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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggatttctcttgtctaatttatatttctgaactcatcagatgagtataacatcacatttttccacttttatggttcatgctcaaatttatttatagGGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAAGATTGCTGATCTGGGACTCGGTAGGGCTTTCACTGTGCCCATGAAAAGC

Basic information

species Zea mays
transcript GRMZM2G495626_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G495626_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g67160.1 (Oryza sativa), 3'ss of exon 2
gttggatt----tctcttg-tctaatttatatttctgaactcatcagatgagtataacatcacatttttccacttttatggttcatgctcaaattta------tttatagGGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAAGATTGCTGATCTGGGACTCGGTAGGGCTTTCACTGTGCCCATGAAAAGC
|||||| |    |||||   | | |||||| || |||  || |||||     || | |||  || || |  | |   |||||| || || |    |       ||| ||| ||||||||||||||||||||| |||| |||||||| ||||| ||| |||| ||||||||||| || || |||||||| |||||||| || |||||||||
gttggactctgttctctccctgtgatttatgttgctgggcttatcagccccatacagcattgcagttgttga-taacatggtttatacttattcctgctcaattttgtagTGATTTAAAGCCACAAAACCTGTTGGTCGACAAGGAAAAGGGGATATTGAAAATTGCTGATCTTGGGCTAGGTAGGGCGTTCACTGTTCCTATGAAAAGC

upper sequence: GRMZM2G495626_T03 (Zea mays), 3'ss of exon 2
lower sequence: EFJ19614 (Selaginella moellendorffii), 3'ss of exon 3
gttggatttctcttgtctaatttatatttctgaactcatcagatgagtataacatcacatttttccacttttatggttcatgctcaaatttatttatagGGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAAGATTGCTGATCTGGGACTCGGTAGGGCTTTCACTGTGCCCATGAAAAGC
                      ||| ||  | |  |  ||            | |   | ||||   ||| |    |||   |     |   |||  |||||  | ||||| |||||||| || || ||||||||||| || ||  | |||||||||||  ||||||||||  ||||||||||||| ||| |||| |||
---------------------gtattttcttaagtttttc------------cttggtagtttttttcttct----ttctaacgagtgtccttttgcagGGACCTCAAGCCGCAAAACCTTCTCGTCGACAAGGAGAAAGGAATCTTAAAGATTGCTGACTTGGGACTCGGCCGGGCTTTCACTGTTCCCTTGAAGAGC

upper sequence: GRMZM2G495626_T03 (Zea mays), 3'ss of exon 2
lower sequence: EFJ06603 (Selaginella moellendorffii), 3'ss of exon 3
gttggatttctcttgtctaatttatatttctgaactcatcagatgagtataacatcacatttttccacttttatggttcatgctcaaatttatttatagGGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAAGATTGCTGATCTGGGACTCGGTAGGGCTTTCACTGTGCCCATGAAAAGC
                                   |  |    | ||| |  | | |  ||||| |   ||| |      ||  |       |||  |||||  | ||||| |||||||| || || ||||||||||| || ||  | |||||||||||  ||||||||||  ||||||||||||| ||| |||| |||
----------------------------------gtattttcttaagtttttccttagtttttttcttctttctaacgagtgtcct------tttgcagGGACCTCAAGCCGCAAAACCTTCTCGTCGACAAGGAGAAAGGAATCTTAAAGATTGCTGACTTGGGACTCGGCCGGGCTTTCACTGTTCCCTTGAAGAGC

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|149101462|gb|EE187582.2|EE187582
EST:     CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCG                         GGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
genomic: CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCGgttggatttc ... ttatttatagGGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
EST: gi|74238747|gb|DT646661.1|DT646661
EST:     CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCG                         GGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
genomic: CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCGgttggatttc ... ttatttatagGGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
EST: gi|101398284|gb|EB821015.1|EB821015
EST:     CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCG                         GGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
genomic: CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCGgttggatttc ... ttatttatagGGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
EST: gi|211530153|gb|FL280582.1|FL280582
EST:     CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCG                         GGATTTAAAGCCA
genomic: CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCGgttggatttc ... ttatttatagGGATTTAAAGCCA
EST: gi|28568987|gb|CB280862.1|CB280862
EST:     CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCG                         GGATTTAAAGCCACAAAACCTGCTGGTGGAC
genomic: CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCGgttggatttc ... ttatttatagGGATTTAAAGCCACAAAACCTGCTGGTGGAC
EST: gi|71771339|gb|DR969276.1|DR969276
EST:     CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCG                         GGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
genomic: CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCGgttggatttc ... ttatttatagGGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
EST: gi|91055879|gb|EB166297.1|EB166297
EST:     CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCG                         GGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
genomic: CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCGgttggatttc ... ttatttatagGGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
EST: gi|87157025|gb|DY401814.1|DY401814
EST:     CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCG                         GGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
genomic: CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCGgttggatttc ... ttatttatagGGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
EST: gi|31612143|gb|CD568765.1|CD568765
EST:     CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCG                         GGATTTAAAGCCACAAAA
genomic: CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCGgttggatttc ... ttatttatagGGATTTAAAGCCACAAAA
EST: gi|91868821|gb|EB400169.1|EB400169
EST:     CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCG                         GGATTTAAAGC
genomic: CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCGgttggatttc ... ttatttatagGGATTTAAAGC
EST: gi|149085475|gb|EE174981.2|EE174981
EST:     CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCG                         GGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
genomic: CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCGgttggatttc ... ttatttatagGGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
EST: gi|71450237|gb|DR831287.1|DR831287
EST:     CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCG                         GGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
genomic: CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCGgttggatttc ... ttatttatagGGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
EST: gi|91872387|gb|EB402344.1|EB402344
EST:     CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCG                         GGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
genomic: CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCGgttggatttc ... ttatttatagGGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
EST: gi|148931796|gb|EC877239.2|EC877239
EST:     CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCCCCG                         GGATTTAAAGC
genomic: CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCGgttggatttc ... ttatttatagGGATTTAAAGC
EST: gi|88755350|gb|DY539491.1|DY539491
EST:     CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCG                         GGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
genomic: CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCGgttggatttc ... ttatttatagGGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
EST: gi|22542240|gb|BU092678.1|BU092678
EST:     CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCG                         GGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
genomic: CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCGgttggatttc ... ttatttatagGGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
EST: gi|78085720|gb|DV514113.1|DV514113
EST:     CAGTTATGCAAAGGAGTTGCACACTGCCATACCCATGGTGTCCTTCACCG                         GGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTG
genomic: CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCGgttggatttc ... ttatttatagGGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTG
EST: gi|76294289|gb|DV033857.1|DV033857
EST:     CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCG                         GGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
genomic: CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCGgttggatttc ... ttatttatagGGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
EST: gi|26559291|gb|CA831526.1|CA831526
EST:     CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCG                         GGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
genomic: CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCGgttggatttc ... ttatttatagGGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
EST: gi|32929643|gb|CF034455.1|CF034455
EST:     CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCG                         GGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
genomic: CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCGgttggatttc ... ttatttatagGGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
EST: gi|94473282|gb|EB702240.1|EB702240
EST:     CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCG                         GGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
genomic: CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCGgttggatttc ... ttatttatagGGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
EST: gi|211362664|gb|FL128442.1|FL128442
EST:     CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCG                         GGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
genomic: CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCGgttggatttc ... ttatttatagGGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
EST: gi|32928347|gb|CF033159.1|CF033159
EST:     CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCG                         GGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
genomic: CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCGgttggatttc ... ttatttatagGGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
EST: gi|91878648|gb|EB408605.1|EB408605
EST:     AGTTATGCAAAGGAGTTTGCCCACTGCCATAGCCATGGTGTCCTTCACCG                         GGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
genomic: AGTTATGCAAAGGAGTT-GCACACTGCCATAGCCATGGTGTCCTTCACCGgttggatttc ... ttatttatagGGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
EST: gi|76289583|gb|DV029151.1|DV029151
EST:     CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCG                         GGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
genomic: CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCGgttggatttc ... ttatttatagGGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
EST: gi|149110996|gb|EE294495.2|EE294495
EST:     CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCG                         GGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
genomic: CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCGgttggatttc ... ttatttatagGGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
EST: gi|71313277|gb|DR793172.1|DR793172
EST:     CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCG                         GGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
genomic: CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCGgttggatttc ... ttatttatagGGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
EST: gi|71431609|gb|DR812659.1|DR812659
EST:     CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCG                         GGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA
genomic: CAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCGgttggatttc ... ttatttatagGGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAA

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: 244

AATTTCCTGTATCAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCGgttggatttc ... ttatttatagGGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAAGATTGCTGATCTGGGACTCGGTAGGGCTTTCACTGTGCCCATGAAAAGC


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 51

AATTTCCTGTATCAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCGgttggatttc ... ttatttatagGGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAAGATTGCTGATCTGGGACTCGGTAGGGCTTTCACTGTGCCCATGAAAAGC


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 33

AATTTCCTGTATCAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCGgttggatttc ... ttatttatagGGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAAGATTGCTGATCTGGGACTCGGTAGGGCTTTCACTGTGCCCATGAAAAGC


Block sizes: 46 (upstream exon), 44 (downstream exon)
Score: 21

AATTTCCTGTATCAGTTATGCAAAGGAGTTGCACACTGCCATAGCCATGGTGTCCTTCACCGgttggatttc ... ttatttatagGGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAAGATTGCTGATCTGGGACTCGGTAGGGCTTTCACTGTGCCCATGAAAAGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtataacatcacatttttccacttttatggttcatgctcaaatttatttatagGGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAAGATTGCTGATCTGGGACTCGGTAGGGCTTTCACTGTGCCCATGAAAAGC
  gtataac  putative branch site (score: 21)
                                            tttattt  putative PPT
                                       tcaaatttatttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggatttctcttgtctaatttatatttctgaactcatcagatgagtataacatcacatttttccacttttatggttcatgctcaaatttatttatagGGATTTAAAGCCACAAAACCTGCTGGTGGACAAGGAGAAGGGTATACTGAAGATTGCTGATCTGGGACTCGGTAGGGCTTTCACTGTGCCCATGAAAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT