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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACGTGTATAGTTTTGGGGTTGTCTTGCTAGAGTTGATTACTGGCCGTAGGGCTATTGACAGCACCAGACCACATGGAGAACAAAATCTTGTCTCATGGgtaagtgatgatctgtttacttgtaaatgatcgcgtgtttccctttttccaatatcttcacatcgttgtatgtctgttggcatcagacactaactacttg...

Basic information

species Zea mays
transcript GRMZM2G140095_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G140095_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g30900.1 (Oryza sativa), 5'ss of exon 4
TGACGTGTATAGTTTTGGGGTTGTCTTGCTAGAGTTGATTACTGGCCGTAGGGCTATTGACAGCACCAGACCACATGGAGAACAAAATCTTGTCTCATGGgtaagtgatgatctgtttacttgtaaatgatcgcgtgtttccctttttccaatatcttcacatcgtt-gtatgtctgttggcatcagacactaactacttg---
||| || ||||| ||||| ||||| ||||| |||||||||||||| ||| |||| || |||||||| || |||||||| || |||||||||||||||||||||||  ||| |||| ||| ||   |     |  |   |     | | | |||| | | | ||  ||  | |||||  |  |  |  |   ||| |  |||   
TGATGTATATAGCTTTGGAGTTGTGTTGCTTGAGTTGATTACTGGTCGTCGGGCGATCGACAGCACTAGGCCACATGGGGAGCAAAATCTTGTCTCATGGgtaagctatgttctgattatttaggagca--catgctatctatatatgctaataacctgaaatgatttatctgtctagtatctcctaag--taattgtttggat

upper sequence: GRMZM2G140095_T03 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA20G39370.2 (Glycine max), 5'ss of exon 3
TGACGTGTATAGTTTTGGGGTTGTCTTGCTAGAGTTGATTACTGGCCGTAGGGCTATTGACAGCACCAGACCACATGGAGAACAAAATCTTGTCTCATGGgtaagtgatgatctgtttacttgtaaatgatcgcgtgtttccctttttccaatatcttcacatcgttgtatgtctgttggcatcagacactaactacttg-----
||| || |||||||||||||| |||||  | ||| |||||||||||||||  || |||||||||||  |||| |||||||||||||| |||||| ||||||||       |  | ||| |||||   |  | |  ||     | ||  |  ||   | || | |  ||   |  || |      ||    ||  |  |||     
TGATGTATATAGTTTTGGGGTAGTCTTCTTGGAGCTGATTACTGGCCGTAAAGCCATTGACAGCACTCGACCCCATGGAGAACAAAACCTTGTCACATGGgtagccctctaa-tctttgcttgtctttattagtttggcatgcattaacttatgcatacataactatg-gggggtggtaatggtag-ttttatttgtttgagcag

upper sequence: GRMZM2G140095_T03 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA10G44580.2 (Glycine max), 5'ss of exon 4
TGACGTGTATAGTTTTGGGGTTGTCTTGCTAGAGTTGATTACTGGCCGTAGGGCTATTGACAGCACCAGACCACATGGAGAACAAAATCTTGTCTCATGGgtaagtgatgatctgtttacttgtaaatgatcgcgtgtttccctttttccaatatcttcacatcgttgtatgtctgttggcatcagacactaactacttg-----
||| || |||||||||||||| |||||  | ||| |||||||||||||||  || |||||||||||  |||| |||||||||||||| |||||| ||||||||                |     |||  | || | | |   ||  |     ||    ||||     |  |  || |       |    ||  |  |||     
TGATGTATATAGTTTTGGGGTAGTCTTCTTGGAGCTGATTACTGGCCGTAAAGCCATTGACAGCACTCGACCCCATGGAGAACAAAACCTTGTCACATGGgtag---------------ccctctaatctttgcttatctttattagtttggcatgcatacataacaatgggggtggtaatggtggtttttatttgtttgagcag

upper sequence: GRMZM2G140095_T03 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA08G47570.1 (Glycine max), 5'ss of exon 4
TGACGTGTATAGTTTTGGGGTTGTCTTGCTAGAGTTGATTACTGGCCGTAGGGCTATTGACAGCACCAGACCACATGGAGAACAAAATCTTGTCTCATGGgtaagtgatgatctgtttacttgtaaatgatcgcgtgtttccctttttccaatatcttcacatcgttgtatgtctgttggcatcagacactaactacttg
||| || |||||||||||||| |||||  ||||| |||||||||||||||  || ||||||||||||   || || |||||||| || |||||| |||||||        ||   ||  ||||| | |  |    |  ||          ||  |     ||   || ||||| |||| |   |||              
TGATGTATATAGTTTTGGGGTGGTCTTCTTAGAGCTGATTACTGGCCGTAAAGCAATTGACAGCACCCAGCCGCAGGGAGAACAGAACCTTGTCACATGGgttttcctctattctttctcttgtcatt--ttaattagtttggcaagcataaactaactgcagttttatatgtatgtttgtg-cag--------------

upper sequence: GRMZM2G140095_T03 (Zea mays), 5'ss of exon 4
lower sequence: Vv01s0146g00250.t01 (Vitis vinifera), 5'ss of exon 4
TGACGTGTATAGTTTTGGGGTTGTCTTGCTAGAGTTGATTACTGGCCGTAGGGCTATTGACAGCACCAGACCACATGGAGAACAAAATCTTGTCTCATGGgtaagtga-----------tgatctgtttactt--gtaaatgatcgcgtgtttccctttttccaatatcttcacatcgttgtatgtctgttggcatcagacactaactacttg-----------------------------------------------------------------------------
||| || || || || ||||| |||||  | ||| |||||||||| ||||  || ||||||||||||  ||| ||||||||||| ||||||||| |||||||||   |           |  | || || | |  |       | | ||    | | | |   | ||      ||||  | | ||  |||     ||        | | | |                                                                              
TGATGTCTACAGCTTCGGGGTGGTCTTCTTGGAGCTGATTACTGGACGTAAAGCCATTGACAGCACCCTACCCCATGGAGAACAGAATCTTGTCACATGGgtaatccactaaattcttgtagtgtggttgcctaagctgcctgtagtgtaggccacatgtctgactactgcaccatcact-tgtgcttgtgattttcctttctccatttccttttggggtttatataagtgcatgcatgtttgtggacaaacagtgcttttctcatatcttgtgttttatgtttttgcag

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|211067144|gb|FL332484.1|FL332484
EST:     -GGCTATTGACAGCACCAGACCACATGGAGAACAAAATCTTGTCTCATGG                         GCACGTCCTCTGTTTAACGACAGAAGAAAGCTCCCTAAGATGGCTGACCCG
genomic: GGGCTATTGACAGCACCAGACCACATGGAGAACAAAATCTTGTCTCATGGgtaagtgatg ... tggttggcagGCACGTCCTCTGTTTAACGACAGAAGAAAGCTCCCTAAGATGGCTGACCCG
EST: gi|211144004|gb|FL467378.1|FL467378
EST:     GGGCTATTGACAGCACCAGACCACATGGAGAACAAAATCTTGTCTCATGG                         GCACGTCCTCTGTTTAACGACAGAAGAAAGCTCCCTAAGATGGCTGACCCG
genomic: GGGCTATTGACAGCACCAGACCACATGGAGAACAAAATCTTGTCTCATGGgtaagtgatg ... tggttggcagGCACGTCCTCTGTTTAACGACAGAAGAAAGCTCCCTAAGATGGCTGACCCG
EST: gi|211365229|gb|FL351453.1|FL351453
EST:     GG-CTATTGACAGCACCAGACCACATGGAGAACAAAATCTTGTCTCATGG                         GCACGTCCTCTGTTTAACGACAGAAGAAAGCTCCCTAAGATGGCTGACCCG
genomic: GGGCTATTGACAGCACCAGACCACATGGAGAACAAAATCTTGTCTCATGGgtaagtgatg ... tggttggcagGCACGTCCTCTGTTTAACGACAGAAGAAAGCTCCCTAAGATGGCTGACCCG
EST: gi|211144003|gb|FL467377.1|FL467377
EST:     CCACATGGAGAACAAAATCTTGTYTCATGG                         GCACGTCCTCTGTTTAACGACAGAAGAAAGCTCCCTAAGATGGCTGACCCG
genomic: CCACATGGAGAACAAAATCTTGTCTCATGGgtaagtgatg ... tggttggcagGCACGTCCTCTGTTTAACGACAGAAGAAAGCTCCCTAAGATGGCTGACCCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGACGTGTATAGTTTTGGGGTTGTCTTGCTAGAGTTGATTACTGGCCGTAGGGCTATTGACAGCACCAGACCACATGGAGAACAAAATCTTGTCTCATGGgtaagtgatgatctgtttacttgtaaatgatcgcgtgtttccctttttccaatatcttcacatcgttgtatgtctgttggcatcagacactaactacttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA