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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acagtagtgatggtagcaattgcctgctaataccagcatatacaagttactttcttacaaatgtatcgaagagtttagttgaccaatgttttgttatcagGTTTTTGGAAATGACAGAAAATATTGGTTCATCCCTGCATATTCAGAAGAGGATCTGAGAAGAATTCCAGCTCTACAGGGTCTTGATTATCCTGTCAGTG

Basic information

species Zea mays
transcript GRMZM2G027307_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G027307_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g58960.1 (Oryza sativa), 3'ss of exon 6
acagtagtgatggtagcaattgcctgctaataccagcatat--acaagttactttcttacaaatgtatcgaagagtttagttgaccaatgttttgttatcagGTTTTTGGAAATGACAGAAAATATTGGTTCATCCCTGCATATTCAGAAGAGGATCTGAGAAGAATTCCAGCTCTACAGGGTCTTGATTATCCTGTCAGTG
 |  |   ||    |  | |   || |    | |  ||| |  | |||| |   |      ||   |  | | || | |  | | || |||| ||||| |||||||||||||||||||  |  ||||||||||||||||| || |||||||||||| |||||||||| |||| ||||||||| |||||||| ||||||||  
cccattccgacatcactactgaact-cagtcagccacatgtgaataagtgaacataactttaacaaaaggcaaagct-aactaaacagtgttctgttaccagGTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCTGCGTACTCAGAAGAGGATTTGAGAAGAATGCCAGTTCTACAGGGCCTTGATTACCCTGTCAGGA
















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|5895854|gb|AW037100.1|AW037100
EST:     CAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAG                         GTTTTTGGAAATGACAGAAAATATTGGTTCATCCCTGCATATTCAGAAGAG
genomic: CAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAGgttaatctgt ... ttgttatcagGTTTTTGGAAATGACAGAAAATATTGGTTCATCCCTGCATATTCAGAAGAG
EST: gi|26455295|gb|CA826878.1|CA826878
EST:     CAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAG                         GTTTTTGGAAATGACAGAAAATATTGGTTCATCCCTGCATATTCAGAAGAG
genomic: CAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAGgttaatctgt ... ttgttatcagGTTTTTGGAAATGACAGAAAATATTGGTTCATCCCTGCATATTCAGAAGAG
EST: gi|149110923|gb|EE294421.2|EE294421
EST:     CAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAG                         GTTTTTGGAAATGACAGAAAATATTGGTTCATCCCTGCATATTCAGAAGAG
genomic: CAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAGgttaatctgt ... ttgttatcagGTTTTTGGAAATGACAGAAAATATTGGTTCATCCCTGCATATTCAGAAGAG
EST: gi|89250234|gb|DY622020.1|DY622020
EST:     CAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGTTCAG                         GTTTTTGGAAATAACAGAAAATATTGGTTCATCCCTGCATATTCAGAAGAG
genomic: CAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAGgttaatctgt ... ttgttatcagGTTTTTGGAAATGACAGAAAATATTGGTTCATCCCTGCATATTCAGAAGAG
EST: gi|148933152|gb|EC876791.2|EC876791
EST:     CAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAG                         GTTTTTGGAAATGACAGAAAATATTGGTTCATCCCTGCATATTCAGAAGAG
genomic: CAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAGgttaatctgt ... ttgttatcagGTTTTTGGAAATGACAGAAAATATTGGTTCATCCCTGCATATTCAGAAGAG
EST: gi|89106782|gb|DY576999.1|DY576999
EST:     CAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAG                         GTTTTTGGAAATGACAGAAAATATTGGTTCATCCCTGCATATTCAGAAGAG
genomic: CAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAGgttaatctgt ... ttgttatcagGTTTTTGGAAATGACAGAAAATATTGGTTCATCCCTGCATATTCAGAAGAG
EST: gi|50326450|gb|CO521576.1|CO521576
EST:     CAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAG                         GTTTTTGGAAATGACAGAAAATATTGGTTCATCCCTGCATATTCAGAAGAG
genomic: CAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAGgttaatctgt ... ttgttatcagGTTTTTGGAAATGACAGAAAATATTGGTTCATCCCTGCATATTCAGAAGAG
EST: gi|61119340|gb|DN560301.1|DN560301
EST:     CAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAG                         GTTTTTGGAAATGACAGAAAATATTGGTTCATCCCTGCATATTCAGAAGAG
genomic: CAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAGgttaatctgt ... ttgttatcagGTTTTTGGAAATGACAGAAAATATTGGTTCATCCCTGCATATTCAGAAGAG
EST: gi|71306346|gb|DR789325.1|DR789325
EST:     CAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAG                         GTTTTTGGAAATGACAGAAAATATTGGTTCATCCCTGCATATTCAGAAGAG
genomic: CAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAGgttaatctgt ... ttgttatcagGTTTTTGGAAATGACAGAAAATATTGGTTCATCCCTGCATATTCAGAAGAG
EST: gi|21390493|gb|BQ528542.1|BQ528542
EST:     CAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAG                         GTTTTTGGAAATGACAGAAAATATTGGTTCATCCCTGCATATTCAGAAGAG
genomic: CAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAGgttaatctgt ... ttgttatcagGTTTTTGGAAATGACAGAAAATATTGGTTCATCCCTGCATATTCAGAAGAG
EST: gi|5917413|gb|AW054204.1|AW054204
EST:     CAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAG                         GTTTTTGGAAATGACAGAAAATATTGGTTCATCCCTGCATATTCAGAAGAG
genomic: CAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAGgttaatctgt ... ttgttatcagGTTTTTGGAAATGACAGAAAATATTGGTTCATCCCTGCATATTCAGAAGAG
EST: gi|101399436|gb|EB821590.1|EB821590
EST:     TTGGCCGGAAGAGGAATTTTGTTCAG                         GTTTTGGGAAATGACAGAAAATATTGGTTCATCCCTGCATATTCAGAAGAG
genomic: TTGGCCGGAAGAGGAATTTTGCTCAGgttaatctgt ... ttgttatcagGTTTTTGGAAATGACAGAAAATATTGGTTCATCCCTGCATATTCAGAAGAG
EST: gi|89106688|gb|DY576905.1|DY576905
EST:     CAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAG                         GTTTTTGGAAATGACAGAAAATATTGGTTCATCCCTGCATATTCAGAAGAG
genomic: CAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAGgttaatctgt ... ttgttatcagGTTTTTGGAAATGACAGAAAATATTGGTTCATCCCTGCATATTCAGAAGAG
EST: gi|110220233|gb|EC902131.1|EC902131
EST:     TTGGCCGGAAGAGGAATTTTGTTCAG                         G-TTTTGGAAATGACAAGAAAATAATGGTTCATCCCTCCATATTCAGAAGA
genomic: TTGGCCGGAAGAGGAATTTTGCTCAGgttaatctgt ... ttgttatcagGTTTTTGGAAATGAC-AGAAAATATTGGTTCATCCCTGCATATTCAGAAGA
EST: gi|149072485|gb|EE160763.2|EE160763
EST:     CAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAG                         GTTTTTGGAAATGACAGAAAATATTGGTTCATCCCTGCATATTCAGAAGAG
genomic: CAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAGgttaatctgt ... ttgttatcagGTTTTTGGAAATGACAGAAAATATTGGTTCATCCCTGCATATTCAGAAGAG

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: 445

GCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAGgttaatctgt ... ttgttatcagGTTTTTGGAAATGACAGAAAATATTGGTTCATCCCTGCATATTCAGAAGAGGATCTGAGAAGAATTCCAGCTCTACAGGGTCTTGATTATCCTGTCAGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 531

GCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAGgttaatctgt ... ttgttatcagGTTTTTGGAAATGACAGAAAATATTGGTTCATCCCTGCATATTCAGAAGAGGATCTGAGAAGAATTCCAGCTCTACAGGGTCTTGATTATCCTGTCAGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 722

GCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAGgttaatctgt ... ttgttatcagGTTTTTGGAAATGACAGAAAATATTGGTTCATCCCTGCATATTCAGAAGAGGATCTGAGAAGAATTCCAGCTCTACAGGGTCTTGATTATCCTGTCAGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 472

GCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAGgttaatctgt ... ttgttatcagGTTTTTGGAAATGACAGAAAATATTGGTTCATCCCTGCATATTCAGAAGAGGATCTGAGAAGAATTCCAGCTCTACAGGGTCTTGATTATCCTGTCAGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttactttcttacaaatgtatcgaagagtttagttgaccaatgttttgttatcagGTTTTTGGAAATGACAGAAAATATTGGTTCATCCCTGCATATTCAGAAGAGGATCTGAGAAGAATTCCAGCTCTACAGGGTCTTGATTATCCTGTCAGTG
                                           ttttgtt  CT-rich tract
                                           ttttgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acagtagtgatggtagcaattgcctgctaataccagcatatacaagttactttcttacaaatgtatcgaagagtttagttgaccaatgttttgttatcagGTTTTTGGAAATGACAGAAAATATTGGTTCATCCCTGCATATTCAGAAGAGGATCTGAGAAGAATTCCAGCTCTACAGGGTCTTGATTATCCTGTCAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - -tgatggt
- - - - - - - - - - tgcctgc
- - - - - - - - - - - - - - - taccagc