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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatacaagataaaagaaaatttaggccttgcatgattattagcattttgcaatgcagcttacctaggtttactgccttgataagctttcgtttatgctcctaagttgtgatttacaaggacaattttgctaccttgtagAAAATACCTCTGATTTTTGGTGAAAGACGCCCAGGTGATGCAGAGATTCTGTTTTCAGAGACTACTAAAGCAGAGAGGGAGCTTAACTGGAA

Basic information

species Zea mays
transcript GRMZM2G469523_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G469523_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g28730.1 (Oryza sativa), 3'ss of exon 7
gtatacaagataaaagaaaatttaggccttgcatgattattagcattttgcaatgcagcttacctaggtttactgccttgataagctttcgtttatgctcctaagttgtgatttacaaggacaattttgctaccttgtagAAAATACCTCTGATTTTTGGTGAAAGACGCCCAGGTGATGCAGAGATTCTGTTTTCAGAGACTACTAAAGCAGAGAGGGAGCTTAACTGGAA
| ||||| ||||||||| | || || | | | || | |||| ||| | || | || ||| | |||| | | ||||| |||||| ||||||||| |||| ||||||||| |||||||| |||||||| |||||| || |||||||||||| ||| || ||||||||
-----------------------------taggtgattgttagcattt---attgtagataaaatgctttctccagcttgcgcgccttgccaggat-ttgctttgttcttattttttttaattgctgtgcta-------gAAAATTCCTCTGATTATTGGCCCAAGACGCCCTGGTGATGCGGAGATTCTATTTTCATTACCTGCTAAAGCAGAGAAGGAACTCAACTGGAA
















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|211051082|gb|FL157953.1|FL157953
EST:     ACATCTGTGCTGGAGATTGTTAAAGCATTTGAGAAGGCTTCTGGGAAG                         AAAATACCTCTGATTTTTGGTGAAAGACGCCCAGGTGATGCAGAGATTCTG
genomic: ACATCTGTGCTGGAGATTGTTAAAGCATTTGAGAAGGCTTCTGGGAAGgtatacaaga ... taccttgtagAAAATACCTCTGATTTTTGGTGAAAGACGCCCAGGTGATGCAGAGATTCTG
EST: gi|32837892|gb|CD977570.1|CD977570
EST:     ACATCTGTGCTGGAGATTGTTAAAGCATTTGAGAAGGCTTCTGGGAAG                         AAAATACCTCTGATTTTTGGTGAAAGGCGCCCAGGTGATGCAGAGATTCTG
genomic: ACATCTGTGCTGGAGATTGTTAAAGCATTTGAGAAGGCTTCTGGGAAGgtatacaaga ... taccttgtagAAAATACCTCTGATTTTTGGTGAAAGACGCCCAGGTGATGCAGAGATTCTG
EST: gi|60352711|gb|DN219684.1|DN219684
EST:     CATCTGTGCTGGAGATTGTTAAAGCATTTGAGAAGGCTTCTGGGAAG                         AAAATACCTCTGATTTTTGGTGAAAGACGCCCAGGTGATGCAGAGATTCTG
genomic: CATCTGTGCTGGAGATTGTTAAAGCATTTGAGAAGGCTTCTGGGAAGgtatacaaga ... taccttgtagAAAATACCTCTGATTTTTGGTGAAAGACGCCCAGGTGATGCAGAGATTCTG
EST: gi|71773386|gb|DR971290.1|DR971290
EST:     TTAAAGCATTTGAGAAGGCTTCTGGGAAG                         AAAATACCTCTGATTTTTGGTGAAAGACGCCCAGGTGATGCAGAGATTCTG
genomic: TTAAAGCATTTGAGAAGGCTTCTGGGAAGgtatacaaga ... taccttgtagAAAATACCTCTGATTTTTGGTGAAAGACGCCCAGGTGATGCAGAGATTCTG
EST: gi|67025401|gb|CO454150.1|CO454150
EST:     GCATTTGAGAAGGCTTCTGGGAAG                         AAAATACCTCTGATTTTTGGTGAAAGACGCCCAGGCGATGCAGAGATTCTG
genomic: GCATTTGAGAAGGCTTCTGGGAAGgtatacaaga ... taccttgtagAAAATACCTCTGATTTTTGGTGAAAGACGCCCAGGTGATGCAGAGATTCTG
EST: gi|24774129|gb|CA409383.1|CA409383
EST:     CTGGAGATTGTTAAAGCATTTGAGAAGGCTTCTGGGAAG                         AAAATACCTCTGATTTTTGGTGAAAGACGCCCAGGTGATGCAGAGATTCTG
genomic: CTGGAGATTGTTAAAGCATTTGAGAAGGCTTCTGGGAAGgtatacaaga ... taccttgtagAAAATACCTCTGATTTTTGGTGAAAGACGCCCAGGTGATGCAGAGATTCTG
EST: gi|67025022|gb|CO453771.1|CO453771
EST:     GTACATCTGTGCTGGAGATTGTTAAAGCATTTGAGAAGGCTTCTGGGAAG                         AAAATACCTCTGATTTTTGGTGAAAGACGCCCAGGTGATGCAGAGATTCTG
genomic: GTACATCTGTGCTGGAGATTGTTAAAGCATTTGAGAAGGCTTCTGGGAAGgtatacaaga ... taccttgtagAAAATACCTCTGATTTTTGGTGAAAGACGCCCAGGTGATGCAGAGATTCTG
EST: gi|71425858|gb|DR806940.1|DR806940
EST:     GTACATCTGTGCTGGAGATTGTTAAAGCATTTGAGAAGGCTTCTGGGAAG                         AAAATACCTCTGATTTTTGGTGAAAGACGCCCAGGTGATGCAGAGATTCTG
genomic: GTACATCTGTGCTGGAGATTGTTAAAGCATTTGAGAAGGCTTCTGGGAAGgtatacaaga ... taccttgtagAAAATACCTCTGATTTTTGGTGAAAGACGCCCAGGTGATGCAGAGATTCTG
EST: gi|32846391|gb|CD986072.1|CD986072
EST:     TACATCTGTGCTGGAGATTGTTAAAGCATTTGAGAAGGCTTCTGGGAAG                         AAAATACCTCTGATTTTTGGTGAAAGGCGCCCAGGTGATGCAGAGATTCTG
genomic: TACATCTGTGCTGGAGATTGTTAAAGCATTTGAGAAGGCTTCTGGGAAGgtatacaaga ... taccttgtagAAAATACCTCTGATTTTTGGTGAAAGACGCCCAGGTGATGCAGAGATTCTG
EST: gi|50326912|gb|CO522038.1|CO522038
EST:     AGATTGTTAAAGCATTTGAGAAGGCTTCTGGGAAG                         A
genomic: AGATTGTTAAAGCATTTGAGAAGGCTTCTGGGAAGgtatacaaga ... taccttgtag-
EST: gi|50326912|gb|CO522038.1|CO522038
EST:     AGATTGTTAAAGCATTTGAGAAGGCTTCTGGGAAG                         A
genomic: AGATTGTTAAAGCATTTGAGAAGGCTTCTGGGAAGgtatacaaga ... taccttgtag-
EST: gi|24773701|gb|CA408955.1|CA408955
EST:     GTACATCTGTGCTGGAGATTGTTAAAGCATTTGAGAAGGCTTCTGGGAAG                         AAAATACCTCTGATTTTTGGTGAAAGACGCCCAGGTGATGCAGAGATTCTG
genomic: GTACATCTGTGCTGGAGATTGTTAAAGCATTTGAGAAGGCTTCTGGGAAGgtatacaaga ... taccttgtagAAAATACCTCTGATTTTTGGTGAAAGACGCCCAGGTGATGCAGAGATTCTG
EST: gi|5739820|gb|AI947510.1|AI947510
EST:     GTACATCTGTGCTGGAGATTGTTAAAGCATTTGAGAAGGCTTCTGGGAAG                         AAAATACCTCTGATTTTTGGTGAAAGACGCCCAGGTGATGCAGAGATTCTG
genomic: GTACATCTGTGCTGGAGATTGTTAAAGCATTTGAGAAGGCTTCTGGGAAGgtatacaaga ... taccttgtagAAAATACCTCTGATTTTTGGTGAAAGACGCCCAGGTGATGCAGAGATTCTG
EST: gi|33468176|gb|CF245225.1|CF245225
EST:     GTACATCTGTGCTGGAGATTGTTAAAGCATTTGAGAAGGCTTCTGGGAAG                         AAAATACCTCTGATTTTTGGTGAAAGACGCCCAGGTGATGCAGAGATTCTG
genomic: GTACATCTGTGCTGGAGATTGTTAAAGCATTTGAGAAGGCTTCTGGGAAGgtatacaaga ... taccttgtagAAAATACCTCTGATTTTTGGTGAAAGACGCCCAGGTGATGCAGAGATTCTG
EST: gi|60354871|gb|DN221844.1|DN221844
EST:     GTACATCTGTGCTGGAGATTGTTAAAGCATTTGAGAAGGCTTCTGGGAAG                         AAAATACCTCTGATTTTTGGTGAAAGACGCCCAGGTGATGCAGAGATTCTG
genomic: GTACATCTGTGCTGGAGATTGTTAAAGCATTTGAGAAGGCTTCTGGGAAGgtatacaaga ... taccttgtagAAAATACCTCTGATTTTTGGTGAAAGACGCCCAGGTGATGCAGAGATTCTG
EST: gi|83278826|gb|DV942834.1|DV942834
EST:     GTGCTGGAGATTGTAAAAGCATTTGAGAAGGCTTCTGGGAAG                         AAAATACCTCTGATTTTTGGTGAAAGACGCCCAGGTGATGCAGAGATTCTG
genomic: GTGCTGGAGATTGTTAAAGCATTTGAGAAGGCTTCTGGGAAGgtatacaaga ... taccttgtagAAAATACCTCTGATTTTTGGTGAAAGACGCCCAGGTGATGCAGAGATTCTG
EST: gi|74245905|gb|DT653819.1|DT653819
EST:     GTACATCTGTGCTGGAGATTGTTAAAGCATTTGAGAAGGCTTCTGGGAAG                         AAAATACCTCTGATTTTTGGTGAAAGACGCCCAGGTGATGCAGAGATTCTG
genomic: GTACATCTGTGCTGGAGATTGTTAAAGCATTTGAGAAGGCTTCTGGGAAGgtatacaaga ... taccttgtagAAAATACCTCTGATTTTTGGTGAAAGACGCCCAGGTGATGCAGAGATTCTG

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), 49 (downstream exon)
Score: 758

GGTGTGAAGCGTACAACCTTGGAACCGGAAGAGGTACATCTGTGCTGGAGATTGTTAAAGCATTTGAGAAGGCTTCTGGGAAGgtatacaaga ... taccttgtagAAAATACCTCTGATTTTTGGTGAAAGACGCCCAGGTGATGCAGAGATTCTGTTTTCAGAGACTACTAAAGCAGAGAGGGAGCTTAACTGGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 873

GGTGTGAAGCGTACAACCTTGGAACCGGAAGAGGTACATCTGTGCTGGAGATTGTTAAAGCATTTGAGAAGGCTTCTGGGAAGgtatacaaga ... taccttgtagAAAATACCTCTGATTTTTGGTGAAAGACGCCCAGGTGATGCAGAGATTCTGTTTTCAGAGACTACTAAAGCAGAGAGGGAGCTTAACTGGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 538

GGTGTGAAGCGTACAACCTTGGAACCGGAAGAGGTACATCTGTGCTGGAGATTGTTAAAGCATTTGAGAAGGCTTCTGGGAAGgtatacaaga ... taccttgtagAAAATACCTCTGATTTTTGGTGAAAGACGCCCAGGTGATGCAGAGATTCTGTTTTCAGAGACTACTAAAGCAGAGAGGGAGCTTAACTGGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 965

GGTGTGAAGCGTACAACCTTGGAACCGGAAGAGGTACATCTGTGCTGGAGATTGTTAAAGCATTTGAGAAGGCTTCTGGGAAGgtatacaaga ... taccttgtagAAAATACCTCTGATTTTTGGTGAAAGACGCCCAGGTGATGCAGAGATTCTGTTTTCAGAGACTACTAAAGCAGAGAGGGAGCTTAACTGGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttcgtttatgctcctaagttgtgatttacaaggacaattttgctaccttgtagAAAATACCTCTGATTTTTGGTGAAAGACGCCCAGGTGATGCAGAGATTCTGTTTTCAGAGACTACTAAAGCAGAGAGGGAGCTTAACTGGAA
                                       ttttgct  CT-rich tract
 atttacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatacaagataaaagaaaatttaggccttgcatgattattagcattttgcaatgcagcttacctaggtttactgccttgataagctttcgtttatgctcctaagttgtgatttacaaggacaattttgctaccttgtagAAAATACCTCTGATTTTTGGTGAAAGACGCCCAGGTGATGCAGAGATTCTGTTTTCAGAGACTACTAAAGCAGAGAGGGAGCTTAACTGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT