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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacatatagttgttcctcaaaaaagggacgtcaaatagttagtttatatatgcagacatattacttatgagttatgataattctcttctgttttcttgcagGCGGACAAGCAAAGACATTGATGTTTGTTCAAATTAATCCGGATACTGAATCATATTCAGAAACAATAAGCACTTTGAAGTTTGCTGAAAGGGTTTCTGG

Basic information

species Zea mays
transcript GRMZM2G323622_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G323622_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g54080.1 (Oryza sativa), 3'ss of exon 17
gtaacatatagttgttcctcaaaaaagggacgtcaaatagttagtttatatatgcagacatattacttatgagttatgataattctcttctgttttcttgcagGCGGACAAGCAAAGACATTGATGTTTGTTCAAATTAATCCGGATACTGAATCATATTCAGAAACAATAAGCACTTTGAAGTTTGCTGAAAGGGTTTCTGG
                          |  || |  | | |||  |  || | | |    |||   ||||  ||||    |||  ||  |  | ||||||| ||| ||||||||||||||| | |||||||||||||| || || |||| |||||||||||||||||| ||||| ||||| || ||||||||||||||||||||
--------------------------gtaacatatagttgttgatagatgtgtacgtggatag-gcttactagtttgcctaa--cttatgcgctttcttgtagGTGGACAAGCAAAGACACTAATGTTTGTTCAAATAAACCCTGATATTGAATCATATTCAGAAACCATAAGTACTTTAAAATTTGCTGAAAGGGTTTCTGG

upper sequence: GRMZM2G323622_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA05G35130.1 (Glycine max), 3'ss of exon 15
gtaacatatagttgttcctcaaaaaagggacgtcaaatagttag---tttatatatgcagacatattacttatgagttatgataattctcttctgttttcttgca--gGCGGACAAGCAAAGACATTGATGTTTGTTCAAATTAATCCGGATACTGAATCATATTCAGAAACAATAAGCACTTTGAAGTTTGCTGAAAGGGTTTCTGG
     | ||  || ||| |||     |  | |||| ||   | |    || | |||| |||    || |||||||  | |||   || ||||   |||| |||||  || |  ||||| |||||| | |||||||||||||||||| | ||       |||||||| |||||| | |||||||| |||||||||||||||||||||||
---gtaaatctttattcatcatt--tgttatgtcacatgccttgaatcttttctatgtagat---tttcttatgatctttgactcttgtctttgattttattgcacagGTGACCAAGCGAAGACACTCATGTTTGTTCAAATTAATTCAGACGTAAGTTCATATTCTGAAACACTGAGCACTTTAAAGTTTGCTGAAAGGGTTTCTGG

upper sequence: GRMZM2G323622_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA05G37800.1 (Glycine max), 3'ss of exon 17
----------------------gtaacatatagttgttcctcaaaaaagggacgtcaaatag----ttagtttatatatgcagacat-attactta-tgagttatgataattctcttctgttttcttg-cagGCGGACAAGCAAAGACATTGATGTTTGTTCAAATTAATCCGGATACTGAATCATATTCAGAAACAATAAGCACTTTGAAGTTTGCTGAAAGGGTTTCTGG
                        ||  || |||  ||  |  |    |   | |    | |    ||  ||||   ||   |   | ||  |||| | | ||   |||  | | | |  | |   ||  ||| || ||||| || ||  | |||||||| ||  ||||||| |||  ||  |||||||| |||||  ||||||| ||||||||||||||| ||||||||||
gtaattgttgccattattggtatcaatttacagt-attgttatatttggtttcatttgtttgcattttgatttaagcatattgcagtcatggcttactaaattgcaatagctttgtccgttgtatatgatagGTGGTCAAGCGAAAACCCTTATGTTTGTACAGCTTAATCCTGATGTTGCTTCATATTCTGAAACTGTAAGCACCTTGAAGTTTGCTGAACGGGTTTCTGG

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|67024383|gb|CO453132.1|CO453132
EST:     TGTTCCTTATCGAAACAGCAAGCTGACTCAAGTTCTACAGAGCTCTTTAG                         GCGGACAAGCAAAGACACTGATGTTTGTTCAAATTAATCCGGATACTGAAT
genomic: TGTTCCTTATCGAAACAGCAAGCTGACTCAAGTTCTACAGAGCTCTTTAGgtaacatata ... tttcttgcagGCGGACAAGCAAAGACATTGATGTTTGTTCAAATTAATCCGGATACTGAAT
EST: gi|211413818|gb|FL421627.1|FL421627
EST:     TGTTCCTTATCGAAACAGCAAGCTGACTCAAGTTCTACAGAGCTCTTTAG                         GCGGACAAGCAAAGACACTGATGTTTGTTCAAATTAATCCGGATACTGAAT
genomic: TGTTCCTTATCGAAACAGCAAGCTGACTCAAGTTCTACAGAGCTCTTTAGgtaacatata ... tttcttgcagGCGGACAAGCAAAGACATTGATGTTTGTTCAAATTAATCCGGATACTGAAT
EST: gi|50323766|gb|CO518892.1|CO518892
EST:     TGTTCCTTATCGAAACAGCAAGCTGACTCAAGTTCTACAGAGCTCTTTAG                         GCGGACAAGCAA
genomic: TGTTCCTTATCGAAACAGCAAGCTGACTCAAGTTCTACAGAGCTCTTTAGgtaacatata ... tttcttgcagGCGGACAAGCAA
EST: gi|211423503|gb|FL387499.1|FL387499
EST:     TGTTCCTTATCGAAACAGCAAGCTGACTCAAGTTCTACAGAGCTCTTTAG                         GCGGACAAGCAAAGACACTGATGTTTGTTCAAATTAATCCGGATACTGAAT
genomic: TGTTCCTTATCGAAACAGCAAGCTGACTCAAGTTCTACAGAGCTCTTTAGgtaacatata ... tttcttgcagGCGGACAAGCAAAGACATTGATGTTTGTTCAAATTAATCCGGATACTGAAT
EST: gi|211097361|gb|FL388137.1|FL388137
EST:     TGTTCCTTATCGAAACAGCAAGCTGACTCAAGTTCTACAGAGCTCTTTAG                         GCGGACAAGCAAAGACACTGATGTTTGTTCAAATTAATCCGGATACTGAAT
genomic: TGTTCCTTATCGAAACAGCAAGCTGACTCAAGTTCTACAGAGCTCTTTAGgtaacatata ... tttcttgcagGCGGACAAGCAAAGACATTGATGTTTGTTCAAATTAATCCGGATACTGAAT
EST: gi|211133186|gb|FL313064.1|FL313064
EST:     TGTTCCTTATCGAAACAGCAAGCTGACTCAAGTTCTACAGAGCTCTTTAG                         GCGGACAAGCAAAGACATTGATGTTTGTTCAAATTAATCCGGATACTGAAT
genomic: TGTTCCTTATCGAAACAGCAAGCTGACTCAAGTTCTACAGAGCTCTTTAGgtaacatata ... tttcttgcagGCGGACAAGCAAAGACATTGATGTTTGTTCAAATTAATCCGGATACTGAAT

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: 433

CTCTCTGCTCTGGGTGATGTGATTTTTGCTTTGGCACAGAAAAATGCTCATGTTCCTTATCGAAACAGCAAGCTGACTCAAGTTCTACAGAGCTCTTTAGgtaacatata ... tttcttgcagGCGGACAAGCAAAGACATTGATGTTTGTTCAAATTAATCCGGATACTGAATCATATTCAGAAACAATAAGCACTTTGAAGTTTGCTGAAAGGGTTTCTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 66

CTCTCTGCTCTGGGTGATGTGATTTTTGCTTTGGCACAGAAAAATGCTCATGTTCCTTATCGAAACAGCAAGCTGACTCAAGTTCTACAGAGCTCTTTAGgtaacatata ... tttcttgcagGCGGACAAGCAAAGACATTGATGTTTGTTCAAATTAATCCGGATACTGAATCATATTCAGAAACAATAAGCACTTTGAAGTTTGCTGAAAGGGTTTCTGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 56

CTCTCTGCTCTGGGTGATGTGATTTTTGCTTTGGCACAGAAAAATGCTCATGTTCCTTATCGAAACAGCAAGCTGACTCAAGTTCTACAGAGCTCTTTAGgtaacatata ... tttcttgcagGCGGACAAGCAAAGACATTGATGTTTGTTCAAATTAATCCGGATACTGAATCATATTCAGAAACAATAAGCACTTTGAAGTTTGCTGAAAGGGTTTCTGG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 297

CTCTCTGCTCTGGGTGATGTGATTTTTGCTTTGGCACAGAAAAATGCTCATGTTCCTTATCGAAACAGCAAGCTGACTCAAGTTCTACAGAGCTCTTTAGgtaacatata ... tttcttgcagGCGGACAAGCAAAGACATTGATGTTTGTTCAAATTAATCCGGATACTGAATCATATTCAGAAACAATAAGCACTTTGAAGTTTGCTGAAAGGGTTTCTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatgcagacatattacttatgagttatgataattctcttctgttttcttgcagGCGGACAAGCAAAGACATTGATGTTTGTTCAAATTAATCCGGATACTGAATCATATTCAGAAACAATAAGCACTTTGAAGTTTGCTGAAAGGGTTTCTGG
                                  ttctcttctgttttct  CT-rich tract
           atattacttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacatatagttgttcctcaaaaaagggacgtcaaatagttagtttatatatgcagacatattacttatgagttatgataattctcttctgttttcttgcagGCGGACAAGCAAAGACATTGATGTTTGTTCAAATTAATCCGGATACTGAATCATATTCAGAAACAATAAGCACTTTGAAGTTTGCTGAAAGGGTTTCTGG

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