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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtctcaagtctattctttaatcccttatggaatttttactgccatgttactgaatactgatctcttattcttctgtgccagAACCATATAAGGGACGATTTGCTACAGCCTGGAAAATTTGATGTGTGCGTGACTAGTTTTGAAATGGCAATCAAAGAAAAATCTGCGTTGAGGCGCTTCA

Basic information

species Zea mays
transcript AC235535.1_FGT001
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 6
----gttggtctcaagtctattctttaatcccttatg-gaatttttactgccatgttactgaatactgatctcttattcttctgtgccagAACCATATAAGGGACGATTTGCTACAGCCTGGAAAATTTGATGTGTGCGTGACTAGTTTTGAAATGGCAATCAAAGAAAAATCTGCGTTGAGGCGCTTCA
    |||    |    ||   |||  || |  |  |  |||    | |||   |  ||||||| | |    |   |||||  |  | |||||||||||||||||  |  |  | ||||| ||||||||||||||||| || |||||||||||||||||||||||||||||| || |  ||| ||| ||||
gttagtttacttagcctccgctctccaaccattcttatgaacaacttctgatgttgtactgaacatt----ttgcattctgtttggtcagAACCATATAAGGGAGAACCTATTGCAGCCAGGAAAATTTGATGTGTGTGTCACTAGTTTTGAAATGGCAATCAAAGAAAAAACTACACTGAAGCGTTTCA

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 6
gttggtctcaagtctattctttaatcccttatggaatttttactgccatgttactgaatactgatctcttattcttctgtgccagAACCATATAAGGGACGATTTGCTACAGCCTGGAAAATTTGATGTGTGCGTGACTAGTTTTGAAATGGCAATCAAAGAAAAATCTGCGTTGAGGCGCTTCA
||    | || ||    ||| | || | |  || | || ||  ||  || || || |   |  || | | || |||    | |||||||||||  ||||  ||||| ||   || || || ||||| || || || |||||||||||||||||||| ||||||||| |||| |||| ||| ||||
gtaatccccatgttatctctgtcattcat-gtgaacttcttg-tggtatattgctaa---catatttgtcatacttg---gtcagAACCATATCCGGGAAAATTTGTTAGTCCCAGGGAAGTTTGACGTCTGTGTTACTAGTTTTGAAATGGCAATTAAAGAAAAAACTGCATTGAAGCGTTTCA

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 6
--------------gttggtctcaagtctattctttaatcccttatggaatttttactgcc-atgttactgaatactgatctcttattcttctgtgccagAACCATATAAGGGACGATTTGCTACAGCCTGGAAAATTTGATGTGTGCGTGACTAGTTTTGAAATGGCAATCAAAGAAAAATCTGCGTTGAGGCGCTTCA
                ||  |  || |   |  |||||      |   |||  || || |  ||| |  ||  || || | |   ||   |      ||||| || ||||| || || || ||     |||| || ||||||||||| || |||||||||||||||| |||||| || || ||||| ||  |||| || |
gtaagactagcctttctgaaccaaattacttgttttaagattgcaattaatgcttgcttctgatgcttttgtctaatggttttaaataactg-----cagAAGCACATAAGAGAGGAGTTACTCGTTGCTGGTAAGTTTGATGTGTGTGTTACTAGTTTTGAAATGGTAATCAAGGAGAAGTCTGCTTTACGGCGATTTA

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|22491353|gb|BU051276.1|BU051276
EST:     TTTGCCCTATCCTACGTGCTGTGAAGTTCTTGGGCAATCCAGAAGAGCGG                         AACCATATAAGGGACGATTTGCTACAGCCT
genomic: TTTGCCCTATCCTACGTGCTGTGAAGTTCTTGGGCAATCCAGAAGAGCGGgttggtctca ... tctgtgccagAACCATATAAGGGACGATTTGCTACAGCCT
EST: gi|20300252|gb|BQ163195.1|BQ163195
EST:     TTTGCCCTATCCTACGTGCTGTGAAGTTCTTGGGCAATCCAGAAGAGCGG                         AACCATATAAGGGACGATTTGCTACAGCCTGGAAAATTTGATGTGTGCGTG
genomic: TTTGCCCTATCCTACGTGCTGTGAAGTTCTTGGGCAATCCAGAAGAGCGGgttggtctca ... tctgtgccagAACCATATAAGGGACGATTTGCTACAGCCTGGAAAATTTGATGTGTGCGTG
EST: gi|19350725|gb|BM895257.1|BM895257
EST:     TTTGCCCTATCCTACGTGCTGTGAAGTTCTTGGGCAATCCAGAAGAGCGG                         AACCATATAAGGGACGATTTGCTACAGCCTTGAAAATTTGATGTGTGCGTG
genomic: TTTGCCCTATCCTACGTGCTGTGAAGTTCTTGGGCAATCCAGAAGAGCGGgttggtctca ... tctgtgccagAACCATATAAGGGACGATTTGCTACAGCCTGGAAAATTTGATGTGTGCGTG
EST: gi|20300542|gb|BQ163485.1|BQ163485
EST:     TTTGCCCTATCCTACGTGCTGTGAAGTTCTTGGGCAATCCAGAAGAGCGG                         AACCATATAAGGGACGATTTGCTACAGCCTGGAAAATTTGATGTGTGCGTG
genomic: TTTGCCCTATCCTACGTGCTGTGAAGTTCTTGGGCAATCCAGAAGAGCGGgttggtctca ... tctgtgccagAACCATATAAGGGACGATTTGCTACAGCCTGGAAAATTTGATGTGTGCGTG
EST: gi|87153564|gb|DY398353.1|DY398353
EST:     TTTGCCCTATCCTACGTGCTGTGAAGTTCTTGGGCAATCCAGAAGAGCGG                         AACCATATAAGGGACGATTTGCTACAGCCTGGAAAATTTGATGTGTGCGTG
genomic: TTTGCCCTATCCTACGTGCTGTGAAGTTCTTGGGCAATCCAGAAGAGCGGgttggtctca ... tctgtgccagAACCATATAAGGGACGATTTGCTACAGCCTGGAAAATTTGATGTGTGCGTG

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: 250

GGTTGCGCCGAAGTCCACCCTTGGCAACTGGATGAAGGAAATCCAACGTTTTTGCCCTATCCTACGTGCTGTGAAGTTCTTGGGCAATCCAGAAGAGCGGgttggtctca ... tctgtgccagAACCATATAAGGGACGATTTGCTACAGCCTGGAAAATTTGATGTGTGCGTGACTAGTTTTGAAATGGCAATCAAAGAAAAATCTGCGTTGAGGCGCTTCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 109

GGTTGCGCCGAAGTCCACCCTTGGCAACTGGATGAAGGAAATCCAACGTTTTTGCCCTATCCTACGTGCTGTGAAGTTCTTGGGCAATCCAGAAGAGCGGgttggtctca ... tctgtgccagAACCATATAAGGGACGATTTGCTACAGCCTGGAAAATTTGATGTGTGCGTGACTAGTTTTGAAATGGCAATCAAAGAAAAATCTGCGTTGAGGCGCTTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 93

GGTTGCGCCGAAGTCCACCCTTGGCAACTGGATGAAGGAAATCCAACGTTTTTGCCCTATCCTACGTGCTGTGAAGTTCTTGGGCAATCCAGAAGAGCGGgttggtctca ... tctgtgccagAACCATATAAGGGACGATTTGCTACAGCCTGGAAAATTTGATGTGTGCGTGACTAGTTTTGAAATGGCAATCAAAGAAAAATCTGCGTTGAGGCGCTTCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 175

GGTTGCGCCGAAGTCCACCCTTGGCAACTGGATGAAGGAAATCCAACGTTTTTGCCCTATCCTACGTGCTGTGAAGTTCTTGGGCAATCCAGAAGAGCGGgttggtctca ... tctgtgccagAACCATATAAGGGACGATTTGCTACAGCCTGGAAAATTTGATGTGTGCGTGACTAGTTTTGAAATGGCAATCAAAGAAAAATCTGCGTTGAGGCGCTTCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggaatttttactgccatgttactgaatactgatctcttattcttctgtgccagAACCATATAAGGGACGATTTGCTACAGCCTGGAAAATTTGATGTGTGCGTGACTAGTTTTGAAATGGCAATCAAAGAAAAATCTGCGTTGAGGCGCTTCA
                            tactgat  putative branch site (score: 175)
                                  tctcttattcttctgt  CT-rich tract
     atttttact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtctcaagtctattctttaatcccttatggaatttttactgccatgttactgaatactgatctcttattcttctgtgccagAACCATATAAGGGACGATTTGCTACAGCCTGGAAAATTTGATGTGTGCGTGACTAGTTTTGAAATGGCAATCAAAGAAAAATCTGCGTTGAGGCGCTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA