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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaccctcttttttccatgcatgtaatctacagtttttaacctgtccatgcctgtaatatacagtgggtagcttggtgttcatagtgtaaagttgaactttgcactgcacacctgcaaaaaagtcactaggatcaaacaagtatgaaagctactgacacctacaatttttgttctcagGTTAGCTGTAGTTTCAATGGCAGGACTGGCTGCTGAAGGTCTAGAATATGACAAAGTTGTAGGTCAATCAGCAGATCTTTTCACCCTTCAG

Basic information

species Zea mays
transcript GRMZM2G004352_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G004352_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os04g54640.1 (Oryza sativa), 3'ss of exon 7
gtaaccctctt---ttttccatgcatgtaatctacagtttttaacctgtccatgcctgtaatatacagtgggtagcttggtgttcatagtgtaaagttgaactttgcactgcacacc-tgcaaaaaagtcactaggatcaaacaagtatgaaagctactgacacctacaatttttgttc--tcagGTTAGCTGTAGTTTCAATGGCAGGACTGGCTGCTGAAGGTCTAGAATATGACAAAGTTGTAGGTCAATCAGCAGATCTTTTCACCCTTCAG
||||| || |     |  | |||| |||| |||  | | |   |  | |   | | |  |||      |   | |  |    |||||||| |    || |||       | || |             | ||   ||  |||||   |  ||  | ||| | |   | ||    | ||   |||||||||||||||| ||||||||||| || |||||||||||||||||||||||||||||||| |||||||| |||||||||||||||||||||
gtaactctgtcaaactcgctatgcttgtagtctgtattgt---atttattttttcttagaatcatgtttattttgtatcagcttcatagtttctgattcaacacaaatatacaaattacatgtgctcattacactgacgaaacatccaaaaacaccactaaaataaataacggatattgtatcagGTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGACAAAGTTGTCGGTCAATCGGCAGATCTTTTCACCCTTCAG

upper sequence: GRMZM2G004352_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv07s0031g01560.t01 (Vitis vinifera), 3'ss of exon 7
gtaaccctcttttttccatgcatgtaatctacagtttttaacctgtccatgcctgtaatatacagtgggtagcttggtgttcatagtgtaaagttgaactttgcact-gcacacctgcaaaaaagtcactaggatcaaacaagtatgaaagctactgacacctacaatttttgttctcagGTTAGCTGTAGTTTCAATGGCAGGACTGGCTGCTGAAGGTCTAGAATATGACAAAGTTGTAGGTCAATCAGCAGATCTTTTCACCCTTCAG
                                                                        | |  |  ||  |  |  |  | | | | || | | |   |  |  |  || |  | |      | |||  |   |       |  |||||  || | || ||| |||||| || || ||  ||||||| ||||| || || ||||| ||  ||||||||||||| || |||||||| || ||||||||||| ||||||
-----------------------------------------------------------------------acataatcctc-catagatagttcggattatggattagttaatttaaattaagggaattgccggtagacagctgaca-------ttccacctttaactgttattc-cagGTTGGCGGTTGTAGCAATGGCTGGACTTGCAGCAGAAGGCCTGCAATATGACAAAGTGGTTGGTCAATCTGCCGATCTTTTCACTCTTCAG
















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|148954649|gb|EC900096.2|EC900096
EST:     TTACAAAAGCTAATATACAGTGGGCAGCTTGATGGAAAAGAACTAGACAG                         GTTAGCTGTAGTTTCAATGGCAGGACTGGCTGCTGAAGGTCTAGAATATGA
genomic: TTACAAAAGCTAATATACAGTGGGCAGCTTGATGGAAAAGAACTAGACAGgtaaccctct ... ttgttctcagGTTAGCTGTAGTTTCAATGGCAGGACTGGCTGCTGAAGGTCTAGAATATGA
EST: gi|149084909|gb|EE174419.2|EE174419
EST:     TTACAAAAGCTAATATACAGTGGGCAGCTTGATGGAAAAGAACTAGACAG                         GTTAGCTGTAGTTTCAATGGCAGGACTGGCTGCTGAAGGTCTAGAATATGA
genomic: TTACAAAAGCTAATATACAGTGGGCAGCTTGATGGAAAAGAACTAGACAGgtaaccctct ... ttgttctcagGTTAGCTGTAGTTTCAATGGCAGGACTGGCTGCTGAAGGTCTAGAATATGA
EST: gi|149100297|gb|EE186362.2|EE186362
EST:     TTACAAAAGCTAATATACAGTGGGCAGCTTGATGGAAAAGAACTAGACAG                         GTTAGCTGTAGTTTCAATGGCAGGACTGGCTGCTGAAGGTCTAGAATATGA
genomic: TTACAAAAGCTAATATACAGTGGGCAGCTTGATGGAAAAGAACTAGACAGgtaaccctct ... ttgttctcagGTTAGCTGTAGTTTCAATGGCAGGACTGGCTGCTGAAGGTCTAGAATATGA
EST: gi|76010526|gb|DT937696.1|DT937696
EST:     TTACAAAAGCTAATATACAGTGGGCAGCTTGATGGAAAGGAACTAGACAG                         GTTAGCTGTAGTTTCAATGGCAGGACTGGCTGCTGAAGGTCTAGAATATGA
genomic: TTACAAAAGCTAATATACAGTGGGCAGCTTGATGGAAAAGAACTAGACAGgtaaccctct ... ttgttctcagGTTAGCTGTAGTTTCAATGGCAGGACTGGCTGCTGAAGGTCTAGAATATGA
EST: gi|71313543|gb|DR793346.1|DR793346
EST:     TTACAAAAGCTAATATACAGTGGGCAGCTTGATGGAAAAGAACTAGACAG                         GTTAGCTGTAGTTTCAATGGCAGGACTGGCTGCTGAAGGTCTAGAATATGA
genomic: TTACAAAAGCTAATATACAGTGGGCAGCTTGATGGAAAAGAACTAGACAGgtaaccctct ... ttgttctcagGTTAGCTGTAGTTTCAATGGCAGGACTGGCTGCTGAAGGTCTAGAATATGA
EST: gi|149100298|gb|EE186363.2|EE186363
EST:     TTACAAAAGCTAATATACAGTGGGCAGCTTGATGGAAAAGAACTAGACAG                         GTTAGCTGTAGTTTCAATGGCAGGACTGGCTGCTGAAGGTCTAGAATATGA
genomic: TTACAAAAGCTAATATACAGTGGGCAGCTTGATGGAAAAGAACTAGACAGgtaaccctct ... ttgttctcagGTTAGCTGTAGTTTCAATGGCAGGACTGGCTGCTGAAGGTCTAGAATATGA
EST: gi|71317337|gb|DR795362.1|DR795362
EST:     TTACAAAAGCTAATATACAGTGGGCAGCTTGATGG--AAGAACTAGACAG                         GTTAGCTGTAGTTTCAATGGCAGGACTGGCTGCTGAAGGTCTAGAATATGA
genomic: TTACAAAAGCTAATATACAGTGGGCAGCTTGATGGAAAAGAACTAGACAGgtaaccctct ... ttgttctcagGTTAGCTGTAGTTTCAATGGCAGGACTGGCTGCTGAAGGTCTAGAATATGA
EST: gi|148930743|gb|EC873038.2|EC873038
EST:     TTACAAAAGCTAATATACAGTGGGCAGCTTGATGGAAAAGAACTAGACAG                         GTTAGCTGTAGTTTCAATGGCAGGACTGGCTGCTGAAGGTCTAGAATATGA
genomic: TTACAAAAGCTAATATACAGTGGGCAGCTTGATGGAAAAGAACTAGACAGgtaaccctct ... ttgttctcagGTTAGCTGTAGTTTCAATGGCAGGACTGGCTGCTGAAGGTCTAGAATATGA
EST: gi|71317339|gb|DR795363.1|DR795363
EST:     TTACAAAAGCTAATATACAGTGGGCAGCTTGATGGAA--GAACTAGACAG                         GTTAGCTGTAGTTTCAATGGCAGGACTGGCTGCTGAAGGTCTAGAATATGA
genomic: TTACAAAAGCTAATATACAGTGGGCAGCTTGATGGAAAAGAACTAGACAGgtaaccctct ... ttgttctcagGTTAGCTGTAGTTTCAATGGCAGGACTGGCTGCTGAAGGTCTAGAATATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcactaggatcaaacaagtatgaaagctactgacacctacaatttttgttctcagGTTAGCTGTAGTTTCAATGGCAGGACTGGCTGCTGAAGGTCTAGAATATGACAAAGTTGTAGGTCAATCAGCAGATCTTTTCACCCTTCAG
                           tactgac  putative branch site (score: 1)
                                          tttttgttctc  putative PPT
                                     tacaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaccctcttttttccatgcatgtaatctacagtttttaacctgtccatgcctgtaatatacagtgggtagcttggtgttcatagtgtaaagttgaactttgcactgcacacctgcaaaaaagtcactaggatcaaacaagtatgaaagctactgacacctacaatttttgttctcagGTTAGCTGTAGTTTCAATGGCAGGACTGGCTGCTGAAGGTCTAGAATATGACAAAGTTGTAGGTCAATCAGCAGATCTTTTCACCCTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT