST:     CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACT                         GTAATGCATATAGCGACGGCCGTTGAGATACATTCGAGGTTTAT
genomic: CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagcctta ... acgtttccagGTAATGCATATAGCGACGGCCGTTGAGATACATTCGAGGTTTAT
EST: gi|211324561|gb|FL223778.1|FL223778
EST:     CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACT                         GTAATGCATATAGCGACGGCCGTTGAGATACATTCGAGGTTTATCCCAAGT
genomic: CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagcctta ... acgtttccagGTAATGCATATAGCGACGGCCGTTGAGATACATTCGAGGTTTATCCCAAGT
EST: gi|78111379|gb|DV529776.1|DV529776
EST:     CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACT                         GTAATGCATATAGCGACGGCCGTTGAGATACATTCGAGGTTTATCCCAAGT
genomic: CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagcctta ... acgtttccagGTAATGCATATAGCGACGGCCGTTGAGATACATTCGAGGTTTATCCCAAGT
EST: gi|211324571|gb|FL223788.1|FL223788
EST:     CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACT                         GTAATGCATATAGCGACGG
genomic: CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagcctta ... acgtttccagGTAATGCATATAGCGACGG
EST: gi|149089384|gb|EE178623.2|EE178623
EST:     CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACT                         GTAATGCATATAGCGACGGCCGTTGAGATACATTCGAGGTTTATCCCAAGT
genomic: CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagcctta ... acgtttccagGTAATGCATATAGCGACGGCCGTTGAGATACATTCGAGGTTTATCCCAAGT
EST: gi|149001505|gb|EE038811.2|EE038811
EST:     CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACT                         GTAATGCATATAGCGACGGCCGTTGAGATACATTCGAGGTTTATCCCAAGT
genomic: CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagcctta ... acgtttccagGTAATGCATATAGCGACGGCCGTTGAGATACATTCGAGGTTTATCCCAAGT
EST: gi|211326730|gb|FL223797.1|FL223797
EST:     AAATGACCATGTGGATAGGTCACAATCCTTCAA-TGATACATTTCCCACT                         GTTATGCATATAG
genomic: AAATGACCATGTGAATAGGTCACAATC-TTCAAATGATACATTTCCCACTgtaagcctta ... acgtttccagGTAATGCATATAG
EST: gi|211324562|gb|FL223779.1|FL223779
EST:     AAATGGAC-ATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACG                         GGAATGCATATAGC
genomic: AAATG-ACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagcctta ... acgtttccagGTAATGCATATAGC
EST: gi|211326731|gb|FL223798.1|FL223798
EST:     CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACT                         GTAATGCATATAGCGACGGCCGTTGAGATACATT
genomic: CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagcctta ... acgtttccagGTAATGCATATAGCGACGGCCGTTGAGATACATT
EST: gi|148951891|gb|EC897665.2|EC897665
EST:     CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACT                         GTAATGCATATAGCGACGGCCGTTGAGATACATTCGAGGTTTATCCCAAGT
genomic: CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagcctta ... acgtttccagGTAATGCATATAGCGACGGCCGTTGAGATACATTCGAGGTTTATCCCAAGT
EST: gi|211324567|gb|FL223784.1|FL223784
EST:     CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACT                         GTAATGCATATAGCGACGGCCGTTGAGATACATTCGAGGTTTATCCCAAGT
genomic: CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagcctta ... acgtttccagGTAATGCATATAGCGACGGCCGTTGAGATACATTCGAGGTTTATCCCAAGT
EST: gi|32798032|gb|CD950268.1|CD950268
EST:     CAAATGACCATGTAAATAGGTCACAATCTTCAAATGATACATTTCCCACT                         GTAATGCATATAGCGACGGCCGTTGAGATACATTCGAGGTTTATCCCAAGT
genomic: CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagcctta ... acgtttccagGTAATGCATATAGCGACGGCCGTTGAGATACATTCGAGGTTTATCCCAAGT
EST: gi|211326725|gb|FL223792.1|FL223792
EST:     CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACT                         GTAATGCATATAGCGACGGCCGTTG
genomic: CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagcctta ... acgtttccagGTAATGCATATAGCGACGGCCGTTG
EST: gi|211324570|gb|FL223787.1|FL223787
EST:     CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACT                         GTAATGCATATAGCGACGGCCGTTGAGATACATTCGAGGTTTATCCCAAGT
genomic: CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagcctta ... acgtttccagGTAATGCATATAGCGACGGCCGTTGAGATACATTCGAGGTTTATCCCAAGT
EST: gi|32797316|gb|CD949552.1|CD949552
EST:     CAAATGACCATGTAAATAGGTCACAATCTTCAAATGATACATTTCCCACT                         GTAATGCATATAGCGACGGCCGTTGAGATACATTCGAGGTTTATCCCAAGT
genomic: CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagcctta ... acgtttccagGTAATGCATATAGCGACGGCCGTTGAGATACATTCGAGGTTTATCCCAAGT
EST: gi|211324572|gb|FL223789.1|FL223789
EST:     CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACT                         GTAATGCATATAGCGACGGCCGTTGAGATAACATTCGAGG
genomic: CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagcctta ... acgtttccagGTAATGCATATAGCGACGGCCGTTGAGATA-CATTCGAGG
EST: gi|211324569|gb|FL223786.1|FL223786
EST:     CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACT                         GTAATGCATATAGCGACGGCCGTTGAGATACATTCGAGGTTTATCCCAAGT
genomic: CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagcctta ... acgtttccagGTAATGCATATAGCGACGGCCGTTGAGATACATTCGAGGTTTATCCCAAGT
EST: gi|91877250|gb|EB407207.1|EB407207
EST:     CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACT                         GTAATGCATATAGCGACGGCCGTTGAGATACATTCGAGGTTTATCCCAAGT
genomic: CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagcctta ... acgtttccagGTAATGCATATAGCGACGGCCGTTGAGATACATTCGAGGTTTATCCCAAGT
EST: gi|211326737|gb|FL223804.1|FL223804
EST:     CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACT                         GTAATGCATATAGCGACGG
genomic: CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagcctta ... acgtttccagGTAATGCATATAGCGACGG
EST: gi|211324565|gb|FL223782.1|FL223782
EST:     CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACT                         GTAATGCATATAGCGACGGCCGTTGAGATACATTCGAGGTTTATCCCAAGT
genomic: CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagcctta ... acgtttccagGTAATGCATATAGCGACGGCCGTTGAGATACATTCGAGGTTTATCCCAAGT
EST: gi|211326729|gb|FL223796.1|FL223796
EST:     CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACT                         GTAATGCATATAGCGACGGCCGTTGAGATACATTCGAGGTTTATCCCAAGT
genomic: CAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagcctta ... acgtttccagGTAATGCATATAGCGACGGCCGTTGAGATACATTCGAGGTTTATCCCAAGT

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: 330

TAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAGTTTGTGCACCCAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagcctta ... acgtttccagGTAATGCATATAGCGACGGCCGTTGAGATACATTCGAGGTTTATCCCAAGTTTGCAACAGTTGCATGATTCACTTCATTCGAAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 355

TAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAGTTTGTGCACCCAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagcctta ... acgtttccagGTAATGCATATAGCGACGGCCGTTGAGATACATTCGAGGTTTATCCCAAGTTTGCAACAGTTGCATGATTCACTTCATTCGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 268

TAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAGTTTGTGCACCCAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagcctta ... acgtttccagGTAATGCATATAGCGACGGCCGTTGAGATACATTCGAGGTTTATCCCAAGTTTGCAACAGTTGCATGATTCACTTCATTCGAAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 351

TAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAGTTTGTGCACCCAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagcctta ... acgtttccagGTAATGCATATAGCGACGGCCGTTGAGATACATTCGAGGTTTATCCCAAGTTTGCAACAGTTGCATGATTCACTTCATTCGAAA