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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgagcggccgaggctcgggttcctctggttgcgctcgcctctcgagtctcgcccggggatgttttcttgtgtttgatttgacgggtgtgtttcgttgccatcgcagGGGTGGTGAGCGGGTTCCTCTCCAATGCGGCTTCGGCGGTGGTGAAGCGGCTGTGGTCGCTCAAATCCACCACCAAGATAG

Basic information

species Zea mays
transcript GRMZM2G075260_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075260_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g49770.1 (Oryza sativa), 3'ss of exon 1
gtgagtgagcggccgaggctcgggttcctctggttgcgctcgcctctcgagtc--tcgcccggggatgttttcttgtgtttgatttgacgggtgtgtttcgttgccatcgcagGGGTGGTGAGCGGGTTCCTCTCCAATGCGGCTTCGGCGGTGGTGAAGCGGCTGTGGTCGCTCAAATCCACCACCAAGATAG
    ||||| | ||  | ||   |   | | || | || | || |||    ||  | ||    |||||| |   ||||| ||  |       || |     ||||||| |||| ||||||||| |||||||||||||| ||||| ||| ||||| ||||||||||||||||||||||||||||||| |||| ||
----gtgagtgaccacgcctgcagcctccccgggttcgttggcttcttcgctcctttgctgatggatgtgtgtgtgtgtgtgtgtgtttttttggggggttttgccattgcagAGGTGGTGAGTGGGTTCCTCTCCAACGCGGCGTCGTCGGTGATGAAGCGGCTGTGGTCGCTCAAATCCACCACGAAGACAG
















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|211499168|gb|FL156948.1|FL156948
EST:     GCTCCTCCTTTGCTCCTTGGCTCCGGCTTCCGCGTCCTCGTACCCCGCAA                         GGGTGGTGAGCGGGTTCCTCTCCAATGCGGCTTCGGCGGTGGTGAAGCGGC
genomic: GCTCCTCCTTTGCTCCTTGGCTCCGGCTTCCGCGTCCTCGTACCCCGCAAgtgagtgagc ... gccatcgcagGGGTGGTGAGCGGGTTCCTCTCCAATGCGGCTTCGGCGGTGGTGAAGCGGC
EST: gi|91048035|gb|EB158453.1|EB158453
EST:     CTCCTCCTTTGCTCCTTGGCTCCGGCTTCCGCGTCCTCGTACCCCCGCAA                         GGGTGGTGAGCGGGTTCCTCTCCAATGCGGCTTCGGCGGTGGTGAAGCGG
genomic: CTCCTCCTTTGCTCCTTGGCTCCGGCTTCCGCGTCCTCGTACCCC-GCAAgtgagtgagc ... gccatcgcagGGGTGGTGAGCGGGTTCCTCTCCAATGCGGCTTCGGCGGTGGTGAAGCGG
EST: gi|211042150|gb|FL156952.1|FL156952
EST:     GCTCCTCCTTTGCTCCTTGGCTCCGGCTTCCGCGTCCTCGTACCCCGCAA                         GGGTGGTGAGCGGGTTCCTCTCCAATGCGGCTTCGGCGGTGGTGAAGCGGC
genomic: GCTCCTCCTTTGCTCCTTGGCTCCGGCTTCCGCGTCCTCGTACCCCGCAAgtgagtgagc ... gccatcgcagGGGTGGTGAGCGGGTTCCTCTCCAATGCGGCTTCGGCGGTGGTGAAGCGGC
EST: gi|50334127|gb|CO529253.1|CO529253
EST:     GCTCCTCCTTTGCTCCTTGGCTCCGGCTTCCGCGTCCTCGTACCCCGCAA                         GGGTGGTGAGCGGGTTCCTCTCCAATGCGGCTTCGGCGGTGGTGAAGCGGC
genomic: GCTCCTCCTTTGCTCCTTGGCTCCGGCTTCCGCGTCCTCGTACCCCGCAAgtgagtgagc ... gccatcgcagGGGTGGTGAGCGGGTTCCTCTCCAATGCGGCTTCGGCGGTGGTGAAGCGGC
EST: gi|71436276|gb|DR817326.1|DR817326
EST:     GCTCCTCCTTTGCTCCTTGGCTCCGGCTTCCGCGTCCTCGTACCCCGCAA                         GGGTGGTGAGCGGGTTCCTCTCCAATGCGGCTTCGGCGGTGGTGAAGCGGC
genomic: GCTCCTCCTTTGCTCCTTGGCTCCGGCTTCCGCGTCCTCGTACCCCGCAAgtgagtgagc ... gccatcgcagGGGTGGTGAGCGGGTTCCTCTCCAATGCGGCTTCGGCGGTGGTGAAGCGGC
EST: gi|31357778|gb|CD442135.1|CD442135
EST:     GCTCCTCCTTTGCTCCTTGGCTCCGGCTTCCGCGTCCTCGTACCCCGCAA                         GGGTGGTGAGCGGGTTCCTCTCCAATGCGGCTTCGGCGGTGGTGAAGCGGC
genomic: GCTCCTCCTTTGCTCCTTGGCTCCGGCTTCCGCGTCCTCGTACCCCGCAAgtgagtgagc ... gccatcgcagGGGTGGTGAGCGGGTTCCTCTCCAATGCGGCTTCGGCGGTGGTGAAGCGGC
EST: gi|78081385|gb|DV509797.1|DV509797
EST:     GCTCCTCCTTTGCTCCTTGGCTCCGGCTTCCGCGTCCTCGTACCCCGCAA                         GGGTGGTGAGCGGGTTCCTCTCCAATGCGGCTTCGGCGGTGGTGAAGCGGC
genomic: GCTCCTCCTTTGCTCCTTGGCTCCGGCTTCCGCGTCCTCGTACCCCGCAAgtgagtgagc ... gccatcgcagGGGTGGTGAGCGGGTTCCTCTCCAATGCGGCTTCGGCGGTGGTGAAGCGGC
EST: gi|71327834|gb|DR800547.1|DR800547
EST:     GCTCCTCCTTTGCTCCTTGGCTCCGGCTTCCGCGTCCTCGTACCCCGCAA                         GGGTGGTGAGCGGGTTCCTCTCCAATGCGGCTTCGGCGGTGGTGAAGCGGC
genomic: GCTCCTCCTTTGCTCCTTGGCTCCGGCTTCCGCGTCCTCGTACCCCGCAAgtgagtgagc ... gccatcgcagGGGTGGTGAGCGGGTTCCTCTCCAATGCGGCTTCGGCGGTGGTGAAGCGGC
EST: gi|148939778|gb|EC884477.2|EC884477
EST:     GCTCCTCCTTTGCTCCTTGGCTCCGGCTTCCGCGTCCTCGTACCCCGCAA                         GGGTGGTGAGCGGGTTCCTCTCCAATGCGGCTTCGGCGGTGGTGAAGCGGC
genomic: GCTCCTCCTTTGCTCCTTGGCTCCGGCTTCCGCGTCCTCGTACCCCGCAAgtgagtgagc ... gccatcgcagGGGTGGTGAGCGGGTTCCTCTCCAATGCGGCTTCGGCGGTGGTGAAGCGGC

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: 228

AAGGGAGGCAACGCGAGGGGCGTCCCGGTGGGGGTGCTGCTGGTGGCCGCGCTCCTCCTTTGCTCCTTGGCTCCGGCTTCCGCGTCCTCGTACCCCGCAAgtgagtgagc ... gccatcgcagGGGTGGTGAGCGGGTTCCTCTCCAATGCGGCTTCGGCGGTGGTGAAGCGGCTGTGGTCGCTCAAATCCACCACCAAGATAG


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

AAGGGAGGCAACGCGAGGGGCGTCCCGGTGGGGGTGCTGCTGGTGGCCGCGCTCCTCCTTTGCTCCTTGGCTCCGGCTTCCGCGTCCTCGTACCCCGCAAgtgagtgagc ... gccatcgcagGGGTGGTGAGCGGGTTCCTCTCCAATGCGGCTTCGGCGGTGGTGAAGCGGCTGTGGTCGCTCAAATCCACCACCAAGATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 43

AAGGGAGGCAACGCGAGGGGCGTCCCGGTGGGGGTGCTGCTGGTGGCCGCGCTCCTCCTTTGCTCCTTGGCTCCGGCTTCCGCGTCCTCGTACCCCGCAAgtgagtgagc ... gccatcgcagGGGTGGTGAGCGGGTTCCTCTCCAATGCGGCTTCGGCGGTGGTGAAGCGGCTGTGGTCGCTCAAATCCACCACCAAGATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 40

AAGGGAGGCAACGCGAGGGGCGTCCCGGTGGGGGTGCTGCTGGTGGCCGCGCTCCTCCTTTGCTCCTTGGCTCCGGCTTCCGCGTCCTCGTACCCCGCAAgtgagtgagc ... gccatcgcagGGGTGGTGAGCGGGTTCCTCTCCAATGCGGCTTCGGCGGTGGTGAAGCGGCTGTGGTCGCTCAAATCCACCACCAAGATAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccggggatgttttcttgtgtttgatttgacgggtgtgtttcgttgccatcgcagGGGTGGTGAGCGGGTTCCTCTCCAATGCGGCTTCGGCGGTGGTGAAGCGGCTGTGGTCGCTCAAATCCACCACCAAGATAG
                        atttgac  putative branch site (score: 40)
                    tttgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgagcggccgaggctcgggttcctctggttgcgctcgcctctcgagtctcgcccggggatgttttcttgtgtttgatttgacgggtgtgtttcgttgccatcgcagGGGTGGTGAGCGGGTTCCTCTCCAATGCGGCTTCGGCGGTGGTGAAGCGGCTGTGGTCGCTCAAATCCACCACCAAGATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC