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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtggccaagtttttttggatttatgaagtttttaggtgtctataacatggttacaatcatccttgctgcagTCACATGATGTATTCACAGAATATCTTGACCTTCTTAATATCTTGGAGGAGGAGCTTTCATCTGTCTCTGATCTTACATTGCAAAATGGACCATTGTCAT

Basic information

species Zea mays
transcript GRMZM2G052750_T02
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052750_T02 (Zea mays), 3'ss of exon 21
lower sequence: LOC_Os02g54500.1 (Oryza sativa), 3'ss of exon 21
-------gttagtggccaagtttttttg---gatttatgaagtttttagg--tgtctataacatggttacaatcatccttgctgcagTCACATGATGTATTCACAGAATATCTTGACCTTCTTAATATCTTGGAGGAGGAGCTTTCATCTGTCTCTGATCTTACATTGCAAAATGGACCATTGTCAT
        | |      |   || ||||   | |||||||| ||| || |  ||||  | || || |||||| || | |    ||||||||||||||| |||| ||| || ||||| |||||||| |  ||||||||||||||||||||||| ||||||||||||||||||||| ||||| ||||||
gtttacaatcataaaatattcttgtttgtacggtttatgaactttctaagaatgtccctgacttgcttacaaacaactt----gcagTCACATGATGTGTTCAGAGAGTACCTTGATCTTCTTAACACTTTGGAGGAGGAGCTTTCATCTGTTTCTGATCTTACATTGCAAAATAGACCAGTGTCAT
















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|32867742|gb|CF007424.1|CF007424
EST:     TCTTTAGGCATGATTTGCGATTGTGGAAAGCATATAGCATTACTCTACAG                         TCACATGATGTATTCACAGAATATCTTGACCTTCTTAATATCTTGGAGGAG
genomic: TCTTTAGGCATGATTTGCGATTGTGGAAAGCATATAGCATTACTCTACAGgttagtggcc ... cttgctgcagTCACATGATGTATTCACAGAATATCTTGACCTTCTTAATATCTTGGAGGAG
EST: gi|211446884|gb|FL341663.1|FL341663
EST:     TCTTTAGGCATGATTTGCGATTGTGGAAAGCATATAGCATTACTCTACAG                         TCACATGATGTATTCACAGAATATCTTGACCTTCTTAATATCTTGGAGGAG
genomic: TCTTTAGGCATGATTTGCGATTGTGGAAAGCATATAGCATTACTCTACAGgttagtggcc ... cttgctgcagTCACATGATGTATTCACAGAATATCTTGACCTTCTTAATATCTTGGAGGAG
EST: gi|211446492|gb|FK979151.1|FK979151
EST:     TCTTTAGGCATGATTTGCGATTGTGGAAAGCATATAGCATTACTCTACAG                         TCACATGATGTATTCACAGAATATCTTGACCTTCTTAATATCTTGGAGGAG
genomic: TCTTTAGGCATGATTTGCGATTGTGGAAAGCATATAGCATTACTCTACAGgttagtggcc ... cttgctgcagTCACATGATGTATTCACAGAATATCTTGACCTTCTTAATATCTTGGAGGAG
EST: gi|211253319|gb|FL352230.1|FL352230
EST:     TCTTTAGGCATGATTTGCGATTGTGGAAAGCATATAGCATTACTCTACAG                         TCACATGATGTATTCACAGAATATCTTGACCTTCTTAATATCTTGGAGGAG
genomic: TCTTTAGGCATGATTTGCGATTGTGGAAAGCATATAGCATTACTCTACAGgttagtggcc ... cttgctgcagTCACATGATGTATTCACAGAATATCTTGACCTTCTTAATATCTTGGAGGAG
EST: gi|32868501|gb|CF008183.1|CF008183
EST:     TCTTTAGGCATGATTTGCGATTGTGGAAAGCATATAGCATTACTCTACAG                         TCACATGATGTATTCACAGAATATCTTGACCTTCTTAATATCTTGGAGGAG
genomic: TCTTTAGGCATGATTTGCGATTGTGGAAAGCATATAGCATTACTCTACAGgttagtggcc ... cttgctgcagTCACATGATGTATTCACAGAATATCTTGACCTTCTTAATATCTTGGAGGAG
EST: gi|83278595|gb|DV942603.1|DV942603
EST:     TCTTTAGGCATGATTTGCGATTGTGGAAAGCATATAGCATTACTCTACAG                         TCACATGATGTATTCACAGAATATCTTGACCTTCTTAATATCTTGGAGGAG
genomic: TCTTTAGGCATGATTTGCGATTGTGGAAAGCATATAGCATTACTCTACAGgttagtggcc ... cttgctgcagTCACATGATGTATTCACAGAATATCTTGACCTTCTTAATATCTTGGAGGAG

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: 94

GTTTTGGTGGATCTCTTTAGGCATGATTTGCGATTGTGGAAAGCATATAGCATTACTCTACAGgttagtggcc ... cttgctgcagTCACATGATGTATTCACAGAATATCTTGACCTTCTTAATATCTTGGAGGAGGAGCTTTCATCTGTCTCTGATCTTACATTGCAAAATGGACCATTGTCAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 86

GTTTTGGTGGATCTCTTTAGGCATGATTTGCGATTGTGGAAAGCATATAGCATTACTCTACAGgttagtggcc ... cttgctgcagTCACATGATGTATTCACAGAATATCTTGACCTTCTTAATATCTTGGAGGAGGAGCTTTCATCTGTCTCTGATCTTACATTGCAAAATGGACCATTGTCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 112

GTTTTGGTGGATCTCTTTAGGCATGATTTGCGATTGTGGAAAGCATATAGCATTACTCTACAGgttagtggcc ... cttgctgcagTCACATGATGTATTCACAGAATATCTTGACCTTCTTAATATCTTGGAGGAGGAGCTTTCATCTGTCTCTGATCTTACATTGCAAAATGGACCATTGTCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 65

GTTTTGGTGGATCTCTTTAGGCATGATTTGCGATTGTGGAAAGCATATAGCATTACTCTACAGgttagtggcc ... cttgctgcagTCACATGATGTATTCACAGAATATCTTGACCTTCTTAATATCTTGGAGGAGGAGCTTTCATCTGTCTCTGATCTTACATTGCAAAATGGACCATTGTCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatttatgaagtttttaggtgtctataacatggttacaatcatccttgctgcagTCACATGATGTATTCACAGAATATCTTGACCTTCTTAATATCTTGGAGGAGGAGCTTTCATCTGTCTCTGATCTTACATTGCAAAATGGACCATTGTCAT
                       ctataac  putative branch site (score: 65)
                                        tcatcctt  putative PPT
         aagttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtggccaagtttttttggatttatgaagtttttaggtgtctataacatggttacaatcatccttgctgcagTCACATGATGTATTCACAGAATATCTTGACCTTCTTAATATCTTGGAGGAGGAGCTTTCATCTGTCTCTGATCTTACATTGCAAAATGGACCATTGTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT