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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCATCGCATAACCACCATTATGTTCATTGTTTATTTAGAATCGTATCCCACTGGTCGTGGAAGAGGACGTGGTGGTGGCAGAAGAGGCAGGGGAAGAGgtatgttctcttgttgtctatatgagcagcaaaggaaacagtcatagtttactggacagtgtctcttataattttgtagtgctgacttgttgatttatgg...

Basic information

species Zea mays
transcript GRMZM2G146472_T03
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G146472_T03 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os11g06760.1 (Oryza sativa), 5'ss of exon 7
GATCATCGCATAACCACCATTATGTTCATTGTTTATTTAGAATCGTATCCCACTGGTCGTGGAAGAGGACGTGGTGGTGGCAGAAGAGGCAGGGGAAGAGgtatgttc--tcttgttgtctatatgagcagcaaaggaaacagtcatagtttactggacagtgtctcttataattttgtagtgctgacttgttgatttatgg
                                        |||| |  ||||||  |||||||||||| |||||||||||||||||||||||||| ||||||||  ||  |||| |    | ||||||||  |||  |       | |    ||  |    |  |   |||   ||   | ||  |      ||   ||   
----------------------------------------AATCTTTCCCCACTAATCGTGGAAGAGGCCGTGGTGGTGGCAGAAGAGGCAGGGGCAGAGgtatcctctttcttatgtcttctatgagcacaaaactaccagactacaacacacatggttattaccagtatctgttaccattgtaggtagcatgccatac--
















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|166685781|gb|EG103044.1|EG103044
EST:     CGTGGTGGTGGCAGAAGAGGCAGGGGAANAG                         GCATGAGCAATGGCCCCCCTCCACCTGCTTATGGTTACAACGAAGAGTGGG
genomic: CGTGGTGGTGGCAGAAGAGGCAGGGGAAGAGgtatgttctc ... atgtgcacagGCATGAGCAATGGCCCCCCTCCACCTGCTTATGGTTACAACGAAGAGTGGG
EST: gi|89755184|gb|DY685709.1|DY685709
EST:     GCAGAAGAGGCAGGGGAAGAG                         GCATGAGCAATGGCCCCCCTCCACCTGCTTATGGTTACAACGAAGAGTGGG
genomic: GCAGAAGAGGCAGGGGAAGAGgtatgttctc ... atgtgcacagGCATGAGCAATGGCCCCCCTCCACCTGCTTATGGTTACAACGAAGAGTGGG
EST: gi|149010217|gb|EE042036.2|EE042036
EST:     TGGAAGAGGACGTGGTGGTGGCAGAAGAGGCAGGGGAAGAG                         GCATGAGCAATGGCCCCCCTCCACCTGCTTATGGTTACAACGAAGAGTGGG
genomic: TGGAAGAGGACGTGGTGGTGGCAGAAGAGGCAGGGGAAGAGgtatgttctc ... atgtgcacagGCATGAGCAATGGCCCCCCTCCACCTGCTTATGGTTACAACGAAGAGTGGG
EST: gi|60346152|gb|DN213125.1|DN213125
EST:     CAGAAGAGGCAGGGGAAGAG                         GCATGAGCAATGGCCCCCCTCCACCTGCTTATGGTTACAACGAAGAGTGGG
genomic: CAGAAGAGGCAGGGGAAGAGgtatgttctc ... atgtgcacagGCATGAGCAATGGCCCCCCTCCACCTGCTTATGGTTACAACGAAGAGTGGG
EST: gi|60401473|gb|DN234280.1|DN234280
EST:     CAGGGGAAGAG                         GCATGAGCAATGGCCCCCCTCCACCTGCTTATGGTTACAACGAAGAGTGGG
genomic: CAGGGGAAGAGgtatgttctc ... atgtgcacagGCATGAGCAATGGCCCCCCTCCACCTGCTTATGGTTACAACGAAGAGTGGG
EST: gi|15632650|gb|BI679743.1|BI679743
EST:     CACTGGTCGTGGAAGAGGACGTGGTGGTGGCAGAAGAGGCAGGGGAAGAG                         GCATGAGCAATGGCCCCCCTCCACCTGCTTATGGTTACAACGAAGAGTGGG
genomic: CACTGGTCGTGGAAGAGGACGTGGTGGTGGCAGAAGAGGCAGGGGAAGAGgtatgttctc ... atgtgcacagGCATGAGCAATGGCCCCCCTCCACCTGCTTATGGTTACAACGAAGAGTGGG
EST: gi|60350971|gb|DN217944.1|DN217944
EST:     CACTGGTCGTGGAAGAGGACGTGGTGGTGGCAGAAGAGGCAGGGGAAGAG                         GCATGAGCAATGGCCCCCCTCCACCTGCTTATGGTTACAACGAAGAGTGGG
genomic: CACTGGTCGTGGAAGAGGACGTGGTGGTGGCAGAAGAGGCAGGGGAAGAGgtatgttctc ... atgtgcacagGCATGAGCAATGGCCCCCCTCCACCTGCTTATGGTTACAACGAAGAGTGGG
EST: gi|149109057|gb|EE189984.2|EE189984
EST:     CACTGGTCGTGGAAGAGGACGTGGTGGTGGCAGAAGAGGCAGGGGAAGAG                         GCATGAGCAATGGCCCCCCTCCACCTGCTTATGGTTA
genomic: CACTGGTCGTGGAAGAGGACGTGGTGGTGGCAGAAGAGGCAGGGGAAGAGgtatgttctc ... atgtgcacagGCATGAGCAATGGCCCCCCTCCACCTGCTTATGGTTA
EST: gi|60357376|gb|DN224349.1|DN224349
EST:     GTCGTGGAAGAGGACGTGGTGGTGGCAGAAGAGGCAGGGGAAGAG                         GCATGAGCAATGGCCCCCCTCCACCTGCTTATGGTTACAACGAAGAGTGGG
genomic: GTCGTGGAAGAGGACGTGGTGGTGGCAGAAGAGGCAGGGGAAGAGgtatgttctc ... atgtgcacagGCATGAGCAATGGCCCCCCTCCACCTGCTTATGGTTACAACGAAGAGTGGG
EST: gi|60396096|gb|DN228965.1|DN228965
EST:     GCAGAAGAGGCAGGGGAAGAG                         GCATGAGCAATGGCCCCCCTCCACCTGCTTATGGTTACAACGAAGAGTGGG
genomic: GCAGAAGAGGCAGGGGAAGAGgtatgttctc ... atgtgcacagGCATGAGCAATGGCCCCCCTCCACCTGCTTATGGTTACAACGAAGAGTGGG
EST: gi|60343821|gb|DN210794.1|DN210794
EST:     CACTGGTCGTGGAAGAGGACGTGGTGGTGGCAGAAGAGGCAGGGGAAGAG                         GCATGAGCAATGGCCCCCCTCCACCTGCTTATGGTTACAACGAAGAGTGGG
genomic: CACTGGTCGTGGAAGAGGACGTGGTGGTGGCAGAAGAGGCAGGGGAAGAGgtatgttctc ... atgtgcacagGCATGAGCAATGGCCCCCCTCCACCTGCTTATGGTTACAACGAAGAGTGGG
EST: gi|60355626|gb|DN222599.1|DN222599
EST:     CGTGGTGGTGGCAGAAGAGGCAGGGGAAGAG                         GCATGAGCAATGGCCCCCCTCCACCTGCTTATGGTTACAACGAAGAGTGGG
genomic: CGTGGTGGTGGCAGAAGAGGCAGGGGAAGAGgtatgttctc ... atgtgcacagGCATGAGCAATGGCCCCCCTCCACCTGCTTATGGTTACAACGAAGAGTGGG
EST: gi|71756347|gb|DR954284.1|DR954284
EST:     CACTGGTCGTGGAAGAGGACGTGGTGGTGGCAGAAGAGGCAGGGGAAGAG                         GCATGAGCAATGGCCCCCCTCCACCTGCTTATGGTTACAACGAAGAGTGGG
genomic: CACTGGTCGTGGAAGAGGACGTGGTGGTGGCAGAAGAGGCAGGGGAAGAGgtatgttctc ... atgtgcacagGCATGAGCAATGGCCCCCCTCCACCTGCTTATGGTTACAACGAAGAGTGGG
EST: gi|60398720|gb|DN231536.1|DN231536
EST:     CACTGGTCGTGGAAGAGGACGTGGTGGTGGCAGAAGAGGCAGGGGAAGAG                         GCATGAGCAATGGCCCCCCTCCACCTGCTTATGGTTACAACGAAGAGTGGG
genomic: CACTGGTCGTGGAAGAGGACGTGGTGGTGGCAGAAGAGGCAGGGGAAGAGgtatgttctc ... atgtgcacagGCATGAGCAATGGCCCCCCTCCACCTGCTTATGGTTACAACGAAGAGTGGG
EST: gi|60337039|gb|DN204012.1|DN204012
EST:     TGGAAGAGGACGTGGTGGTGGCAGAAGAGGCAGGGGAAGAG                         GCATGAGCAATGGCCCCCCTCCACCTGCTTATGGTTACAACGAAGAGTGGG
genomic: TGGAAGAGGACGTGGTGGTGGCAGAAGAGGCAGGGGAAGAGgtatgttctc ... atgtgcacagGCATGAGCAATGGCCCCCCTCCACCTGCTTATGGTTACAACGAAGAGTGGG
EST: gi|60350068|gb|DN217041.1|DN217041
EST:     AGGCAGGGGAAGAG                         GCATGAGCAATGGCCCCCCTCCACCTGCTTATGGTTACAACGAAGAGTGGG
genomic: AGGCAGGGGAAGAGgtatgttctc ... atgtgcacagGCATGAGCAATGGCCCCCCTCCACCTGCTTATGGTTACAACGAAGAGTGGG

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), 49 (downstream exon)
Score: 2820

GATCATCGCATAACCACCATTATGTTCATTGTTTATTTAGAATCGTATCCCACTGGTCGTGGAAGAGGACGTGGTGGTGGCAGAAGAGGCAGGGGAAGAGgtatgttctc ... atgtgcacagGCATGAGCAATGGCCCCCCTCCACCTGCTTATGGTTACAACGAAGAGTGGGAGGAGGAAGGAGATTATTATAACAGAGGGCGCGGGAGAGGGCGGCTACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 2991

GATCATCGCATAACCACCATTATGTTCATTGTTTATTTAGAATCGTATCCCACTGGTCGTGGAAGAGGACGTGGTGGTGGCAGAAGAGGCAGGGGAAGAGgtatgttctc ... atgtgcacagGCATGAGCAATGGCCCCCCTCCACCTGCTTATGGTTACAACGAAGAGTGGGAGGAGGAAGGAGATTATTATAACAGAGGGCGCGGGAGAGGGCGGCTACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1990

GATCATCGCATAACCACCATTATGTTCATTGTTTATTTAGAATCGTATCCCACTGGTCGTGGAAGAGGACGTGGTGGTGGCAGAAGAGGCAGGGGAAGAGgtatgttctc ... atgtgcacagGCATGAGCAATGGCCCCCCTCCACCTGCTTATGGTTACAACGAAGAGTGGGAGGAGGAAGGAGATTATTATAACAGAGGGCGCGGGAGAGGGCGGCTACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1999

GATCATCGCATAACCACCATTATGTTCATTGTTTATTTAGAATCGTATCCCACTGGTCGTGGAAGAGGACGTGGTGGTGGCAGAAGAGGCAGGGGAAGAGgtatgttctc ... atgtgcacagGCATGAGCAATGGCCCCCCTCCACCTGCTTATGGTTACAACGAAGAGTGGGAGGAGGAAGGAGATTATTATAACAGAGGGCGCGGGAGAGGGCGGCTACG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATCATCGCATAACCACCATTATGTTCATTGTTTATTTAGAATCGTATCCCACTGGTCGTGGAAGAGGACGTGGTGGTGGCAGAAGAGGCAGGGGAAGAGgtatgttctcttgttgtctatatgagcagcaaaggaaacagtcatagtttactggacagtgtctcttataattttgtagtgctgacttgttgatttatgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaggaaa