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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTCAACCATCTGAAAACCCTGCACATAAATGGGGTGGTCTCGGAGAGGTCCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAAgtatgcttgccttatcttgacatcctcctgaagtttgttttttcttggactgtgtattgatgcatgtttgtttctgtgactgaattgatttattttgttggcttttcattttattgtttcttttgttttag

Basic information

species Zea mays
transcript GRMZM2G087212_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G087212_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os11g07910.1 (Oryza sativa), 5'ss of exon 2
TGTCAACCATCTGAAAACCCTGCACATAAATGGGGTGGTCTCGGAGAGGTCCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAAgtatgcttgccttatcttgacatcctcctgaagtttgttttttcttggactgtgtattgatgcatgtttgtttctgtgactgaattgatttattttgttggcttttcattttattgtttcttttgttttag
||||| |||||||||||||| ||||| ||||||||||||||||||||||||||||| || ||||||||||| ||||||||| | |||||||||||  |||||| | |   ||| ||   | | ||||||  | ||| |||  | ||||| |||| ||  ||| |||||  ||   |  ||| ||  |||||    ||     ||| ||||  | |      ||||||||||
TGTCAGCCATCTGAAAACCCCGCACACAAATGGGGTGGTCTCGGAGAGGTCCTTGGCGGCAATGAGCTGATCGATAGTCAGGTTGATATAAAGTTTTTAAgtaagttgatcttttc---ataccctccttgattttatttacttttggaatgtgcatcaatgtatgttcctt---gcaact-aaccgattt-ccctgaccattttacattaaact----tctttgttttag

upper sequence: GRMZM2G087212_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA08G20100.1 (Glycine max), 5'ss of exon 2
TGTCAACCATCTGAAAACCCTGCACATAAATGGGGTGGTCTCGGAGAGGTCCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAAgtatgcttgccttatcttgacatcctcctgaagtttgttttttcttggactgtgtattgatgcatgtttgtttctgtgactgaattg-atttattttgttggcttttcattttattgtttcttttgttttag
|| |   || |||  || |||||||| |||||||||||||| || |||||||| ||||| ||||| || |||||||| ||  | || ||||||||| || |||||   |  |  |     ||||||       ||| |||  |   |  |  |   ||||   |   | | ||       |   ||  | ||| ||| |  |                              
TGCCGTTCACCTGGTAATCCTGCACACAAATGGGGTGGTCTTGGTGAGGTCCTGGGTGGCAATGAACTCATTGATAGCCAACTTGAGATAAAGTTCCTAGgtatggaggtttcttt----catcct------atttatttcataa-gacccatcagttgaca-aaactggctttaacagttattttataattaatttttaag------------------------------

upper sequence: GRMZM2G087212_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA12G29120.1 (Glycine max), 5'ss of exon 2
TGTCAACCATCTGAAAACCCTGCACATAAATGGGGTGGTCTCGGAGAGGTCCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAAgtatg----cttgccttatcttgacatcctcctgaagtttgttttttcttggactgtgtattgatgcatgtttgtttctgtgactgaattgatttattttgttggcttttcattttattgtttcttttgttttag
|| |  ||| |||  ||  ||||||| |||||||||||||| || |||||||| ||||| |||||||| |||||||| ||  | || ||||||||| || |||||     ||   | ||| |       || | |    | |   |      |||| |  || |  ||  ||| |||   | | |   || |                                           
TGCCGTCCACCTGGTAATACTGCACACAAATGGGGTGGTCTTGGTGAGGTCCTGGGTGGCAATGAGCTCATTGATAGCCAACTTGAGATAAAGTTCCTAGgtatggaggtttctttcatcctatttatttcataagacctatcagtagacaaactg-gctttaa--cagattttttttaattatttttttaag------------------------------------------

upper sequence: GRMZM2G087212_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA08G13370.1 (Glycine max), 5'ss of exon 2
-TGTCAACCATCTGAAAACCCTGCACATAAATGGGGTGGTCTCGGAGAGGTCCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAAgtatg------cttgccttatcttgacatcctcctgaagtttgttttttcttggactgtgtattgatgcatgtttgtttctgtgactgaattgatttattttgttggcttttcattttattgtttcttttgttttag
   || |  |  ||  |   ||||||| |||||||||||||| || |||||||| ||||| |||||||| || ||||| || || || |||||||||  |||||||        ||   ||   ||   | |     |     ||   ||     |||| |  || ||| ||  |  | | |                                                        
CCATCTAGTAG-TGCTAGTGCTGCACACAAATGGGGTGGTCTTGGTGAGGTCCTGGGTGGCAATGAGCTCATCGATAGCCAAATTGAAATAAAGTTCCAAAgtatgaaggtttctgttgtactatgtatttcatagaagagccgtcagttgacaaactg-gctttaatggatactattgttttcag----------------------------------------------------

upper sequence: GRMZM2G087212_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA05G30210.1 (Glycine max), 5'ss of exon 2
-TGTCAACCATCTGAAAACCCTGCACATAAATGGGGTGGTCTCGGAGAGGTCCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAAgtatgcttgccttatcttgacatcctcctgaagtttgttttttcttggactgtgtattgatgc--atgtttgtttctgtgactgaattgatttattttgttggcttttcattttattgtttcttttgttttag
   || |  |  ||  |   ||||||| |||||||||||||| || |||||||| ||||| |||||||| || ||||| ||  | || || ||||||  |||||||   |  |  |    ||    |  | || |        | |||||  |   | ||      |||  || |  |||                                                      
CCATCTAGTAG-TGCTAGTGCTGCACACAAATGGGGTGGTCTTGGTGAGGTCCTGGGTGGCAATGAGCTCATCGATAGCCAACTTGAAATTAAGTTCCAAAgtatgaaggtttctttcgtactatgtatttaa-tagaagagctgttggatggcaaaatggctttaatgcatgctattgttttcag------------------------------------------------

upper sequence: GRMZM2G087212_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT1G10950.1 (Arabidopsis thaliana), 5'ss of exon 2
TGTCAACCATCTGAAAACCCTGCACATAAATGGGGTGGTCTCGGAGAGGTCCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAAgtatgcttgccttatcttgacatcctcctgaagtttgttttttcttggactgtgtattgat-gcatgtttgtttctgtgactgaattgatttattttgttggcttttcattttattgtttcttttgttttag
|| |  ||||||| ||||  ||  || |||||||||||||| || || || || |||||||||||||||||||| ||| |||| |  ||||| ||||| |||| | ||     ||  | | |        ||| || |||||  |   | |    | | || | |  || ||   | |     | ||    ||  || |  | ||||                         
TGCCGCCCATCTGGAAACAATGTTCACAAATGGGGTGGTCTTGGTGAAGTTCTAGGTGGAAATGAGCTGATTGACAGTGAGATTGCGATAAAATTCATGAgtacgttt---caattcttatac-------aagcttctttttcatactagttaacagttatcgtacattcgtacttattctctagttacaataccttttctgttttttccacag------------------

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|32932214|gb|CF037026.1|CF037026
EST:     CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAA                         AAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGG
genomic: CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAAgtatgcttgc ... tttgttttagAAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGG
EST: gi|32932817|gb|CF037629.1|CF037629
EST:     CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAA                         AAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGG
genomic: CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAAgtatgcttgc ... tttgttttagAAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGG
EST: gi|211326237|gb|FL421004.1|FL421004
EST:     CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAA                         AAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGG
genomic: CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAAgtatgcttgc ... tttgttttagAAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGG
EST: gi|29543705|gb|CB604085.1|CB604085
EST:     CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAA                         AAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGG
genomic: CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAAgtatgcttgc ... tttgttttagAAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGG
EST: gi|71313654|gb|DR793406.1|DR793406
EST:     CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAA                         AAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGG
genomic: CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAAgtatgcttgc ... tttgttttagAAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGG
EST: gi|148939673|gb|EC884332.2|EC884332
EST:     CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAA                         AAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGG
genomic: CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAAgtatgcttgc ... tttgttttagAAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGG
EST: gi|211343700|gb|FL394270.1|FL394270
EST:     CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAA                         AAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGG
genomic: CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAAgtatgcttgc ... tttgttttagAAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGG
EST: gi|211140426|gb|FL390015.1|FL390015
EST:     CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAA                         AAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGA
genomic: CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAAgtatgcttgc ... tttgttttagAAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGA
EST: gi|18649711|gb|BM498530.1|BM498530
EST:     CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGCTCATAA                         AAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAA
genomic: CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAAgtatgcttgc ... tttgttttagAAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAA
EST: gi|78087321|gb|DV515714.1|DV515714
EST:     CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAA                         AAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGG
genomic: CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAAgtatgcttgc ... tttgttttagAAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGG
EST: gi|211511643|gb|FL407274.1|FL407274
EST:     CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAA                         AAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGG
genomic: CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAAgtatgcttgc ... tttgttttagAAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGG
EST: gi|18649080|gb|BM497899.1|BM497899
EST:     CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAA                         AAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGG
genomic: CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAAgtatgcttgc ... tttgttttagAAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGG
EST: gi|211317119|gb|FL381345.1|FL381345
EST:     CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAA                         AAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGG
genomic: CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAAgtatgcttgc ... tttgttttagAAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGG
EST: gi|211369216|gb|FL412418.1|FL412418
EST:     CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAA                         AAAATGTGGACA
genomic: CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAAgtatgcttgc ... tttgttttagAAAATGTGGACA
EST: gi|211410531|gb|FL375648.1|FL375648
EST:     CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAA                         AAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGG
genomic: CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAAgtatgcttgc ... tttgttttagAAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGG
EST: gi|149088767|gb|EE177890.2|EE177890
EST:     CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAA                         AAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGG
genomic: CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAAgtatgcttgc ... tttgttttagAAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGG
EST: gi|19351785|gb|BM896317.1|BM896317
EST:     CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAA                         AAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGG
genomic: CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAAgtatgcttgc ... tttgttttagAAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGG
EST: gi|87153936|gb|DY398725.1|DY398725
EST:     CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAA                         AAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGG
genomic: CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAAgtatgcttgc ... tttgttttagAAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGG
EST: gi|19350701|gb|BM895233.1|BM895233
EST:     ATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAA                         AAAATGTGGNCAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGG
genomic: ATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAAgtatgcttgc ... tttgttttagAAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGG
EST: gi|211051804|gb|FL416956.1|FL416956
EST:     CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAA                         AAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGG
genomic: CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAAgtatgcttgc ... tttgttttagAAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGG
EST: gi|149107593|gb|EE189475.2|EE189475
EST:     CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAA                         AAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGG
genomic: CCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAAgtatgcttgc ... tttgttttagAAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGG

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: 39 (upstream exon), 49 (downstream exon)
Score: 142

TGTCAACCATCTGAAAACCCTGCACATAAATGGGGTGGTCTCGGAGAGGTCCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAAgtatgcttgc ... tttgttttagAAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGGTTCAGCAATTTGCTAATGCCATTGAAAACTCATATTGGTTTGAGCTTTT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 112

TGTCAACCATCTGAAAACCCTGCACATAAATGGGGTGGTCTCGGAGAGGTCCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAAgtatgcttgc ... tttgttttagAAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGGTTCAGCAATTTGCTAATGCCATTGAAAACTCATATTGGTTTGAGCTTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 114

TGTCAACCATCTGAAAACCCTGCACATAAATGGGGTGGTCTCGGAGAGGTCCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAAgtatgcttgc ... tttgttttagAAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGGTTCAGCAATTTGCTAATGCCATTGAAAACTCATATTGGTTTGAGCTTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 168

TGTCAACCATCTGAAAACCCTGCACATAAATGGGGTGGTCTCGGAGAGGTCCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAAgtatgcttgc ... tttgttttagAAAATGTGGACAAGGGGGCCATTTGCACAATTGAACTTGATGTTCAAAAGGTTCAGCAATTTGCTAATGCCATTGAAAACTCATATTGGTTTGAGCTTTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTCAACCATCTGAAAACCCTGCACATAAATGGGGTGGTCTCGGAGAGGTCCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAAgtatgcttgccttatcttgacatcctcctgaagtttgttttttcttggactgtgtattgatgcatgtttgtttctgtgactgaattgatttattttgttggcttttcattttattgtttcttttgttttag

- - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT