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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attcaactccagctaactttacgtgcgtttcgctagcgtgccattcagtgtcctcgaccctttcggcgatcgcagctgattgcttgtgtgccggcctcagGTACCGCGCCATCACGAGCGCATACTACCGCGGCGCGGTGGGCGCGCTGGTGGTGTACGACGTGAGCCGCCGCACCACCTTCGACAACGCGGAGCGCTGG

Basic information

species Zea mays
transcript GRMZM2G023436_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023436_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g47730.1 (Oryza sativa), 3'ss of exon 1
attcaactccagctaactttacgtgcgtttcgc-tagcgtgcc--attcagtgtcc--tcgaccctttcggcgatcgcagctgattgcttgtgtgccggcctcagGTACCGCGCCATCACGAGCGCATACTACCGCGGCGCGGTGGGCGCGCTGGTGGTGTACGACGTGAGCCGCCGCACCACCTTCGACAACGCGGAGCGCTGG
   |   | || ||  || | | |   ||| ||  |  |      |||   | |||  | ||   ||     || | | | ||  | |       ||  || |||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||  ||||||| ||| ||||| ||||||||||| |||
--acgtgttcaactcgctatgcttcacttttgcgcaatggattggattggatatccctttgatatttggattgacctc-gttggcttcccccccccc--ccccagGTACCGCGCCATCACGAGCGCCTACTACCGCGGCGCGGTGGGCGCGCTGGTGGTGTACGACGTGACGCGCCGCATCACGTTCGAGAACGCGGAGCGGTGG
















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|50323773|gb|CO518899.1|CO518899
EST:     CGGGCAGGAGAG                         GTACCGCGCCATCACGAGCGCATACTACCGCGGCGCGGTGGGCGCGCTGGT
genomic: CGGGCAGGAGAGgtacgccctt ... ccggcctcagGTACCGCGCCATCACGAGCGCATACTACCGCGGCGCGGTGGGCGCGCTGGT
EST: gi|211108241|gb|FL033718.1|FL033718
EST:     ACGANCA-GCTCGTCAAGGCACAGATCTGGGACACCGCCGGGCAGGAGAG                         GTACCGCGCCATCACGAGC
genomic: ACGA-CAAGCTCGTCAAGGCACAGATCTGGGACACCGCCGGGCAGGAGAGgtacgccctt ... ccggcctcagGTACCGCGCCATCACGAGC
EST: gi|71428472|gb|DR809522.1|DR809522
EST:     GGGACACCGCCGGGCAGGAGAG                         GTACCGCGCCATCACGAGCGCATACTACCGCGGCGCGGTGGGCGCGCTGGT
genomic: GGGACACCGCCGGGCAGGAGAGgtacgccctt ... ccggcctcagGTACCGCGCCATCACGAGCGCATACTACCGCGGCGCGGTGGGCGCGCTGGT
EST: gi|149099759|gb|EE185811.2|EE185811
EST:     GACGACAAGCTCGTCAAGGCACAGATCTGGGACACCGCCGGGCAGGAGAG                         GTACCGCGCCATCACGAGCGCATACTACCGCGGCGCGGTGGGCGCGCTGGT
genomic: GACGACAAGCTCGTCAAGGCACAGATCTGGGACACCGCCGGGCAGGAGAGgtacgccctt ... ccggcctcagGTACCGCGCCATCACGAGCGCATACTACCGCGGCGCGGTGGGCGCGCTGGT
EST: gi|211108239|gb|FL033716.1|FL033716
EST:     AACAACAAGCTCGTCAAGGCACATATCTGGGACACCGCCGGGCAGGAGAG                         GTACCGCGCCATCACGAGCGCATACTACCGCGGCGCG
genomic: GACGACAAGCTCGTCAAGGCACAGATCTGGGACACCGCCGGGCAGGAGAGgtacgccctt ... ccggcctcagGTACCGCGCCATCACGAGCGCATACTACCGCGGCGCG
EST: gi|78082032|gb|DV510444.1|DV510444
EST:     GACGACAAGCTCGTCAAGGCACAGATCTGGGACACCGCCGGGCAGGAGAG                         GTACCGCGCCATCACGAGCGCATACTACCGCGGCGCGGTGGGCGCGCTGGT
genomic: GACGACAAGCTCGTCAAGGCACAGATCTGGGACACCGCCGGGCAGGAGAGgtacgccctt ... ccggcctcagGTACCGCGCCATCACGAGCGCATACTACCGCGGCGCGGTGGGCGCGCTGGT
EST: gi|71425397|gb|DR806648.1|DR806648
EST:     TCAAGGCACAGATCTGGGACACCGCCGGGCAGGAGAG                         GTACCGCGCCATCACGAGCGCATACTACCGCGGCGCGGTGGGCGCGCTGGT
genomic: TCAAGGCACAGATCTGGGACACCGCCGGGCAGGAGAGgtacgccctt ... ccggcctcagGTACCGCGCCATCACGAGCGCATACTACCGCGGCGCGGTGGGCGCGCTGGT
EST: gi|71425398|gb|DR806649.1|DR806649
EST:     GACGACAAGCTCGTCAAGGCACAGATCTGGGACACCGCCGGGCAGGAGAG                         GTACCGCGCCATCACGAGCGCATACTACCGCGGCGCGGTGGGCGCGCTGGT
genomic: GACGACAAGCTCGTCAAGGCACAGATCTGGGACACCGCCGGGCAGGAGAGgtacgccctt ... ccggcctcagGTACCGCGCCATCACGAGCGCATACTACCGCGGCGCGGTGGGCGCGCTGGT
EST: gi|211108238|gb|FL033715.1|FL033715
EST:     GACGACAAGCTCGTCAAGGCACAGATCTGGGACACCGCCGGGCAGGAGAG                         GTACCGCGCCATCACGAGCGCATACTACCGCGGCGCGGTGGGCGCGCTGGT
genomic: GACGACAAGCTCGTCAAGGCACAGATCTGGGACACCGCCGGGCAGGAGAGgtacgccctt ... ccggcctcagGTACCGCGCCATCACGAGCGCATACTACCGCGGCGCGGTGGGCGCGCTGGT
EST: gi|71428473|gb|DR809523.1|DR809523
EST:     GACGACAAGCTCGTCAAGGCACAGATCTGGGACACCGCCGGGCAGGAGAG                         GTACCGCGCCATCACGAGCGCATACTACCGCGGCGCGGTGGGCGCGCTGGT
genomic: GACGACAAGCTCGTCAAGGCACAGATCTGGGACACCGCCGGGCAGGAGAGgtacgccctt ... ccggcctcagGTACCGCGCCATCACGAGCGCATACTACCGCGGCGCGGTGGGCGCGCTGGT
EST: gi|50323774|gb|CO518900.1|CO518900
EST:     GACGACAAGCTCGTCAAGGCACAGATCTGGGACACCGCCGGGCAGGAGAG                         GTACCGCGCCATCACGAGCGCATACTACCGCGGCGCGGTGGGCGCGCTGGT
genomic: GACGACAAGCTCGTCAAGGCACAGATCTGGGACACCGCCGGGCAGGAGAGgtacgccctt ... ccggcctcagGTACCGCGCCATCACGAGCGCATACTACCGCGGCGCGGTGGGCGCGCTGGT
EST: gi|211108243|gb|FL033720.1|FL033720
EST:     GACGACAAGCTCGTCAAGGCACAGATCTGGGACACCGCCGGGCAGGAGAG                         GTACCGCGCCATCACGAGCGCATACTACCGCGGCGCGGTGGGCGCGCTGGT
genomic: GACGACAAGCTCGTCAAGGCACAGATCTGGGACACCGCCGGGCAGGAGAGgtacgccctt ... ccggcctcagGTACCGCGCCATCACGAGCGCATACTACCGCGGCGCGGTGGGCGCGCTGGT

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 34

AGACCAGGTCCACCATCGGCGTCGAGTTCGCCACCAAGACCGTCCAGGTCGACGACAAGCTCGTCAAGGCACAGATCTGGGACACCGCCGGGCAGGAGAGgtacgccctt ... ccggcctcagGTACCGCGCCATCACGAGCGCATACTACCGCGGCGCGGTGGGCGCGCTGGTGGTGTACGACGTGAGCCGCCGCACCACCTTCGACAACGCGGAGCGCTGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 45

AGACCAGGTCCACCATCGGCGTCGAGTTCGCCACCAAGACCGTCCAGGTCGACGACAAGCTCGTCAAGGCACAGATCTGGGACACCGCCGGGCAGGAGAGgtacgccctt ... ccggcctcagGTACCGCGCCATCACGAGCGCATACTACCGCGGCGCGGTGGGCGCGCTGGTGGTGTACGACGTGAGCCGCCGCACCACCTTCGACAACGCGGAGCGCTGG


Block sizes: 42 (upstream exon), 48 (downstream exon)
Score: 18

AGACCAGGTCCACCATCGGCGTCGAGTTCGCCACCAAGACCGTCCAGGTCGACGACAAGCTCGTCAAGGCACAGATCTGGGACACCGCCGGGCAGGAGAGgtacgccctt ... ccggcctcagGTACCGCGCCATCACGAGCGCATACTACCGCGGCGCGGTGGGCGCGCTGGTGGTGTACGACGTGAGCCGCCGCACCACCTTCGACAACGCGGAGCGCTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtgtcctcgaccctttcggcgatcgcagctgattgcttgtgtgccggcctcagGTACCGCGCCATCACGAGCGCATACTACCGCGGCGCGGTGGGCGCGCTGGTGGTGTACGACGTGAGCCGCCGCACCACCTTCGACAACGCGGAGCGCTGG
                            agctgat  putative branch site (score: 18)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attcaactccagctaactttacgtgcgtttcgctagcgtgccattcagtgtcctcgaccctttcggcgatcgcagctgattgcttgtgtgccggcctcagGTACCGCGCCATCACGAGCGCATACTACCGCGGCGCGGTGGGCGCGCTGGTGGTGTACGACGTGAGCCGCCGCACCACCTTCGACAACGCGGAGCGCTGG

- - - ctccagc
- - - - - - - - - - - - - - - - - -gcgtgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcagctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttgt