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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttctactctatatttgctccttcagaatggtttaataaatccttgttttgctagcagctcttaatgttctttcattgttaattgcattcttttgtgcagCTGAGAAGAGGGTGATACCTGGTTCCGCTGATGGCCAGTTTGAATTTGGTTCATTCATGTCAGCTACACTGAGCTGTGACCACAGGGTTATAGATG

Basic information

species Zea mays
transcript GRMZM2G015132_T01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G015132_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os02g01500.1 (Oryza sativa), 3'ss of exon 17
-----tttctactctatatttgctccttcagaatggtttaataaatccttgttttgctagcagctcttaatgttctttcattgttaa--ttgcattcttttgtgcagCTGAGAAGAGGGTGATACCTGGTTCCGCTGATGGCCAGTTTGAATTTGGTTCATTCATGTCAGCTACACTGAGCTGTGACCACAGGGTTATAGATG
      |||| ||    |   |  | ||||   ||    | |   | |||||  || |  ||     |    || |||  ||  |    ||   ||  ||||  |||||||||||||||||||||||||   ||  || ||||||| ||| |||||||| |||||||| || ||| |||||||||| ||||||||||| ||||
ataaacttctgctaagaag--gtccattcacgttg---cagtg--ttcttgtgatgattacatagggtgtcattatttacttaatggccttttttttgtttggacagCTGAGAAGAGGGTGATACCTGGCAGCGTAGACGGCCAGTATGAGTTTGGTTCCTTCATGTCGGCAACAATGAGCTGTGATCACAGGGTTATTGATG

upper sequence: GRMZM2G015132_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os07g22720.1 (Oryza sativa), 3'ss of exon 17
tttctactctatatttgctccttcagaatggtttaataaatccttgttttgctagcagctcttaatgttctttcattg--ttaattgcattctt--ttgtgcagCTGAGAAGAGGGTGATACCTGGTTCCGCTGATGGCCAGTTTGAATTTGGTTCATTCATGTCAGCTACACTGAGCTGTGACCACAGGGTTATAGATG
    |    | ||||||||    |||  |  || | | | || |  | ||     | |  | ||  | |   |  ||   | || ||| || ||  ||| |||||||||| |||||||||||||||   |||  |||| || |  || |||||||| |||||||| || ||| |||||||||| ||||||||||| ||||
---atgtattctatttgctagg-caggctcattcacttagtcatgctgttttagtccgtacatagggattcatttttaactcaactgcttttttgcttgggcagCTGAGAGGAGGGTGATACCTGGCAGCGCCAATGGTCAATACGAGTTTGGTTCCTTCATGTCGGCAACAATGAGCTGTGATCACAGGGTTATTGATG
















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|29576885|gb|CB616997.1|CB616997
EST:     CTGCGCCATCATAAATCCTCCCCAGTCAGCAATTTTGGCCATTGGTTCTG                         CTGAGAAGAGGGTGATACCTGGTTCCGCTGATGGCCAGTTTGAATTTGGTT
genomic: CTGCGCCATCATAAATCCTCCCCAGTCAGCAATTTTGGCCATTGGTTCTGgtaatgagtc ... ttttgtgcagCTGAGAAGAGGGTGATACCTGGTTCCGCTGATGGCCAGTTTGAATTTGGTT
EST: gi|71761137|gb|DR959074.1|DR959074
EST:     TTGCGCCATCATAAATCCTCCCCAGTCAGCAATTTTGGCCATTGGTTTTG                         CTGAGAAGAGGGTGATACCTGGTTCCGCTGATGGCCAGTTTGAATTTGGTT
genomic: CTGCGCCATCATAAATCCTCCCCAGTCAGCAATTTTGGCCATTGGTTCTGgtaatgagtc ... ttttgtgcagCTGAGAAGAGGGTGATACCTGGTTCCGCTGATGGCCAGTTTGAATTTGGTT
EST: gi|76932163|gb|DV172956.1|DV172956
EST:     CTGCGCCATCATAAATCCTCCCCAGTCAGCAATTTTGGCCATTGGTTCTG                         CTGAGAAGAGGGTGATACCTGGTTCCGCTGATGGCCAGTTTGAATTTGGTT
genomic: CTGCGCCATCATAAATCCTCCCCAGTCAGCAATTTTGGCCATTGGTTCTGgtaatgagtc ... ttttgtgcagCTGAGAAGAGGGTGATACCTGGTTCCGCTGATGGCCAGTTTGAATTTGGTT
EST: gi|71333154|gb|DR803611.1|DR803611
EST:     TTGCGCCATCATAAATCCTCCCCAGTCAGCAATTTTGGCCATTGGTTCTG                         CTGAGAAGAGGGTGATACCTGGTTCCGCTGATGGCCAGTTTGAATTTGGTT
genomic: CTGCGCCATCATAAATCCTCCCCAGTCAGCAATTTTGGCCATTGGTTCTGgtaatgagtc ... ttttgtgcagCTGAGAAGAGGGTGATACCTGGTTCCGCTGATGGCCAGTTTGAATTTGGTT
EST: gi|211011840|gb|FL066266.1|FL066266
EST:     CTGCGCCATCATAAATCCTCCCCAGTCAGCAATTTTGGCCATTGGTTCTG                         CTGAGAATAGGGTGATACCTGTTTCCGCTGATGGCCAGTTTGAATTTGGTT
genomic: CTGCGCCATCATAAATCCTCCCCAGTCAGCAATTTTGGCCATTGGTTCTGgtaatgagtc ... ttttgtgcagCTGAGAAGAGGGTGATACCTGGTTCCGCTGATGGCCAGTTTGAATTTGGTT
EST: gi|78091151|gb|DV519525.1|DV519525
EST:     CTGCGCCATCATAAATCCTCCCCAGTCAGCAATTTTGGCCATTGGTTCTG                         CTGAGAAGAGGGTGATACCTGGTTCCGCTGATGGCCAGTTTGAATTTGGTT
genomic: CTGCGCCATCATAAATCCTCCCCAGTCAGCAATTTTGGCCATTGGTTCTGgtaatgagtc ... ttttgtgcagCTGAGAAGAGGGTGATACCTGGTTCCGCTGATGGCCAGTTTGAATTTGGTT

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: 454

GGCACCTTCACTGTATCAAATTTGGGAGGTCCCTTCGGAATTAAACAATTCTGCGCCATCATAAATCCTCCCCAGTCAGCAATTTTGGCCATTGGTTCTGgtaatgagtc ... ttttgtgcagCTGAGAAGAGGGTGATACCTGGTTCCGCTGATGGCCAGTTTGAATTTGGTTCATTCATGTCAGCTACACTGAGCTGTGACCACAGGGTTATAGATG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 768

GGCACCTTCACTGTATCAAATTTGGGAGGTCCCTTCGGAATTAAACAATTCTGCGCCATCATAAATCCTCCCCAGTCAGCAATTTTGGCCATTGGTTCTGgtaatgagtc ... ttttgtgcagCTGAGAAGAGGGTGATACCTGGTTCCGCTGATGGCCAGTTTGAATTTGGTTCATTCATGTCAGCTACACTGAGCTGTGACCACAGGGTTATAGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 467

GGCACCTTCACTGTATCAAATTTGGGAGGTCCCTTCGGAATTAAACAATTCTGCGCCATCATAAATCCTCCCCAGTCAGCAATTTTGGCCATTGGTTCTGgtaatgagtc ... ttttgtgcagCTGAGAAGAGGGTGATACCTGGTTCCGCTGATGGCCAGTTTGAATTTGGTTCATTCATGTCAGCTACACTGAGCTGTGACCACAGGGTTATAGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 936

GGCACCTTCACTGTATCAAATTTGGGAGGTCCCTTCGGAATTAAACAATTCTGCGCCATCATAAATCCTCCCCAGTCAGCAATTTTGGCCATTGGTTCTGgtaatgagtc ... ttttgtgcagCTGAGAAGAGGGTGATACCTGGTTCCGCTGATGGCCAGTTTGAATTTGGTTCATTCATGTCAGCTACACTGAGCTGTGACCACAGGGTTATAGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttgctagcagctcttaatgttctttcattgttaattgcattcttttgtgcagCTGAGAAGAGGGTGATACCTGGTTCCGCTGATGGCCAGTTTGAATTTGGTTCATTCATGTCAGCTACACTGAGCTGTGACCACAGGGTTATAGATG
                               tgttaat  putative branch site (score: 936)
                                        cattctttt  putative PPT
                         tttcattgttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttctactctatatttgctccttcagaatggtttaataaatccttgttttgctagcagctcttaatgttctttcattgttaattgcattcttttgtgcagCTGAGAAGAGGGTGATACCTGGTTCCGCTGATGGCCAGTTTGAATTTGGTTCATTCATGTCAGCTACACTGAGCTGTGACCACAGGGTTATAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - -tgctcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - gcagctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcattc