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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttgagtgttcgacatgccttttaatcacatcataactatagtatttttttgtgatttgatacttctttggtctaaaatttagttttatgtacccttagATCAATAGTCTTATTGGAACTAAGGTGGAGTGGGTTTATCATATGTTACAAGCATTCAACAGCGGCAACCTTGCCCTCTACCAAGAACTTTGCAGGGTTC

Basic information

species Zea mays
transcript GRMZM5G868757_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G868757_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g11570.1 (Oryza sativa), 3'ss of exon 3
-gtttgagtgttcgacatgccttttaatcacatcataactatagtatttttttgtgatttgatacttctttggtctaaa--atttagttttatgtacccttagATCAATAGTCTTATTGGAACTAAGGTGGAGTGGGTTTATCATATGTTACAAGCATTCAACAGCGGCAACCTTGCCCTCTACCAAGAACTTTGCAGGGTTC
 | ||||    | ||   |||  | ||||  || ||| |   | ||| |  |||| ||||| ||| ||| ||    ||    ||||  ||| | || ||||||||||| |||||||||||||| |||||||||||||| ||||||||||||||||||||||||| ||||||||| || |||||||||||||| || ||||| |
ggattgaaatattgaatggcccctaaatc-tat-atatcggca-tatatggttgtcatttggtacatctctgtctgaagttgtttatatttttatatccttagATCAACAGTCTTATTGGAACCAAGGTGGAGTGGGTCTATCATATGTTACAAGCATTCAACACCGGCAACCTAGCTCTCTACCAAGAACTATGTAGGGTCC

upper sequence: GRMZM5G868757_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g32800.1 (Oryza sativa), 3'ss of exon 3
------gtttgagtgttcgacatgccttttaatc-acatcataactatagtatttttttgtgatttgatacttctttggtctaaaatttagttttatgtacccttagATCAATAGTCTTATTGGAACTAAGGTGGAGTGGGTTTATCATATGTTACAAGCATTCAACAGCGGCAACCTTGCCCTCTACCAAGAACTTTGCAGGGTTC
       ||| | || | ||   |||  | |||| |  |||  | ||||||  |        ||||||||| ||| || ||| ||| |    ||| |  | ||||||||||| ||||| |||||||| |||||||||||||| ||||||||||| |||||||||||||  |||||||| || ||||||||||||||||||| ||| |
ggtgtttttttaatgcttgaatggcccctaaatctatgtcagca-tatagttgtc------aatttgatacatctctgttctgaaactgctattttttaatccttagATCAACAGTCTAATTGGAACCAAGGTGGAGTGGGTCTATCATATGTTGCAAGCATTCAACACTGGCAACCTAGCTCTCTACCAAGAACTTTGCAAGGTCC
















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|194716906|gb|FK934065.1|FK934065
EST:     TGCTGGGTGATAACATTTACAACTTTGGGGAGTTGTTAGCTCACCCGATT                         ATCAATAGTCTTATTGGAACTAAGGTGGAGTGGGTTTATCATATGTTACAA
genomic: TGCTGGGTGATAACATTTACAACTTTGGGGAGTTGTTAGCTCACCCGATTgtaagtaatt ... gtacccttagATCAATAGTCTTATTGGAACTAAGGTGGAGTGGGTTTATCATATGTTACAA
EST: gi|148930110|gb|EC872431.2|EC872431
EST:     TGCTGGGTGATAACATTTACAACTTTGGGGAGTTGTTAGCTCACCCGATT                         ATCAATAGTCTTATTGGAACTAAGGTGGAGTGGGTTTATCATATGTTACAA
genomic: TGCTGGGTGATAACATTTACAACTTTGGGGAGTTGTTAGCTCACCCGATTgtaagtaatt ... gtacccttagATCAATAGTCTTATTGGAACTAAGGTGGAGTGGGTTTATCATATGTTACAA
EST: gi|211082970|gb|FL307146.1|FL307146
EST:     TGCTGGGTGATAACATTTACAACTTTGGGGAGTTGTTAGCTCACCCGATT                         ATCAATAGTCTTATTGGAACTAAGGTGGAGTGGGTTTATCATATGTTACAA
genomic: TGCTGGGTGATAACATTTACAACTTTGGGGAGTTGTTAGCTCACCCGATTgtaagtaatt ... gtacccttagATCAATAGTCTTATTGGAACTAAGGTGGAGTGGGTTTATCATATGTTACAA
EST: gi|28987392|gb|CB351612.1|CB351612
EST:     TGCTGGG-GATAACATTTACAAC-TTGGGGAG-TGTTAGCTCACCCGATT                         ATCAATAGTCTTA-TGGAACTAAGGTGGAGTGGGTTTATCATATGTTACAA
genomic: TGCTGGGTGATAACATTTACAACTTTGGGGAGTTGTTAGCTCACCCGATTgtaagtaatt ... gtacccttagATCAATAGTCTTATTGGAACTAAGGTGGAGTGGGTTTATCATATGTTACAA
EST: gi|6020572|gb|AW065605.1|AW065605
EST:     TGCTGGGTGATAACATTTACAACTTTGGGGAATTGTTAGCTCACCCGATT                         ATCAATAGTCTTATTGGAACCAAGGTGGAGTGGGTTTATCATATGTTACAA
genomic: TGCTGGGTGATAACATTTACAACTTTGGGGAGTTGTTAGCTCACCCGATTgtaagtaatt ... gtacccttagATCAATAGTCTTATTGGAACTAAGGTGGAGTGGGTTTATCATATGTTACAA
EST: gi|149078129|gb|EE166878.2|EE166878
EST:     TGCTGGGTGATAACATTTACAACTTTGGGGAGTTGTTAGCTCACCCGATT                         ATCAATAGTCTTATTGGAACTAAAGTGGAGTGGGTTTATCATATG
genomic: TGCTGGGTGATAACATTTACAACTTTGGGGAGTTGTTAGCTCACCCGATTgtaagtaatt ... gtacccttagATCAATAGTCTTATTGGAACTAAGGTGGAGTGGGTTTATCATATG

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: 132

GACTTGGCTTTTGATCTATCTCTAGCAGCCTTGCTGGGTGATAACATTTACAACTTTGGGGAGTTGTTAGCTCACCCGATTgtaagtaatt ... gtacccttagATCAATAGTCTTATTGGAACTAAGGTGGAGTGGGTTTATCATATGTTACAAGCATTCAACAGCGGCAACCTTGCCCTCTACCAAGAACTTTGCAGGGTTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 129

GACTTGGCTTTTGATCTATCTCTAGCAGCCTTGCTGGGTGATAACATTTACAACTTTGGGGAGTTGTTAGCTCACCCGATTgtaagtaatt ... gtacccttagATCAATAGTCTTATTGGAACTAAGGTGGAGTGGGTTTATCATATGTTACAAGCATTCAACAGCGGCAACCTTGCCCTCTACCAAGAACTTTGCAGGGTTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 121

GACTTGGCTTTTGATCTATCTCTAGCAGCCTTGCTGGGTGATAACATTTACAACTTTGGGGAGTTGTTAGCTCACCCGATTgtaagtaatt ... gtacccttagATCAATAGTCTTATTGGAACTAAGGTGGAGTGGGTTTATCATATGTTACAAGCATTCAACAGCGGCAACCTTGCCCTCTACCAAGAACTTTGCAGGGTTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 56

GACTTGGCTTTTGATCTATCTCTAGCAGCCTTGCTGGGTGATAACATTTACAACTTTGGGGAGTTGTTAGCTCACCCGATTgtaagtaatt ... gtacccttagATCAATAGTCTTATTGGAACTAAGGTGGAGTGGGTTTATCATATGTTACAAGCATTCAACAGCGGCAACCTTGCCCTCTACCAAGAACTTTGCAGGGTTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttttgtgatttgatacttctttggtctaaaatttagttttatgtacccttagATCAATAGTCTTATTGGAACTAAGGTGGAGTGGGTTTATCATATGTTACAAGCATTCAACAGCGGCAACCTTGCCCTCTACCAAGAACTTTGCAGGGTTC
                          gtctaaa  putative branch site (score: 56)
                                              taccctt  putative PPT
                           tctaaaatttagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgagtgttcgacatgccttttaatcacatcataactatagtatttttttgtgatttgatacttctttggtctaaaatttagttttatgtacccttagATCAATAGTCTTATTGGAACTAAGGTGGAGTGGGTTTATCATATGTTACAAGCATTCAACAGCGGCAACCTTGCCCTCTACCAAGAACTTTGCAGGGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC