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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtgatggtgatgtccctctctgtttctctgcttcttgctccacagaacagagcttttagctaagcaatgggacattttttttcgcagGAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTGTCAACGCAGCTTTCCTTGCTTCTTTATACAGCGACTATCTTGAAGCGGC

Basic information

species Zea mays
transcript GRMZM2G147849_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147849_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g52630.1 (Oryza sativa), 3'ss of exon 4
gttggtgatggtgatgt-ccctctctgtttctctgcttcttgctccacagaacagagcttttagctaagcaatgggacattttttttcgcagGAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTGTCAACGCAGCTTTCCTTGCTTCTTTATACAGCGACTATCTTGAAGCGGC
      |  |||| ||| ||| || ||  |||||  || |  ||| |     || |  |   || ||| ||||||||  |||       |||||||| | |||||||||||||| ||||||||||| || |||||||| | |||||| || ||||||||||| ||| |||||||||| || || || || ||
------gtcggtgctgttccccctttgcctctctttttttctctcta---gccacaaatggaagttaaacaatgggaggttt------acagGAGGAATGATACAGCTCAACCACGGAAGGCCTCAGCCACTTCAGTATGTTGTCAATGCGGCTTTCCTTGCCTCTCTATACAGCGATTACCTGGATGCTGC
















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|211472968|gb|FL344046.1|FL344046
EST:     CGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAG                         GAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTG
genomic: CGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAGgttggtgatg ... tttttcgcagGAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTG
EST: gi|160481653|gb|EY254223.1|EY254223
EST:     CGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAG                         GAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTG
genomic: CGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAGgttggtgatg ... tttttcgcagGAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTG
EST: gi|211308480|gb|FL124618.1|FL124618
EST:     CGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAG                         GAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTG
genomic: CGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAGgttggtgatg ... tttttcgcagGAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTG
EST: gi|74239514|gb|DT647428.1|DT647428
EST:     CGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAG                         GAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTG
genomic: CGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAGgttggtgatg ... tttttcgcagGAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTG
EST: gi|211467558|gb|FL331131.1|FL331131
EST:     CGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAG                         GAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTG
genomic: CGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAGgttggtgatg ... tttttcgcagGAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTG
EST: gi|211279182|gb|FL307694.1|FL307694
EST:     CGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAG                         GAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTG
genomic: CGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAGgttggtgatg ... tttttcgcagGAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTG
EST: gi|211001820|gb|FL229076.1|FL229076
EST:     CATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAG                         GAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTG
genomic: CATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAGgttggtgatg ... tttttcgcagGAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTG
EST: gi|67010311|gb|CO439060.1|CO439060
EST:     CGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAG                         GAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTG
genomic: CGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAGgttggtgatg ... tttttcgcagGAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTG
EST: gi|211532037|gb|FL347050.1|FL347050
EST:     CGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAG                         GAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTG
genomic: CGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAGgttggtgatg ... tttttcgcagGAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTG

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), 48 (downstream exon)
Score: 74

GGGTACCCTTACGAAGAAATACTGAGGACATTCCACAACCAAACCGACAACGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAGgttggtgatg ... tttttcgcagGAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTGTCAACGCAGCTTTCCTTGCTTCTTTATACAGCGACTATCTTGAAGCGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 206

GGGTACCCTTACGAAGAAATACTGAGGACATTCCACAACCAAACCGACAACGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAGgttggtgatg ... tttttcgcagGAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTGTCAACGCAGCTTTCCTTGCTTCTTTATACAGCGACTATCTTGAAGCGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 119

GGGTACCCTTACGAAGAAATACTGAGGACATTCCACAACCAAACCGACAACGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAGgttggtgatg ... tttttcgcagGAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTGTCAACGCAGCTTTCCTTGCTTCTTTATACAGCGACTATCTTGAAGCGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 493

GGGTACCCTTACGAAGAAATACTGAGGACATTCCACAACCAAACCGACAACGTCATGTGCTCGTATTTACCTGTATTCAATTCATTCAACTTCACCAAAGgttggtgatg ... tttttcgcagGAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTGTCAACGCAGCTTTCCTTGCTTCTTTATACAGCGACTATCTTGAAGCGGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgctccacagaacagagcttttagctaagcaatgggacattttttttcgcagGAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTGTCAACGCAGCTTTCCTTGCTTCTTTATACAGCGACTATCTTGAAGCGGC
                                        cattttttttc  CT-rich tract
                                       acatttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtgatggtgatgtccctctctgtttctctgcttcttgctccacagaacagagcttttagctaagcaatgggacattttttttcgcagGAGGATTAATACAGCTCAACCATGGAAGGCCTCAACCGCTTCAGTACGCTGTCAACGCAGCTTTCCTTGCTTCTTTATACAGCGACTATCTTGAAGCGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC