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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actaggcaactagacacaaactgatgatatcttatatttggggaaacaaaccaacacagctcgttgccaagaacaaactgatactgcaacatccttacagGTTCCTTGACCCCATTGTACATGGACGGTACCCGTACTCGATGCAAGAGATTGCCAAAGACAGGCTACCGTTGTTCAGCGATGAAGAAGCCAGGATGGTG

Basic information

species Zea mays
transcript GRMZM2G148176_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G148176_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os07g46280.1 (Oryza sativa), 3'ss of exon 7
----------------------------------------------------------------------------actaggcaactagacacaaactgatgatat--cttatatttggggaaacaaaccaacacagctcgttgccaagaacaaactgatactgcaacatccttacagGTTCCTTGACCCCATTGTACATGGACGGTACCCGTACTCGATGCAAGAGATTGCCAAAGACAGGCTACCGTTGTTCAGCGATGAAGAAGCCAGGATGGTG
                                                                            | |||    |||||       ||||  | |  |    |  ||        ||   || |   |  |||  |  | |||||||| |||   |  |||||| |||||||||||||||||| | ||||| |||||||| ||||||||||  || || | ||| |||||| | ||    ||||| ||||| ||  |||||||||||
gtaaaaatctgaaaacaccatctggttcaggatcaaattatcgattatttactccagagttcagatgctcaggtctagtagcagtctagattttttgtgatagtgtagccacaaactgaaagtctgaaagtacccttttttttgg-atcagcaaactgacactatgatctccttaaagGTTCCTTGACCCCATTATCCATGGTCGGTACCCATACTCGATGCTCGAAATCGTCAAGGACAGGATGCCAACCTTCAGTGATGAGGAGTCCAGGATGGTG
















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|87157450|gb|DY402239.1|DY402239
EST:     AATGCGGACCAGGCTGCAGCACAGCGAGCCAGGGACTTCCACCTAGGCTG                         GTTCCTTGACCCCATTGTACATGGACGGTACCCGTACTCGATGCAAGAGAT
genomic: AATGCGGACCAGGCTGCAGCACAGCGAGCCAGGGACTTCCACCTAGGCTGgtaaacgcct ... atccttacagGTTCCTTGACCCCATTGTACATGGACGGTACCCGTACTCGATGCAAGAGAT
EST: gi|22819206|gb|BU499296.1|BU499296
EST:     AATGCGGACCAGGCTGCAGCACAGCGAGCCAGGGACTTCCACCTAGGCTG                         GTTCCTTGACCCCATTGTACATGGACGGTACCCGTACTCGATGCAAGAGAT
genomic: AATGCGGACCAGGCTGCAGCACAGCGAGCCAGGGACTTCCACCTAGGCTGgtaaacgcct ... atccttacagGTTCCTTGACCCCATTGTACATGGACGGTACCCGTACTCGATGCAAGAGAT
EST: gi|18659302|gb|BM500266.1|BM500266
EST:     AATGCGGACCAGGCTGCAGCACAGCGAGCCAGGGACTTCCACCTAGGCTG                         GTTCCTTGACCCCATTGTACATGGACGGTACCCGTACTCGATGCAAGAGAT
genomic: AATGCGGACCAGGCTGCAGCACAGCGAGCCAGGGACTTCCACCTAGGCTGgtaaacgcct ... atccttacagGTTCCTTGACCCCATTGTACATGGACGGTACCCGTACTCGATGCAAGAGAT
EST: gi|211158739|gb|FL327709.1|FL327709
EST:     AATGCGGACCAGGCTGCAGCACAGCGAGCCAGGGACTTCCACCTAGGCTG                         GTTCCTTGACCCCATTGTACATGGACGG
genomic: AATGCGGACCAGGCTGCAGCACAGCGAGCCAGGGACTTCCACCTAGGCTGgtaaacgcct ... atccttacagGTTCCTTGACCCCATTGTACATGGACGG
EST: gi|71333296|gb|DR803703.1|DR803703
EST:     AATGCGGACCAGGCTGCAGCACAGCGAGCCAGGGATTTCCACCTAGGCTG                         GTTCCTTGACCCCATTGTACATGGACGGTACCCGTACTCGATGCAAGAGAT
genomic: AATGCGGACCAGGCTGCAGCACAGCGAGCCAGGGACTTCCACCTAGGCTGgtaaacgcct ... atccttacagGTTCCTTGACCCCATTGTACATGGACGGTACCCGTACTCGATGCAAGAGAT
EST: gi|6851479|gb|AW352489.1|AW352489
EST:     AATGCGGACCAGGCTGCAGCACAGCGAGCCAGGGACTTCCACCTAGGCTG                         GTTCCTTGACCCCATTGTACATGGACGGTACCCGTACTCGATGCAAGAGAT
genomic: AATGCGGACCAGGCTGCAGCACAGCGAGCCAGGGACTTCCACCTAGGCTGgtaaacgcct ... atccttacagGTTCCTTGACCCCATTGTACATGGACGGTACCCGTACTCGATGCAAGAGAT
EST: gi|26559781|gb|CA832016.1|CA832016
EST:     GCAGCACAGCGAGCCAGGGACTTCCACCTAGGCTG                         G-TCCTTGACCCCATTGTACATGGACGGTACCCGTACTCGATGCAAGAGAT
genomic: GCAGCACAGCGAGCCAGGGACTTCCACCTAGGCTGgtaaacgcct ... atccttacagGTTCCTTGACCCCATTGTACATGGACGGTACCCGTACTCGATGCAAGAGAT

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), 47 (downstream exon)
Score: 222

AGATTGGAATTCTCCTGGATTTCGTGTGGTACGAACCTTTCAGCGACAGCAATGCGGACCAGGCTGCAGCACAGCGAGCCAGGGACTTCCACCTAGGCTGgtaaacgcct ... atccttacagGTTCCTTGACCCCATTGTACATGGACGGTACCCGTACTCGATGCAAGAGATTGCCAAAGACAGGCTACCGTTGTTCAGCGATGAAGAAGCCAGGATGGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 111

AGATTGGAATTCTCCTGGATTTCGTGTGGTACGAACCTTTCAGCGACAGCAATGCGGACCAGGCTGCAGCACAGCGAGCCAGGGACTTCCACCTAGGCTGgtaaacgcct ... atccttacagGTTCCTTGACCCCATTGTACATGGACGGTACCCGTACTCGATGCAAGAGATTGCCAAAGACAGGCTACCGTTGTTCAGCGATGAAGAAGCCAGGATGGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 73

AGATTGGAATTCTCCTGGATTTCGTGTGGTACGAACCTTTCAGCGACAGCAATGCGGACCAGGCTGCAGCACAGCGAGCCAGGGACTTCCACCTAGGCTGgtaaacgcct ... atccttacagGTTCCTTGACCCCATTGTACATGGACGGTACCCGTACTCGATGCAAGAGATTGCCAAAGACAGGCTACCGTTGTTCAGCGATGAAGAAGCCAGGATGGTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 76

AGATTGGAATTCTCCTGGATTTCGTGTGGTACGAACCTTTCAGCGACAGCAATGCGGACCAGGCTGCAGCACAGCGAGCCAGGGACTTCCACCTAGGCTGgtaaacgcct ... atccttacagGTTCCTTGACCCCATTGTACATGGACGGTACCCGTACTCGATGCAAGAGATTGCCAAAGACAGGCTACCGTTGTTCAGCGATGAAGAAGCCAGGATGGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaaaccaacacagctcgttgccaagaacaaactgatactgcaacatccttacagGTTCCTTGACCCCATTGTACATGGACGGTACCCGTACTCGATGCAAGAGATTGCCAAAGACAGGCTACCGTTGTTCAGCGATGAAGAAGCCAGGATGGTG
                              aactgat  putative branch site (score: 76)
                                            catcctt  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actaggcaactagacacaaactgatgatatcttatatttggggaaacaaaccaacacagctcgttgccaagaacaaactgatactgcaacatccttacagGTTCCTTGACCCCATTGTACATGGACGGTACCCGTACTCGATGCAAGAGATTGCCAAAGACAGGCTACCGTTGTTCAGCGATGAAGAAGCCAGGATGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - -acacaaa
- - - - - - - - - - -tgatgat
- - - - - - - - - - - - - - - - - - - - - -aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - ccaacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttgcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgcaac