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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGTAGATTGCCGTATCTGTGGTGATCCTAACTCAGTGCTTCGTTTTGCTTTTATCGAGTTTGCTGATGACGgtagtagcttttgacatgacaattgtcatttgatagtcctatgttggtgtaagaaacattctttaacaaagctgtttttctgcag

Basic information

species Zea mays
transcript GRMZM5G814159_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G814159_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os06g35030.3 (Oryza sativa), 5'ss of exon 4
GTGGTAGATTGCCGTATCTGTGGTGATCCTAACTCAGTGCTTCGTTTTGCTTTTATCGAGTTTGCTGATGACGgtagtagcttttgacatgacaattgtcatttgatagtcctatgttggtgtaagaaacattctttaacaaagctg---tttttctgcag
||||||||||||||||| |||||||| || || |||||||| |||||||| |||||||||||||| ||||| |||| |     |  ||   | ||||  ||| |   |  |  || ||| || ||||| || || | ||  ||| |    |||| ||||||
GTGGTAGATTGCCGTATATGTGGTGACCCAAATTCAGTGCTGCGTTTTGCCTTTATCGAGTTTGCCGATGATGgtaat-----tcaacgcaa-aatt--catctcgcatgctcat-ttgttgcaagaagcaatcctgaatgaagttccctttttcctgcag

upper sequence: GRMZM5G814159_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA08G18810.1 (Glycine max), 5'ss of exon 4
GTGGTAGATTGCCGTATCTGTGGTGATCCTAACTCAGTGCTTCGTTTTGCTTTTATCGAGTTTGCTGATGACGgtagtagcttttgacatgacaattgt---catttgatagtcctatgttggtgta---agaaac---attctttaacaaagctgtttttctgcag------------------------
||  | |||||||| || |||||||||||  | ||||| || |||||||||||| | |||||||| |||||  || |||  | ||| | ||  |||  |   || || | | ||   |        |   ||| ||   ||| |||  |||  |   |||  ||||                         
GTAATTGATTGCCGAATTTGTGGTGATCCACATTCAGTTCTCCGTTTTGCTTTTGTTGAGTTTGCAGATGA--GT-

upper sequence: GRMZM5G814159_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv19s0176g00140.t01 (Vitis vinifera), 5'ss of exon 4
GTGGTAGATTGCCGTATCTGTGGTGATCCTAACTCAGTGCTTCGTTTTGCTTTTATCGAGTTTGCTGATGACGgtag-------tagctttt---gacatgacaattgtcat-ttgatagtcct--atgttggtgtaagaaacattctttaacaaa-------gctgtttttctgcag
|| || ||||| ||  | |||||||||||  | ||||| ||||||||||| ||| | ||||||||||||||  |||        ||  ||||   | ||| ||| || ||   ||| |  |  |  | ||  || || |  |  ||   || || |       | | | | ||  |||
GTTGTTGATTGTCGAGTTTGTGGTGATCCGCATTCAGTTCTTCGTTTTGCATTTGTGGAGTTTGCTGATGAGCgtaagtttttttatttttttgggccataacatttttctcattggtgttgttgaaagtgtgtctatgtgatttttcatatcatactcacttggtatatgtcaacag

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|32911170|gb|CF015982.1|CF015982
EST:     TGATCCTAACTCAGTGCTTCGTTTTGCTTTTATCGAGTTTGCTGATGACG                         TTGCTGCACAAGCAGCACTAGCACTTGGTGGAACCGTGCTTGGCTTTTATA
genomic: TGATCCTAACTCAGTGCTTCGTTTTGCTTTTATCGAGTTTGCTGATGACGgtagtagctt ... ttttctgcagTTGCTGCACAAGCAGCACTAGCACTTGGTGGAACCGTGCTTGGCTTTTATC
EST: gi|71772178|gb|DR970115.1|DR970115
EST:     AGTTTGCTGATGACG                         TTGCTGCACAAGCAGCACTAGCACTTGGTGGAACCGTGCTTGGCTTTTATC
genomic: AGTTTGCTGATGACGgtagtagctt ... ttttctgcagTTGCTGCACAAGCAGCACTAGCACTTGGTGGAACCGTGCTTGGCTTTTATC
EST: gi|110932361|gb|EE152587.1|EE152587
EST:     TTATGGAGTTTGCTGATGACG                         TTGCTGCACAAGCAGCACTAGCACTTGGTGGAACCGTGCTTGGCTTTTATC
genomic: TTATCGAGTTTGCTGATGACGgtagtagctt ... ttttctgcagTTGCTGCACAAGCAGCACTAGCACTTGGTGGAACCGTGCTTGGCTTTTATC
EST: gi|18164011|gb|BM333850.1|BM333850
EST:     TGATCCTAACTCAGTGCTTCGTTTTGCTTTTATCGAGTTTGCTGATGACG                         TTGCTGCACAAGCAGCACTAGCACTTGGTGGAACCGTGCTTGGCTTTTATC
genomic: TGATCCTAACTCAGTGCTTCGTTTTGCTTTTATCGAGTTTGCTGATGACGgtagtagctt ... ttttctgcagTTGCTGCACAAGCAGCACTAGCACTTGGTGGAACCGTGCTTGGCTTTTATC
EST: gi|6851486|gb|AW352496.1|AW352496
EST:     TGATCCTAACTCAGTGCTTCGTTTTGCTTTTATCGAGTTTGCTGATGACG                         TTGCTGCACAAGCAGCACTAGCACTTGGTGGAACCGTGCTTGGCTTTTATC
genomic: TGATCCTAACTCAGTGCTTCGTTTTGCTTTTATCGAGTTTGCTGATGACGgtagtagctt ... ttttctgcagTTGCTGCACAAGCAGCACTAGCACTTGGTGGAACCGTGCTTGGCTTTTATC
EST: gi|31909457|gb|CD650928.1|CD650928
EST:     TGATCCTAACTCAGTGCTTCGTTTTGCTTTTATCGAGTTTGCTGATGACG                         TTGCTGCACAAGCAGCACTAGCACTTGGTGG
genomic: TGATCCTAACTCAGTGCTTCGTTTTGCTTTTATCGAGTTTGCTGATGACGgtagtagctt ... ttttctgcagTTGCTGCACAAGCAGCACTAGCACTTGGTGG
EST: gi|32914736|gb|CF019548.1|CF019548
EST:     TGATCCTAACTCAGTGCTTCGTTTTGCTTTTATCGAGTTTGCTGATGACG                         TTGCTGCACAAGCAGCACTAGCACTTGGTGGAACCGTGCTTGGCTTTTATC
genomic: TGATCCTAACTCAGTGCTTCGTTTTGCTTTTATCGAGTTTGCTGATGACGgtagtagctt ... ttttctgcagTTGCTGCACAAGCAGCACTAGCACTTGGTGGAACCGTGCTTGGCTTTTATC
EST: gi|37395891|gb|CF635231.1|CF635231
EST:     TGATCCTAACTCAGTGCTTCGTTTTGCTTTTATCGAGTTTGCTGATGACG                         TTGCTGCACAATCAGCACTAGCACTTGGTGGAACCGTGCTTGGCTTTTATC
genomic: TGATCCTAACTCAGTGCTTCGTTTTGCTTTTATCGAGTTTGCTGATGACGgtagtagctt ... ttttctgcagTTGCTGCACAAGCAGCACTAGCACTTGGTGGAACCGTGCTTGGCTTTTATC
EST: gi|67021641|gb|CO450390.1|CO450390
EST:     TGATCCTAACTCAGTGCTTCGTTTTGCTTTTATCGAGTTTGCTGATGACG                         TTGCTGCACAAGCAGCACTAGCACTTGGTGGAACCGTGCTTGGCTTTTATC
genomic: TGATCCTAACTCAGTGCTTCGTTTTGCTTTTATCGAGTTTGCTGATGACGgtagtagctt ... ttttctgcagTTGCTGCACAAGCAGCACTAGCACTTGGTGGAACCGTGCTTGGCTTTTATC
EST: gi|149099389|gb|EE185429.2|EE185429
EST:     TTTGCTGATGACG                         TTGCTGCACAAGCAGCACTAGCACTTGGTGGAACCGTGCTTGGCTTTTATC
genomic: TTTGCTGATGACGgtagtagctt ... ttttctgcagTTGCTGCACAAGCAGCACTAGCACTTGGTGGAACCGTGCTTGGCTTTTATC
EST: gi|31362976|gb|CD447333.1|CD447333
EST:     TGATCCTAACTCAGTGCTTCGTTTTGCTTTTATCGAGTTTGCTGATGACG                         TTGCTGCACAAGCAGCACTAGCACTTGGTGGAACCGTGCTTGGCTTTTATC
genomic: TGATCCTAACTCAGTGCTTCGTTTTGCTTTTATCGAGTTTGCTGATGACGgtagtagctt ... ttttctgcagTTGCTGCACAAGCAGCACTAGCACTTGGTGGAACCGTGCTTGGCTTTTATC

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: 48 (upstream exon), 47 (downstream exon)
Score: 268

GTGGTAGATTGCCGTATCTGTGGTGATCCTAACTCAGTGCTTCGTTTTGCTTTTATCGAGTTTGCTGATGACGgtagtagctt ... ttttctgcagTTGCTGCACAAGCAGCACTAGCACTTGGTGGAACCGTGCTTGGCTTTTATCCTGTCAAGGTTCTGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 208

GTGGTAGATTGCCGTATCTGTGGTGATCCTAACTCAGTGCTTCGTTTTGCTTTTATCGAGTTTGCTGATGACGgtagtagctt ... ttttctgcagTTGCTGCACAAGCAGCACTAGCACTTGGTGGAACCGTGCTTGGCTTTTATCCTGTCAAGGTTCTGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 261

GTGGTAGATTGCCGTATCTGTGGTGATCCTAACTCAGTGCTTCGTTTTGCTTTTATCGAGTTTGCTGATGACGgtagtagctt ... ttttctgcagTTGCTGCACAAGCAGCACTAGCACTTGGTGGAACCGTGCTTGGCTTTTATCCTGTCAAGGTTCTGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 342

GTGGTAGATTGCCGTATCTGTGGTGATCCTAACTCAGTGCTTCGTTTTGCTTTTATCGAGTTTGCTGATGACGgtagtagctt ... ttttctgcagTTGCTGCACAAGCAGCACTAGCACTTGGTGGAACCGTGCTTGGCTTTTATCCTGTCAAGGTTCTGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGTAGATTGCCGTATCTGTGGTGATCCTAACTCAGTGCTTCGTTTTGCTTTTATCGAGTTTGCTGATGACGgtagtagcttttgacatgacaattgtcatttgatagtcctatgttggtgtaagaaacattctttaacaaagctgtttttctgcag

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