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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgagagattcaggttgaggttgaaaaccagtctgatcgctttcattttaaatcctgtgactgctgccaataaaaatagaagttattttttttgcatgcagGTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCATGAGTCCAAGTATAACT

Basic information

species Zea mays
transcript GRMZM2G145029_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G145029_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g34180.1 (Oryza sativa), 3'ss of exon 1
-tgagagattcaggttgaggttgaaaaccagtctgatcgctttcattttaaatcctgtgactgctgccaataaaaatagaagttattttttttgcatgcagGTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCATGAGTCCAAGTATAACT
 |       |  ||| || | |||     |    | ||      |  | | ||    |  ||   | ||| || | |      |   |||||  | |||||||| ||||||||||| ||||| ||||| ||||| |||||||| |||||||||||||
tttgtgccgtggggtggaagatgagctggaaatagctcctgagaaaatcacatttcatttct-tagacaacaatactgagcaatccgtttttaccctgcagGTGTATTTTAGTGGACGAACAGGACAACGTCATTGGCCATGATTCCAAGTATAACT

upper sequence: GRMZM2G145029_T02 (Zea mays), 3'ss of exon 1
lower sequence: EFJ31498 (Selaginella moellendorffii), 3'ss of exon 1
---------------------tgagagattcaggtt---gaggttgaaaaccagtctgatcg---ctttcattttaaatcctgtgactgctgccaataaaaatagaagttattttttttgcatgcagGTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCATGAGTCCAAGTATAACT
                     |       ||  |||    || | | ||| |  || ||  |   ||||   | |   |  || | |      |  | |   | |   || | || | |  |   ||||| ||  | ||||| ||  | ||||||||| |||||||||| |||||||||||||
gtaagctttgactctcttctttatcttgctcgtgtttcaaagttcgcaaatctatcggagtgattcttttgctcttggttttgaggcaaggatc--tgacgctcgctcttgtgttgtgtcta---agGTGTATCCTGGTGGACGAGAAGGACAATGTCGTCGGCCATGACTCCAAGTATAACT
















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|211100857|gb|FL320689.1|FL320689
EST:     GCCGACGTCGGGATGGACGCCGTCCAGCGGCGGCTCATGTTTGAGGACGA                         GTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCACGAGTCCAAGTA
genomic: GCCGACGTCGGGATGGACGCCGTCCAACGGCGGCTCATGTTTGAGGACGAgtgagttgcc ... ttgcatgcagGTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCATGAGTCCAAGTA
EST: gi|211043409|gb|FL322272.1|FL322272
EST:     GCCGACGTCGGGATGGACGCCGTCCAGCGGCGGCTCATGTTTTAGGACGA                         GTGCATTTTTAGTGGATGAACAAGACAATGTCATCGGCCACGAGTCCAAGT
genomic: GCCGACGTCGGGATGGACGCCGTCCAACGGCGGCTCATGTTTGAGGACGAgtgagttgcc ... ttgcatgcagGTGCATTTT-AGTGGATGAACAAGACAATGTCATCGGCCATGAGTCCAAGT
EST: gi|211523188|gb|FL353428.1|FL353428
EST:     GCCGACGTCGGGATGGACGCCGTCCAGCGGCGGCTCATGTTTGAGGACGA                         GTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCACGAGTCCAAGTA
genomic: GCCGACGTCGGGATGGACGCCGTCCAACGGCGGCTCATGTTTGAGGACGAgtgagttgcc ... ttgcatgcagGTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCATGAGTCCAAGTA
EST: gi|211514701|gb|FL326221.1|FL326221
EST:     GCCGACGTCGGGATGGACGCCGTCCAGCGGCGGCTCATGTTTGAGGACGA                         GTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCACGAGTCCAAGTA
genomic: GCCGACGTCGGGATGGACGCCGTCCAACGGCGGCTCATGTTTGAGGACGAgtgagttgcc ... ttgcatgcagGTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCATGAGTCCAAGTA
EST: gi|148948634|gb|EC898546.2|EC898546
EST:     GCCGACGTCGGGATGGACGCCGTCCAACGGCGGCTCATGTTTGAGGACGA                         GTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCATGAGTCCAAGTA
genomic: GCCGACGTCGGGATGGACGCCGTCCAACGGCGGCTCATGTTTGAGGACGAgtgagttgcc ... ttgcatgcagGTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCATGAGTCCAAGTA
EST: gi|15313313|gb|BI478657.1|BI478657
EST:     GCCGACGTCGGGATGGACGCCGTCCAACGGCGGCTCATGTTTGAGGACGA                         GTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCATGAGTCCAAGTA
genomic: GCCGACGTCGGGATGGACGCCGTCCAACGGCGGCTCATGTTTGAGGACGAgtgagttgcc ... ttgcatgcagGTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCATGAGTCCAAGTA
EST: gi|148930170|gb|EC872550.2|EC872550
EST:     GCCGACGTCGGGATGGACGCCGTCCAACGGCGGCTCATGTTTGAGGACGA                         GTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCATGAGTCCAAGTA
genomic: GCCGACGTCGGGATGGACGCCGTCCAACGGCGGCTCATGTTTGAGGACGAgtgagttgcc ... ttgcatgcagGTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCATGAGTCCAAGTA
EST: gi|211410145|gb|FL360134.1|FL360134
EST:     GCCGACGTCGGGATGGATGCCGTCCAGCGGCGGCTCATGTTTGAGGACGA                         GTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCACGAGTCCAAGTA
genomic: GCCGACGTCGGGATGGACGCCGTCCAACGGCGGCTCATGTTTGAGGACGAgtgagttgcc ... ttgcatgcagGTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCATGAGTCCAAGTA

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: 39 (upstream exon), 49 (downstream exon)
Score: 28

CCTCCGCACGGGGCGCCGTGATGGGGAACCCAGGCCCCGGCGCCGTTGACGCCGACGTCGGGATGGACGCCGTCCAACGGCGGCTCATGTTTGAGGACGAgtgagttgcc ... ttgcatgcagGTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCATGAGTCCAAGTATAACT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 148

CCTCCGCACGGGGCGCCGTGATGGGGAACCCAGGCCCCGGCGCCGTTGACGCCGACGTCGGGATGGACGCCGTCCAACGGCGGCTCATGTTTGAGGACGAgtgagttgcc ... ttgcatgcagGTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCATGAGTCCAAGTATAACT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 161

CCTCCGCACGGGGCGCCGTGATGGGGAACCCAGGCCCCGGCGCCGTTGACGCCGACGTCGGGATGGACGCCGTCCAACGGCGGCTCATGTTTGAGGACGAgtgagttgcc ... ttgcatgcagGTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCATGAGTCCAAGTATAACT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 191

CCTCCGCACGGGGCGCCGTGATGGGGAACCCAGGCCCCGGCGCCGTTGACGCCGACGTCGGGATGGACGCCGTCCAACGGCGGCTCATGTTTGAGGACGAgtgagttgcc ... ttgcatgcagGTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCATGAGTCCAAGTATAACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaaatcctgtgactgctgccaataaaaatagaagttattttttttgcatgcagGTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCATGAGTCCAAGTATAACT
                                    ttatttttttt  CT-rich tract
                      aataaaaatagaagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgagagattcaggttgaggttgaaaaccagtctgatcgctttcattttaaatcctgtgactgctgccaataaaaatagaagttattttttttgcatgcagGTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCATGAGTCCAAGTATAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA