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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatcttggatgtgtatctgtactctgtgtgtgtcattgccttttgttttctctaaagtaatcatataatgtgcattaaaacatgtgagagcccttgtagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTTCGTGGGGCCTCTTGGGCTGGATGTAGTGGTCTTGACCGCTCATCTGCAGATTACATCGG

Basic information

species Zea mays
transcript GRMZM2G149535_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149535_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g73450.1 (Oryza sativa), 3'ss of exon 3
---tgatcttg-gatgtgtatctgtactctgtgtgtgtcattgccttttgttttctctaaagta--atcatataatgtgcattaaaacatgtgagagcccttgtagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTTCGTGGGGCCTCTTGGGCTGGATGTAGTGGTCTTGACCGCTCATCTGCAGATTACATCGG
   || ||    || |||    | | || ||||| |||     ||| |||| |||||||  |||  | |||||  ||| |||||||  ||  | || |||||| ||||||||||||||||||| || ||||||||||| || |||||||||||||||||||||||||| || ||||||||||| ||||||||||| ||
ctgtgttccaacgaagtggtattatgctatgtgtatgtt----cctcttgtcttctctattgtagaaacatatgctgtacattaaag-at-cgggaacccttgcagGTTGCTATTGTTGTTGGTGGCGGCAATATCTTCCGCGGGGCCTCTTGGGCTGGATGTAGTGGACTCGACCGCTCATCAGCAGATTACATTGG

upper sequence: GRMZM2G149535_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA05G32340.1 (Glycine max), 3'ss of exon 3
----tgatcttggatgtgtatctgtactctgtgtgtgtcattgccttttgttttctctaaagtaatcatataatgtgcattaaaacatgtgagagcccttgtagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTTCGTGGGGCCTCTTGGGCTGGATGTAGTGGTCTTGACCGCTCATCTGCAGATTACATCGG
    |||| |||  ||    |  | ||  |     ||   ||       | ||| |     ||  ||| |   | ||  |||||  ||  |   |   ||  |||||||  | || ||||| || || || ||||| |||||  |||| ||||||||| ||||||| || |||||||||||||| ||||| || ||
tttatgatattgc-tgcaagttagaacatttgacttgaagttattcaaagctttttactg-gttttcagac--tttggtttaaacgattaggctgatgtttcagGTTGCACTGGTAGTTGGTGGGGGTAACATCTTCCGTGGATCCTCCTGGGCTGGAAGTAGTGGACTAGACCGCTCATCTGCGGATTATATTGG

upper sequence: GRMZM2G149535_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT3G18680.1 (Arabidopsis thaliana), 3'ss of exon 3
tgatcttggatgtg-tatctgtactctg--tgtgtgtcattgccttttgttttctctaaagtaatcatataatgtgcattaaaacatgtgagagccctt--gtagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTTCGTGGGGCCTCTTGGGCTGGATGTAGTGGTCTTGACCGCTCATCTGCAGATTACATCGG
     ||  |  |  |||  |    | |    ||||||   | | ||     ||  |  | |  |  | |    |   |   | | | | |   |  |    ||||||||||| |||||||| || || ||||||||||||||  |  | |||||||| || ||||| ||||| ||||| ||||| ||||| |||||
----tttaaacatactatacggcaacagatcatgtgtctgggtcattaagaatcattgcaatg-ttgtgtgtgctctgtctgatcttcttacgcctttacaatagGTTGCTATAGTTGTTGGAGGAGGAAATATCTTTCGTGGATCTACCTGGGCTGGGTGCAGTGGCCTTGATCGCTCCTCTGCTGATTATATCGG

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|211408335|gb|FL400099.1|FL400099
EST:     CAATGGCTATTGCAAGAGAGGTTGCTTCTGTCACCAAGCTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGGTGGCAATATCTTTCGTGGGGCCTCTT
genomic: CAATGGCTATTGCAAGAGAGGTTGCTTCTGTCACCAAGCTAGGTGTAGAGgtgtgtcctc ... gcccttgtagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTTCGTGGGGCCTCTT
EST: gi|211217192|gb|FL385722.1|FL385722
EST:     CAATGGCTATTGCAAGAGAGGTTGCTTCTGTCACCAAGCTAGGTGTAGAG                         GTTGCTATTGTTGT
genomic: CAATGGCTATTGCAAGAGAGGTTGCTTCTGTCACCAAGCTAGGTGTAGAGgtgtgtcctc ... gcccttgtagGTTGCTATTGTTGT
EST: gi|211481824|gb|FL383632.1|FL383632
EST:     CAATGGCTATTGCAAGAGAGGTTGCTTCTGTCACCAAGCTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGGTGGCAATATCTTTCGTGGGGCCTCTTGGGCT
genomic: CAATGGCTATTGCAAGAGAGGTTGCTTCTGTCACCAAGCTAGGTGTAGAGgtgtgtcctc ... gcccttgtagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTTCGTGGGGCCTCTTGGGCT
EST: gi|211329721|gb|FL371074.1|FL371074
EST:     CAATGGCTATTGCAAGAGAGGTTGCTTCTGTCACCAAGCTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGG
genomic: CAATGGCTATTGCAAGAGAGGTTGCTTCTGTCACCAAGCTAGGTGTAGAGgtgtgtcctc ... gcccttgtagGTTGCTATTGTTGTTGGCGG
EST: gi|211119381|gb|FL414343.1|FL414343
EST:     CAATGGCTATTGCAAGAGAGGTTGCTTCTGTCACCAAGCTAGGTGTAGAG                         GTTGCTATTGTTGTTTGGCGGTGGC
genomic: CAATGGCTATTGCAAGAGAGGTTGCTTCTGTCACCAAGCTAGGTGTAGAGgtgtgtcctc ... gcccttgtagGTTGCTATTGTTGTT-GGCGGTGGC
EST: gi|211434254|gb|FL404586.1|FL404586
EST:     CAATGGCTATTGCAAGAGAGGTTGCTTCTGTCACCAAGCTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGGTGGCAATATCTTTCGTGGGGCCTCTTGGGCT
genomic: CAATGGCTATTGCAAGAGAGGTTGCTTCTGTCACCAAGCTAGGTGTAGAGgtgtgtcctc ... gcccttgtagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTTCGTGGGGCCTCTTGGGCT
EST: gi|71312662|gb|DR792853.1|DR792853
EST:     CAATGGCTATTGCAAGAGAGGTTGCTTCTGTCACCAAGCTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGGTGGCAATATCTTTCGTGGGGCCTCTTGGGCT
genomic: CAATGGCTATTGCAAGAGAGGTTGCTTCTGTCACCAAGCTAGGTGTAGAGgtgtgtcctc ... gcccttgtagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTTCGTGGGGCCTCTTGGGCT
EST: gi|78105364|gb|DV523782.1|DV523782
EST:     CAATGGCTATTGCAAGAGAGGTTGCTTCTGTCACCAAGCTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGG
genomic: CAATGGCTATTGCAAGAGAGGTTGCTTCTGTCACCAAGCTAGGTGTAGAGgtgtgtcctc ... gcccttgtagGTTGCTATTGTTGTTGGCGG
EST: gi|149000676|gb|EE037886.2|EE037886
EST:     CAATGGCTATTGCAAGAGAGGTTGCTTCTGTCACCAAGCTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGGTGGCAATATCTTTCGTGGGGCCTCTTGGGCT
genomic: CAATGGCTATTGCAAGAGAGGTTGCTTCTGTCACCAAGCTAGGTGTAGAGgtgtgtcctc ... gcccttgtagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTTCGTGGGGCCTCTTGGGCT

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: 29

ATTACAATGGCTATTGCAAGAGAGGTTGCTTCTGTCACCAAGCTAGGTGTAGAGgtgtgtcctc ... gcccttgtagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTTCGTGGGGCCTCTTGGGCTGGATGTAGTGGTCTTGACCGCTCATCTGCAGATTACATCGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 23

ATTACAATGGCTATTGCAAGAGAGGTTGCTTCTGTCACCAAGCTAGGTGTAGAGgtgtgtcctc ... gcccttgtagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTTCGTGGGGCCTCTTGGGCTGGATGTAGTGGTCTTGACCGCTCATCTGCAGATTACATCGG


Block sizes: 40 (upstream exon), 40 (downstream exon)
Score: 6

ATTACAATGGCTATTGCAAGAGAGGTTGCTTCTGTCACCAAGCTAGGTGTAGAGgtgtgtcctc ... gcccttgtagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTTCGTGGGGCCTCTTGGGCTGGATGTAGTGGTCTTGACCGCTCATCTGCAGATTACATCGG


Block sizes: 32 (upstream exon), 49 (downstream exon)
Score: 29

ATTACAATGGCTATTGCAAGAGAGGTTGCTTCTGTCACCAAGCTAGGTGTAGAGgtgtgtcctc ... gcccttgtagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTTCGTGGGGCCTCTTGGGCTGGATGTAGTGGTCTTGACCGCTCATCTGCAGATTACATCGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttctctaaagtaatcatataatgtgcattaaaacatgtgagagcccttgtagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTTCGTGGGGCCTCTTGGGCTGGATGTAGTGGTCTTGACCGCTCATCTGCAGATTACATCGG
     ctctaaa  putative branch site (score: 29)
                                              cccttgt  putative PPT
        taaagtaatcatataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatcttggatgtgtatctgtactctgtgtgtgtcattgccttttgttttctctaaagtaatcatataatgtgcattaaaacatgtgagagcccttgtagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTTCGTGGGGCCTCTTGGGCTGGATGTAGTGGTCTTGACCGCTCATCTGCAGATTACATCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - -ggatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgtga