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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctatctgctttgacttgtcggtttgtgttcatagtggcatataaggtgagcgtcgtttcactgatctgtgcagGGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAG

Basic information

species Zea mays
transcript GRMZM2G375002_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G375002_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g58730.2 (Oryza sativa), 3'ss of exon 5
-------gtatgctatctgctttgacttgt-cggtttgtgttcatagtggcatataaggtgagcgtcgtttcactgatctgtgcagGGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAG
               | |||||  | || |   | ||     ||| ||  || |     | |   |  |||  || |||  || ||||||||||||||||||| || |||||||| || || ||||| ||||||||||||||||| ||||| 
gtattcaaagcttagtttgcttgtatttttgttgcttcccagcattgttacacaagtcattaaaattattttgctaatcaatgtagGGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAA

upper sequence: GRMZM2G375002_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ16760 (Selaginella moellendorffii), 3'ss of exon 5
gtatgctatctgctttgacttgtcggtttgtgttcatagtggcatataaggtgagcgtcgtttcactgatctgtgcagGGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAG
             |   |    |  |||| ||||| |  |  |  ||     ||  ||| | |   || | |   ||||||||||| |||||||||| ||| |||||||| ||||||||||| || || || ||||||||||||
------------gtacaaaaaatatgtttttgttcgttctttctaatgccccga--gtcatattcgtgtttt--ccagGGCGAAGAACTGAGGAAGCAAATCGGTGCTGCTGCCTACATCGAGTGTAGCTCGAAAACCCAGCAG

upper sequence: GRMZM2G375002_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ09765 (Selaginella moellendorffii), 3'ss of exon 5
gtatgctatctgctttgacttgtcggtttgtgttcatagtggcatataaggtgagcgtcgtttcactgatctgtgcagGGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAG
   |  || |  ||||| ||||||   | |  |   || ||  || ||   | |||  |||    |||       |||||||||||||||||||||| ||| || || || ||||||||||| || || ||||| || ||||||
--gtcataacacctttg-cttgtc---tcgactctttactga-attta---taagccacgtgatgctg-------cagGGCGAAGAGCTGAGGAAGCAAATCGGGGCGGCTGCCTACATCGAGTGTAGCTCAAAGACGCAGCAG

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|211386802|gb|FL474297.1|FL474297
EST:     AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAG                         GGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
genomic: AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAGgtatgctatc ... atctgtgcagGGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
EST: gi|5055407|gb|AI734294.1|AI734294
EST:     AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAG                         GGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
genomic: AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAGgtatgctatc ... atctgtgcagGGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
EST: gi|6973662|gb|AW438236.1|AW438236
EST:     AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAG                         GGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
genomic: AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAGgtatgctatc ... atctgtgcagGGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
EST: gi|71302719|gb|DR787472.1|DR787472
EST:     AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAG                         GGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
genomic: AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAGgtatgctatc ... atctgtgcagGGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
EST: gi|16926993|gb|BM080061.1|BM080061
EST:     AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAG                         GGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
genomic: AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAGgtatgctatc ... atctgtgcagGGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
EST: gi|8383272|gb|BE056215.1|BE056215
EST:     AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAG                         GGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
genomic: AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAGgtatgctatc ... atctgtgcagGGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
EST: gi|67018898|gb|CO447647.1|CO447647
EST:     AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAG                         GGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
genomic: AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAGgtatgctatc ... atctgtgcagGGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
EST: gi|16925708|gb|BM078776.1|BM078776
EST:     AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAG                         GGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
genomic: AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAGgtatgctatc ... atctgtgcagGGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
EST: gi|5510771|gb|AI857155.1|AI857155
EST:     AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAG                         GGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
genomic: AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAGgtatgctatc ... atctgtgcagGGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
EST: gi|211356949|gb|FL222513.1|FL222513
EST:     AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAG                         GGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
genomic: AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAGgtatgctatc ... atctgtgcagGGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
EST: gi|78107806|gb|DV526224.1|DV526224
EST:     AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAG                         GGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
genomic: AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAGgtatgctatc ... atctgtgcagGGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
EST: gi|37391181|gb|CF632832.1|CF632832
EST:     AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAG                         GGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
genomic: AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAGgtatgctatc ... atctgtgcagGGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
EST: gi|16918068|gb|BM073562.1|BM073562
EST:     AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAG                         GGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
genomic: AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAGgtatgctatc ... atctgtgcagGGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
EST: gi|16925543|gb|BM078611.1|BM078611
EST:     AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAG                         GGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
genomic: AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAGgtatgctatc ... atctgtgcagGGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
EST: gi|4646692|gb|AI491552.2|AI491552
EST:     AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCNCTGCCCAG                         GGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
genomic: AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAGgtatgctatc ... atctgtgcagGGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
EST: gi|28930831|gb|CB334192.1|CB334192
EST:     AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAG                         GGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
genomic: AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAGgtatgctatc ... atctgtgcagGGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
EST: gi|10697643|gb|BE997367.1|BE997367
EST:     AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAG                         GGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
genomic: AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAGgtatgctatc ... atctgtgcagGGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
EST: gi|28986594|gb|CB351213.1|CB351213
EST:     AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAG                         GGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
genomic: AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAGgtatgctatc ... atctgtgcagGGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
EST: gi|101401925|gb|EB822590.1|EB822590
EST:     AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAG                         GGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
genomic: AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAGgtatgctatc ... atctgtgcagGGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
EST: gi|18174791|gb|BM350179.1|BM350179
EST:     AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAG                         GGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
genomic: AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAGgtatgctatc ... atctgtgcagGGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
EST: gi|32828059|gb|CD967737.1|CD967737
EST:     AGCAGTTTTTTGTTGATCACCCAGGTGCTGTTCCAATTTCCACTGCCCAG                         GGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT
genomic: AGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAGgtatgctatc ... atctgtgcagGGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGT

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), 45 (downstream exon)
Score: 169

ATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAGgtatgctatc ... atctgtgcagGGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 205

ATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAGgtatgctatc ... atctgtgcagGGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 275

ATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAGgtatgctatc ... atctgtgcagGGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 238

ATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAGgtatgctatc ... atctgtgcagGGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggtttgtgttcatagtggcatataaggtgagcgtcgtttcactgatctgtgcagGGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAG
                                        cactgat  putative branch site (score: 238)
                    atataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctatctgctttgacttgtcggtttgtgttcatagtggcatataaggtgagcgtcgtttcactgatctgtgcagGGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC