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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACTACTCAGTTTGATTGAGTACAAAACACTTGTGATGCGTGGGGATTTGGAACATGCGAATATTATTTTACCATCCATACCAAAGGAACAACACAACAGgtgccatcctgtttgtctgttcaaaattttgtagtggttgttaatttaaacttttatgtgccccaatgtttatatgatttacttttggcttgcag

Basic information

species Zea mays
transcript GRMZM2G443953_T03
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G443953_T03 (Zea mays), 5'ss of exon 18
lower sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 17
TACTACTCAGTTTGATTGAGTACAAAACACTTGTGATGCGTGGGGATTTGGAACATGCGAATATTATTTTACCATCCATACCAAAGGAACAACACAACAGgtgccatcctgtttgtctgttcaaaattttgtagtggttgttaatttaaacttttatgtgccccaatgtttatatgatttac-----ttttggcttgcag---
| ||  | || |||||||||||||| ||||||||||||||||| |||||||||   || |||   ||| ||||||| || || || || || || |||||||   |      ||||      | |||  |  | |   | | ||| |  |    ||||   |   || | | ||  | |||      |||| | |  |||   
TGCTTTTAAGCTTGATTGAGTACAAGACACTTGTGATGCGTGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATCCCCAAAGAGCATCATAACAGgtaggacttaccttgttgcaagacaatgattgattttctttcaatatgtagaaatatg---cttgatatgtgtagaaattaaaaatgtttttggtaacagaat

upper sequence: GRMZM2G443953_T03 (Zea mays), 5'ss of exon 18
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 17
TACTACTCAGTTTGATTGAGTACAAAACACTTGTGATGCGTGGGGATTTGGAACATGCGAATATTATTTTACCATCCATACCAAAGGAACAACACAACAGgtgccatcctgtttgtctgtt-caaaattttgtagtggttgttaatttaaacttttatgtgccccaatgttt-atatgatttacttttggcttgcag--------
||||  | ||||||||||| ||||| |||||||| |||||||| |||||||||   || |||   ||| ||||||| || || || || || || |||||||   |   | ||| ||||||      ||  | | ||    ||| |||   ||||  |  |     |||||| ||||| |||      |||||            
TACTTTTAAGTTTGATTGAATACAAGACACTTGTCATGCGTGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATTCCTAAAGAGCATCATAACAGgtagtagt-tattt-tctgttatgttgttacggaatgacccttacttt---ctttatttagaaattatgtttgatatgttttgagaaaggcttttttgtaagggt

upper sequence: GRMZM2G443953_T03 (Zea mays), 5'ss of exon 18
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 17
TACTACTCAGTTTGATTGAGTACAAAACACTTGTGATGCGTGGGGATTTGGAACATGCGAATATTATTTTACCATCCATACCAAAGGAACAACACAACAGgtgccatcctgtttgtctgttcaaaattttgtagtggttgttaatttaaacttttatgtgccccaatgtttatatgatttacttttggcttgcag--------
| ||  | || |||||||||||||| ||||||||||||||||| |||||||||   || |||  |||| | ||||| || || || || || || |||||||   |    |||    |||   |  ||      |  |  |||||||     |||   |      |  | |   |||| |   |     ||  |         
TGCTTTTAAGCTTGATTGAGTACAAGACACTTGTGATGCGTGGTGATTTGGAAAGGGCCAATGATATTCTGCCATCAATCCCCAAAGAGCATCATAACAGgtagaagttagttaccttgtgttacgttgcaagataatgattaattt---tctttcaatatgttgaaatatgcttgatatgtgtagaaattaaaaatgctttt

upper sequence: GRMZM2G443953_T03 (Zea mays), 5'ss of exon 18
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 21
TACTACTCAGTTTGATTGAGTACAAAACACTTGTGATGCGTGGGGATTTGGAACATGCGAATATTATTTTACCATCCATACCAAAGGAACAACACAACAGgtgccatcctgtttgtctgttcaaaattttgtagtggttgt----taatttaaacttttatgtgccccaatgtttata-tgatttacttttggcttgcag---------------------------------------------------------
||||  | ||||||||||||||||| || |||||||||||||| ||||||||||| || |||    | ||||| || || || ||||| || || || ||||   |   |||   |    ||  | | | ||    | ||     |  | | |      ||||  || |      ||| || ||||  ||    |   |                                                          
TACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCTAAGGAGCACCATAATAGgtatgagaatgtgctttccctcgcattatggttacagctggattatggtgttagtaaacatgtatccaaggtcacataatggtttaaattgttttcctaaattcacgcattcctacttttctgattctcgacttcaaaatcctgttcgttttgtcag

upper sequence: GRMZM2G443953_T03 (Zea mays), 5'ss of exon 18
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 17
TACTACTCAGTTTGATTGAGTACAAAACACTTGTGATGCGTGGGGATTTGGAACATGCGAATATTATTTTACCATCCATACCAAAGGAACAACACAACAGgtgcc-atcctgtttgtctgttcaaaattttgtagtggttgttaatttaaactttta--tgtgccccaatgtttatatgatttacttt--tggcttgcag----
|||| |||| ||||||||||||||| |||||||| |||||||| || ||  ||| ||| | |   |||||||| |  || ||  | || ||  |||| |||| |  |   |  | || |  | | |     ||| | || || ||||| |   | ||  |||| ||  | |||    |  | |  |||  | ||||||      
TACTTCTCAATTTGATTGAGTACAAGACACTTGTAATGCGTGGAGACTTTCAACGTGCAAGTGAAATTTTACCTTTGATTCCTCAAGAGCACTACAATAGgtactgaaattcatagtatactgacagcaaagtaattgt-gtgaatttgatggtgtagatgtgtcctcaggtt---gtagtctgatttgatagcttgctagatt

upper sequence: GRMZM2G443953_T03 (Zea mays), 5'ss of exon 18
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 17
TACTACTCAGTTTGATTGAGTACAAAACACTTGTGATGCGTGGGGATTTGGAACATGCGAATATTATTTTACCATCCATACCAAAGGAACAACACAACAGgtgccatcctgtt--tgtctgttcaaaattttgtagtggttgttaatttaaacttttatgtgccccaatgtttatatgatttacttttggcttgcag-------
|||| |||||||||||||||||||| || |||||||||||||| ||  ||||||  || |||    ||||||| || || || || ||||| || || ||||    | ||  |  || |||||   ||      |||        |   ||||  |||        | | |||  ||  || |  ||| |   | |        
TACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCCAAAGAACATCATAATAGgtaaatttctactgttggctgttggtaaaca-acagtaaaataagaggcaaacacttacaa--tgtagtatttggatc-ttcatgttttgtggggaattttgta

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|5895850|gb|AW037096.1|AW037096
EST:     GAACATGCGAATATTATTTTACCATCCATACCAAAGGAACAACACAACAG                         TGTGGCACATTTCCTTGAATCACGTGGCATGTTGGAGGAAGCCCTTGATAT
genomic: GAACATGCGAATATTATTTTACCATCCATACCAAAGGAACAACACAACAGgtgccatcct ... tggcttgcagTGTGGCACATTTCCTTGAATCACGTGGCATGTTGGAGGAAGCCCTTGATAT
EST: gi|160481629|gb|EY254461.1|EY254461
EST:     GAACATGCGAATATTATTTTACCATCCATACCAAAGGAACAACACAACAG                         TGTGGCACATTTCCTTGAATCACGTGGCATGTTGAAGAAAGCCCT
genomic: GAACATGCGAATATTATTTTACCATCCATACCAAAGGAACAACACAACAGgtgccatcct ... tggcttgcagTGTGGCACATTTCCTTGAATCACGTGGCATGTTGGAGGAAGCCCT
EST: gi|78116813|gb|DV535200.1|DV535200
EST:     GAACATGCGAATATTATTTTACCATCCATACCAAAGGAACAACACAACAG                         TGTGGCACATTTCCTTGAATCACGTGGCATGTTGGAGGAAGCCCTTGATAT
genomic: GAACATGCGAATATTATTTTACCATCCATACCAAAGGAACAACACAACAGgtgccatcct ... tggcttgcagTGTGGCACATTTCCTTGAATCACGTGGCATGTTGGAGGAAGCCCTTGATAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACTACTCAGTTTGATTGAGTACAAAACACTTGTGATGCGTGGGGATTTGGAACATGCGAATATTATTTTACCATCCATACCAAAGGAACAACACAACAGgtgccatcctgtttgtctgttcaaaattttgtagtggttgttaatttaaacttttatgtgccccaatgtttatatgatttacttttggcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA