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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgttggactgtagtgtaaatatgtatttacatatgtgtagatcctacccattttgttccttagttgaggtttgattcaattctattggacctttgcagGCTGCTGCTTCGTGATCTGCCCATCAAGGGAGGAGGCTGATAAGGCTGTGACTACATACCACAACAAGCGCACACTACCTGGG

Basic information

species Zea mays
transcript GRMZM2G177001_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G177001_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g30980.1 (Oryza sativa), 3'ss of exon 1
cttgttggactgtagtgtaaatatgtatttacatatg-----tgtagatcctacccattttgttccttagttgaggtttgattcaat-tctattggaccttt-gcagGCTGCTGCTTCGTGATCTGCCCATCAAGGGAGGAGGCTGATAAGGCTGTGACTACATACCACAACAAGCGCACACTACCTGGG
        | | |  |   |   | | ||| || |||       ||  || |   ||  |||| | | | ||     |||||| ||  |  | ||||||||| ||||||||||||||  |||||||||||||||||||||||||||| ||||| |||| | |||| |||||||||||||| || || |||
------aaagtatc-tactaccttttctttccagatgacattcttaattcttgatcaacttgtccatcattttgaccttgatttaagatgcactggaccttttgcagGCTGCTGCTTTTTGATCTGCCCATCAAGGGAGGAGGCTGACAAGGCGGTGAATGCATATCACAACAAGCGCACCCTTCCAGGG
















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|149108797|gb|EE189842.2|EE189842
EST:     CGTCGACGAGGTCACTGTCATCCGCGACAGGGTCACCAGGGTCTCGCGAG                         GCTGCTGCTTCGTGATCTGCCCATCAAGGGAGGAGGCTGATAAGGCTGTGA
genomic: CGTCGACGAGGTCACTGTCATCCGCGACAGGGTCACCAGGGTCTCGCGAGgtccggatcc ... acctttgcagGCTGCTGCTTCGTGATCTGCCCATCAAGGGAGGAGGCTGATAAGGCTGTGA
EST: gi|60400937|gb|DN233744.1|DN233744
EST:     CGTCGACGAGGTCACTGTCATCCGCGACAGGGTCACCAGGGTCTCGCGAG                         GCTGCTGCTTCGTGATCTGCCCATCAAGGGAGGAGGCTGATAAGGCTGTGA
genomic: CGTCGACGAGGTCACTGTCATCCGCGACAGGGTCACCAGGGTCTCGCGAGgtccggatcc ... acctttgcagGCTGCTGCTTCGTGATCTGCCCATCAAGGGAGGAGGCTGATAAGGCTGTGA
EST: gi|149098711|gb|EE184722.2|EE184722
EST:     CGTCGACGAGGTCACTGTCATCCGCGACAGGGTCACCAGGGTCTCGCGAG                         GCTGCTGCTTCGTGATCTGCCCATCAAGGGAGGAGGCTGATAAGGCTGTGA
genomic: CGTCGACGAGGTCACTGTCATCCGCGACAGGGTCACCAGGGTCTCGCGAGgtccggatcc ... acctttgcagGCTGCTGCTTCGTGATCTGCCCATCAAGGGAGGAGGCTGATAAGGCTGTGA
EST: gi|71438922|gb|DR819972.1|DR819972
EST:     CTGTCATCCGCGACAGGGTCACCAGGGTCTCGCGAG                         GCTGCTGCTTCGTGATCTGCCCATCAAGGGAGGAGGCTGATAAGGCTGTGA
genomic: CTGTCATCCGCGACAGGGTCACCAGGGTCTCGCGAGgtccggatcc ... acctttgcagGCTGCTGCTTCGTGATCTGCCCATCAAGGGAGGAGGCTGATAAGGCTGTGA
EST: gi|211051931|gb|FL422541.1|FL422541
EST:     TCCGCGACAGGGTCACCAGGGTCTCGCGAG                         GCTGCTGCTTCGTGATCTGCCCATCAAGGGAGGAGGCTGATAAGGCTGTGA
genomic: TCCGCGACAGGGTCACCAGGGTCTCGCGAGgtccggatcc ... acctttgcagGCTGCTGCTTCGTGATCTGCCCATCAAGGGAGGAGGCTGATAAGGCTGTGA
EST: gi|60396221|gb|DN229090.1|DN229090
EST:     CGTCGACGAGGTCACTGTCATCCGCGACAGGGTCACCAGGGTCTCGCGAG                         GCTGCTGCTTCGTGATCTGCCCATCAAGGGAGGAGGCTGATAAGGCTGTGA
genomic: CGTCGACGAGGTCACTGTCATCCGCGACAGGGTCACCAGGGTCTCGCGAGgtccggatcc ... acctttgcagGCTGCTGCTTCGTGATCTGCCCATCAAGGGAGGAGGCTGATAAGGCTGTGA
EST: gi|6564129|gb|AW231751.1|AW231751
EST:     CGTCGACGAGGTCACCGTCATCCGCGACAGGGTCACCAGGATCTCGCGAG                         GCTGCTGCTTCGTGATCTGCCCATCAAGGGAGGAGGCTGATAAGGCTGTGA
genomic: CGTCGACGAGGTCACTGTCATCCGCGACAGGGTCACCAGGGTCTCGCGAGgtccggatcc ... acctttgcagGCTGCTGCTTCGTGATCTGCCCATCAAGGGAGGAGGCTGATAAGGCTGTGA

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: 47 (upstream exon), 47 (downstream exon)
Score: 88

AAGCAGATGTCCGAGGCCGAGCTCGCTGCCATGTTCCGCAGCGTCGCCCTCGTCGACGAGGTCACTGTCATCCGCGACAGGGTCACCAGGGTCTCGCGAGgtccggatcc ... acctttgcagGCTGCTGCTTCGTGATCTGCCCATCAAGGGAGGAGGCTGATAAGGCTGTGACTACATACCACAACAAGCGCACACTACCTGGG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 44

AAGCAGATGTCCGAGGCCGAGCTCGCTGCCATGTTCCGCAGCGTCGCCCTCGTCGACGAGGTCACTGTCATCCGCGACAGGGTCACCAGGGTCTCGCGAGgtccggatcc ... acctttgcagGCTGCTGCTTCGTGATCTGCCCATCAAGGGAGGAGGCTGATAAGGCTGTGACTACATACCACAACAAGCGCACACTACCTGGG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 62

AAGCAGATGTCCGAGGCCGAGCTCGCTGCCATGTTCCGCAGCGTCGCCCTCGTCGACGAGGTCACTGTCATCCGCGACAGGGTCACCAGGGTCTCGCGAGgtccggatcc ... acctttgcagGCTGCTGCTTCGTGATCTGCCCATCAAGGGAGGAGGCTGATAAGGCTGTGACTACATACCACAACAAGCGCACACTACCTGGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 32

AAGCAGATGTCCGAGGCCGAGCTCGCTGCCATGTTCCGCAGCGTCGCCCTCGTCGACGAGGTCACTGTCATCCGCGACAGGGTCACCAGGGTCTCGCGAGgtccggatcc ... acctttgcagGCTGCTGCTTCGTGATCTGCCCATCAAGGGAGGAGGCTGATAAGGCTGTGACTACATACCACAACAAGCGCACACTACCTGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctacccattttgttccttagttgaggtttgattcaattctattggacctttgcagGCTGCTGCTTCGTGATCTGCCCATCAAGGGAGGAGGCTGATAAGGCTGTGACTACATACCACAACAAGCGCACACTACCTGGG
                         gtttgat  putative branch site (score: 32)
                                              cctttgc  putative PPT
                                  aattctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttgttggactgtagtgtaaatatgtatttacatatgtgtagatcctacccattttgttccttagttgaggtttgattcaattctattggacctttgcagGCTGCTGCTTCGTGATCTGCCCATCAAGGGAGGAGGCTGATAAGGCTGTGACTACATACCACAACAAGCGCACACTACCTGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - -tggactg
- - - - - - - - - - atatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgattca