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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaatggacgattgtcctttgaacccttcagaaagatcaatttgtatttgtgatccaccaaaaagagtaaccctttttctatactactacatacaggatggtccatatcatttacttaaagtgttcttttccttttcctgccagGTTGTCTTTATCCCAAATTACAATGTATCAGTGGCTGAAGTGCTTATTCCTGGTAGCGAATTGTCACAGCATATTAGTACTGCTGGTATGGAAGCAAGTG

Basic information

species Zea mays
transcript GRMZM2G085577_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085577_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os01g63270.2 (Oryza sativa), 3'ss of exon 12
gtatgaatggacgattgtcctttgaacccttcagaaagatcaatttgtatttgtgatccaccaaaaagagtaaccctttttctatactactacatacaggatggtccatatcatttacttaaagtgttcttttcctt-ttcctgccagGTTGTCTTTATCCCAAATTACAATGTATCAGTGGCTGAAGTGCTTATTCCTGGTAGCGAATTGTCACAGCATATTAGTACTGCTGGTATGGAAGCAAGTG
                                                || |       |  |  ||||  | |    ||| || |    |||| | |   | |    ||   || | ||||| |||     ||||| |||||  ||||| || || || || || ||||||||||| ||||| || ||||| |||||||| || ||| |||||||||| || ||||| || || |||||||||||||
-----------------------------------------------catatagtgagtaatattaagataatctagatttgta-atccttacacaaatatttgattgtaattttgaattaaaatgtggacctccttgttcctctcagGTGGTGTTCATTCCCAACTACAATGTATCTGTGGCCGAGGTGCTCATTCCTGGGAGTGAACTGTCACAGCACATCAGTACCGCAGGCATGGAAGCAAGTG

upper sequence: GRMZM2G085577_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA18G07480.1 (Glycine max), 3'ss of exon 12
gtatgaatggacgattgtcctttgaacccttcagaaagatcaatttgtatttgtgatccaccaaaaagagtaaccctttttctatactactacatacaggatggtccatatcattta---cttaaagtgttcttttcc--ttttcctgccagGTTGTCTTTATCCCAAATTACAATGTATCAGTGGCTGAAGTGCTTATTCCTGGTAGCGAATTGTCACAGCATATTAGTACTGCTGGTATGGAAGCAAGTG
                                                   | |  | ||  || |  || |  | | | |||  |  | ||   |    ||  |   |       |     |||| |||| || |     |||  || |||||||| ||| | |||||||||||||| || ||||| || ||||| ||||| || || ||  | || ||||||||||| ||||| || |||||||||||||
---------------------------------------------------tctactgcatgaacacaagca-tcatgtatctgcatgattattaaacttattcttagtggggaacaaaatctaaactgtttttattaaacttttttgtcagGTTGTGTTTGTTCCAAATTACAATGTGTCTGTGGCAGAGGTGCTGATTCCAGGAAGTGAGCTTTCTCAGCATATTAGCACTGCAGGCATGGAAGCAAGTG

upper sequence: GRMZM2G085577_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA08G45210.1 (Glycine max), 3'ss of exon 13
gtatgaatggacgattgtcctttgaacccttcagaaagatcaatttgtatttgtgatccaccaaaaagagtaaccctttttctatactactacatacaggatggtccatatcatttacttaaagtgttctt-ttccttttcctgccagGTTGTCTTTATCCCAAATTACAATGTATCAGTGGCTGAAGTGCTTATTCCTGGTAGCGAATTGTCACAGCATATTAGTACTGCTGGTATGGAAGCAAGTG
                                          |  || ||    |    |   |   |  | |  ||  |   | |||  |||    |    |   || |      |  |||| || |||| ||    ||  || |||||||| ||| |||||||||||||||| || ||||| || ||||| ||||| || || ||  | || ||||||||||| ||||| || |||||||||||||
----------------------------------------tcacatgaatacaggcattatgtatctgcatgattctaatatcaaact--tacgcttaatgagaaacaaa------atctaaactgctcttatttaactttttgtcagGTTGTGTTTGTCCCAAATTACAATGTGTCTGTGGCAGAGGTGCTGATTCCAGGAAGTGAGCTTTCTCAGCATATTAGCACTGCAGGCATGGAAGCAAGTG

upper sequence: GRMZM2G085577_T01 (Zea mays), 3'ss of exon 12
lower sequence: Vv06s0004g06020.t01 (Vitis vinifera), 3'ss of exon 12
gtatgaatggacgattgtcctttgaacccttcagaaagatcaatttgtatttgtgatccaccaaaaagagtaaccctttttctatactac-tac-atacaggatggtccatatcatttacttaaagtgttcttttccttttcctgccagGTTGTCTTTATCCCAAATTACAATGTATCAGTGGCTGAAGTGCTTATTCCTGGTAGCGAATTGTCACAGCATATTAGTACTGCTGGTATGGAAGCAAGTG
                                  |    |    ||   |||  | |     | |   || || | ||||| | || ||  | | | ||  | || | |||  |||     ||||    | |              |||||||| ||| | |||||||| ||||| || ||||| || ||||||||||| || || || ||||||||||| || || || ||||| |||||||| ||||
-------------------------------tgtatgttttggctt---tttaagcttttttatattcagcaatcttttttttttagtatatgctacacttgctgatgcat-ccataactgtaaaaaaattt--------------cagGTTGTTTTTGTTCCAAATTATAATGTGTCTGTGGCAGAGGTGCTTATTCCAGGAAGTGAGTTGTCACAGCACATCAGCACAGCTGGCATGGAAGCCAGTG

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|91049536|gb|EB159954.1|EB159954
EST:     ATGTTGGTGCTGTTGTGAACAATGATCCCGAAGTTAACAAATATCTGAAG                         GTTGTCTTTATCCCAAATTACAATGTATCAGTGGCTGAAGTGCTTATTCCT
genomic: ATGTTGGTGCTGTTGTGAACAATGATCCCGAAGTTAACAAATATCTGAAGgtatgaatgg ... ttcctgccagGTTGTCTTTATCCCAAATTACAATGTATCAGTGGCTGAAGTGCTTATTCCT
EST: gi|32833216|gb|CD972894.1|CD972894
EST:     ATGTTGGTGCTGTTGTGAACAATGATCCCGAAGTTAACAAATATCTGAAG                         GTTGTCTTTATCCCAAATTACAATGTATCAGTGGCTGAAGTGCTTATTAGC
genomic: ATGTTGGTGCTGTTGTGAACAATGATCCCGAAGTTAACAAATATCTGAAGgtatgaatgg ... ttcctgccagGTTGTCTTTATCCCAAATTACAATGTATCAGTGGCTGAAGTGCTTATTC-C
EST: gi|60358978|gb|DN225951.1|DN225951
EST:     ATGTTGGTGCTGTTGTGAACAATGACCCCGAAGTTAACAAATATCTGAAG                         GTTGTCTTTATCCCAAATTACAATGTATCAGTGGCTGAAGTGCTTATTCCT
genomic: ATGTTGGTGCTGTTGTGAACAATGATCCCGAAGTTAACAAATATCTGAAGgtatgaatgg ... ttcctgccagGTTGTCTTTATCCCAAATTACAATGTATCAGTGGCTGAAGTGCTTATTCCT
EST: gi|32855932|gb|CD995613.1|CD995613
EST:     ATGTTGGTGCTGTTGTGAACAATGATCCCGAAGTTAACAAATATCTGAAG                         GTTGTCTTTATCCCAAATTACAATGTATCAGTGGCTGAAGTGCTTATTCCT
genomic: ATGTTGGTGCTGTTGTGAACAATGATCCCGAAGTTAACAAATATCTGAAGgtatgaatgg ... ttcctgccagGTTGTCTTTATCCCAAATTACAATGTATCAGTGGCTGAAGTGCTTATTCCT
EST: gi|60354619|gb|DN221592.1|DN221592
EST:     ATGTTGGTGCTGTTGTGAACAATGATCCCGAAGTTAACAAATATCTGAAG                         GTTGTCTTTATCCCAAATTACAATGTATCAGTGGCTGAAGTGCTTATTCCT
genomic: ATGTTGGTGCTGTTGTGAACAATGATCCCGAAGTTAACAAATATCTGAAGgtatgaatgg ... ttcctgccagGTTGTCTTTATCCCAAATTACAATGTATCAGTGGCTGAAGTGCTTATTCCT
EST: gi|32832224|gb|CD971902.1|CD971902
EST:     ATGTTGGTGCTGTTGTGAACAATGATCCCGAAGTTAACAAATATCTGAAG                         GTTGTCTTTATCCCAAATTACAATGTATCAGTGGCTGAAGTGCTTATTCCT
genomic: ATGTTGGTGCTGTTGTGAACAATGATCCCGAAGTTAACAAATATCTGAAGgtatgaatgg ... ttcctgccagGTTGTCTTTATCCCAAATTACAATGTATCAGTGGCTGAAGTGCTTATTCCT
EST: gi|24934476|gb|CA452694.1|CA452694
EST:     ATGTTGGTGCTGTTGTGAACAATGATCCCGAAGTTAACAAATATCTGAAG                         GTTGTCTTTATCCCAAATTACAATGTATCAATGGCTGAAGTGCTTATTCCT
genomic: ATGTTGGTGCTGTTGTGAACAATGATCCCGAAGTTAACAAATATCTGAAGgtatgaatgg ... ttcctgccagGTTGTCTTTATCCCAAATTACAATGTATCAGTGGCTGAAGTGCTTATTCCT
EST: gi|76924590|gb|DV170029.1|DV170029
EST:     TGTTGGTGCTGTTGTGAAACA-TGATCCCGAAGTTAACAA-TATCTGAAG                         GTTGTCTTTATCC-AAATTACCATGTATCAGTGGCTGAAGTGCTTATTCCT
genomic: TGTTGGTGCTGTTGTGAA-CAATGATCCCGAAGTTAACAAATATCTGAAGgtatgaatgg ... ttcctgccagGTTGTCTTTATCCCAAATTACAATGTATCAGTGGCTGAAGTGCTTATTCCT
EST: gi|94472102|gb|EB701060.1|EB701060
EST:     ATGTTGGTGCTGTTGTGAACAATGATCCCGAAGTTAACAAATATCTGAAG                         GTTGTCTTTATCCCAAATTACAATGTATCAGTGGCTGAAGTGCTTATTCCT
genomic: ATGTTGGTGCTGTTGTGAACAATGATCCCGAAGTTAACAAATATCTGAAGgtatgaatgg ... ttcctgccagGTTGTCTTTATCCCAAATTACAATGTATCAGTGGCTGAAGTGCTTATTCCT
EST: gi|211204436|gb|FL394622.1|FL394622
EST:     ATGTTGGTGCTGTTGTGAACAATGATCCCGAAGTTAACAAATATCTGAAG                         GTTGTCTTTATCCCAAATTACAATGTATCAGTGGCTGAAGTGCTTATTCCT
genomic: ATGTTGGTGCTGTTGTGAACAATGATCCCGAAGTTAACAAATATCTGAAGgtatgaatgg ... ttcctgccagGTTGTCTTTATCCCAAATTACAATGTATCAGTGGCTGAAGTGCTTATTCCT
EST: gi|211521628|gb|FL412959.1|FL412959
EST:     ATGTTGGTGCTGTTGTGAACAATGATCCCGAAGTTAACAAATATCTGAAG                         GTTGTCTTTATCCCAAATTACAATGTATCAGTGGCTGAAGTGCTTATTCCT
genomic: ATGTTGGTGCTGTTGTGAACAATGATCCCGAAGTTAACAAATATCTGAAGgtatgaatgg ... ttcctgccagGTTGTCTTTATCCCAAATTACAATGTATCAGTGGCTGAAGTGCTTATTCCT

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), 48 (downstream exon)
Score: 276

AGCGTTTGCAACATACACTAATGCCAAAAGAATAGTGAAATTGGTGAATGATGTTGGTGCTGTTGTGAACAATGATCCCGAAGTTAACAAATATCTGAAGgtatgaatgg ... ttcctgccagGTTGTCTTTATCCCAAATTACAATGTATCAGTGGCTGAAGTGCTTATTCCTGGTAGCGAATTGTCACAGCATATTAGTACTGCTGGTATGGAAGCAAGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 249

AGCGTTTGCAACATACACTAATGCCAAAAGAATAGTGAAATTGGTGAATGATGTTGGTGCTGTTGTGAACAATGATCCCGAAGTTAACAAATATCTGAAGgtatgaatgg ... ttcctgccagGTTGTCTTTATCCCAAATTACAATGTATCAGTGGCTGAAGTGCTTATTCCTGGTAGCGAATTGTCACAGCATATTAGTACTGCTGGTATGGAAGCAAGTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 68

AGCGTTTGCAACATACACTAATGCCAAAAGAATAGTGAAATTGGTGAATGATGTTGGTGCTGTTGTGAACAATGATCCCGAAGTTAACAAATATCTGAAGgtatgaatgg ... ttcctgccagGTTGTCTTTATCCCAAATTACAATGTATCAGTGGCTGAAGTGCTTATTCCTGGTAGCGAATTGTCACAGCATATTAGTACTGCTGGTATGGAAGCAAGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 235

AGCGTTTGCAACATACACTAATGCCAAAAGAATAGTGAAATTGGTGAATGATGTTGGTGCTGTTGTGAACAATGATCCCGAAGTTAACAAATATCTGAAGgtatgaatgg ... ttcctgccagGTTGTCTTTATCCCAAATTACAATGTATCAGTGGCTGAAGTGCTTATTCCTGGTAGCGAATTGTCACAGCATATTAGTACTGCTGGTATGGAAGCAAGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catacaggatggtccatatcatttacttaaagtgttcttttccttttcctgccagGTTGTCTTTATCCCAAATTACAATGTATCAGTGGCTGAAGTGCTTATTCCTGGTAGCGAATTGTCACAGCATATTAGTACTGCTGGTATGGAAGCAAGTG
                                tgttcttttccttttc  CT-rich tract
               atatcatttacttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaatggacgattgtcctttgaacccttcagaaagatcaatttgtatttgtgatccaccaaaaagagtaaccctttttctatactactacatacaggatggtccatatcatttacttaaagtgttcttttccttttcctgccagGTTGTCTTTATCCCAAATTACAATGTATCAGTGGCTGAAGTGCTTATTCCTGGTAGCGAATTGTCACAGCATATTAGTACTGCTGGTATGGAAGCAAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG