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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaaccagatcctattttcctcccaagccaggacgctctagctcgttctctgacatgtccatgcgccgcgcgcgccagCGCGATCAGGCAGGCCGACTGCCTCCGCCGGGACGGCGCCGGCGCCGGCGCGCGCTGCGACGCGCCAGGGACCGTGCTGATGCTGGCGTTCAGCGTGGTC

Basic information

species Zea mays
transcript GRMZM2G096407_T01
intron # 3
splice site 3'
intron type U2

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|50324689|gb|CO519815.1|CO519815
EST:     CTGTGGGGCACCATGGTCGGGTACACCATCACGGCGACCATAAGCATGGC                         CGCGATCAGGCAGGCCGACTGCCTCCGCCGGGACGGCGCCGGCGCCGGCGC
genomic: CTGTGGGGCACCATGGTCGGGTACACCATCACGGCGACCATAAGCATGGCgtgagtaacc ... cgcgcgccagCGCGATCAGGCAGGCCGACTGCCTCCGCCGGGACGGCGCCGGCGCCGGCGC
EST: gi|148939591|gb|EC884211.2|EC884211
EST:     CTGTGGGGCACCATGGTCGGGTACACCATCACGGCGACCATAAGCATGGC                         CGCGATCAGGCAGGCCGACTGCCTCCGCCGGGACGGCGCCGGCGCCGGCGC
genomic: CTGTGGGGCACCATGGTCGGGTACACCATCACGGCGACCATAAGCATGGCgtgagtaacc ... cgcgcgccagCGCGATCAGGCAGGCCGACTGCCTCCGCCGGGACGGCGCCGGCGCCGGCGC
EST: gi|74241093|gb|DT649007.1|DT649007
EST:     CTGTGGGGCACCATGGTCGGGTACACCATCACGGCGACCATAAGCATGGC                         CGCGATCAGGCAGGCCGACTGCCTCCGCCGGGACGGCGCCGGCGCCGGCGC
genomic: CTGTGGGGCACCATGGTCGGGTACACCATCACGGCGACCATAAGCATGGCgtgagtaacc ... cgcgcgccagCGCGATCAGGCAGGCCGACTGCCTCCGCCGGGACGGCGCCGGCGCCGGCGC
EST: gi|148991824|gb|EE033411.2|EE033411
EST:     CTGTGGGGCACCATGGTCGGGTACACCATCACGGCGACCATAAGCATGGC                         CGCGATCAGGCAGGCCGACTGCCTCCGCCGGGACGGCGCCGGCGCCGGCGC
genomic: CTGTGGGGCACCATGGTCGGGTACACCATCACGGCGACCATAAGCATGGCgtgagtaacc ... cgcgcgccagCGCGATCAGGCAGGCCGACTGCCTCCGCCGGGACGGCGCCGGCGCCGGCGC
EST: gi|76013340|gb|DT940510.1|DT940510
EST:     CTGTGGGGCACCATGGTCGGGTACACCATCACGGCGACCATAAGCATGGC                         CGCGATCAGGCAGGCCGACTGCCTCCGCCGGGACGGCGCCGGCGCCGGCGC
genomic: CTGTGGGGCACCATGGTCGGGTACACCATCACGGCGACCATAAGCATGGCgtgagtaacc ... cgcgcgccagCGCGATCAGGCAGGCCGACTGCCTCCGCCGGGACGGCGCCGGCGCCGGCGC
EST: gi|101393258|gb|EB818560.1|EB818560
EST:     CTGTGGGGCACCATGATCGGGTACACCATCACGGCGACCATAAGCATGGC                         CGCGATCAGGCAGGCCGACTGCCTCCGCCGGGACGGCGCCGGCGCCGGCGC
genomic: CTGTGGGGCACCATGGTCGGGTACACCATCACGGCGACCATAAGCATGGCgtgagtaacc ... cgcgcgccagCGCGATCAGGCAGGCCGACTGCCTCCGCCGGGACGGCGCCGGCGCCGGCGC

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: 42 (upstream exon), 15 (downstream exon)
Score: 4

GTCCCAGGGAGGTGTTCATGTGCGGGGTCGCGCAGTACGTGAACCTGTGGGGCACCATGGTCGGGTACACCATCACGGCGACCATAAGCATGGCgtgagtaacc ... cgcgcgccagCGCGATCAGGCAGGCCGACTGCCTCCGCCGGGACGGCGCCGGCGCCGGCGCGCGCTGCGACGCGCCAGGGACCGTGCTGATGCTGGCGTTCAGCGTGGTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 16

GTCCCAGGGAGGTGTTCATGTGCGGGGTCGCGCAGTACGTGAACCTGTGGGGCACCATGGTCGGGTACACCATCACGGCGACCATAAGCATGGCgtgagtaacc ... cgcgcgccagCGCGATCAGGCAGGCCGACTGCCTCCGCCGGGACGGCGCCGGCGCCGGCGCGCGCTGCGACGCGCCAGGGACCGTGCTGATGCTGGCGTTCAGCGTGGTC


Block sizes: 30 (upstream exon), 30 (downstream exon)
Score: 5

GTCCCAGGGAGGTGTTCATGTGCGGGGTCGCGCAGTACGTGAACCTGTGGGGCACCATGGTCGGGTACACCATCACGGCGACCATAAGCATGGCgtgagtaacc ... cgcgcgccagCGCGATCAGGCAGGCCGACTGCCTCCGCCGGGACGGCGCCGGCGCCGGCGCGCGCTGCGACGCGCCAGGGACCGTGCTGATGCTGGCGTTCAGCGTGGTC


Block sizes: 33 (upstream exon), 25 (downstream exon)
Score: 3

GTCCCAGGGAGGTGTTCATGTGCGGGGTCGCGCAGTACGTGAACCTGTGGGGCACCATGGTCGGGTACACCATCACGGCGACCATAAGCATGGCgtgagtaacc ... cgcgcgccagCGCGATCAGGCAGGCCGACTGCCTCCGCCGGGACGGCGCCGGCGCCGGCGCGCGCTGCGACGCGCCAGGGACCGTGCTGATGCTGGCGTTCAGCGTGGTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagccaggacgctctagctcgttctctgacatgtccatgcgccgcgcgcgccagCGCGATCAGGCAGGCCGACTGCCTCCGCCGGGACGGCGCCGGCGCCGGCGCGCGCTGCGACGCGCCAGGGACCGTGCTGATGCTGGCGTTCAGCGTGGTC
                        ctctgac  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtaaccagatcctattttcctcccaagccaggacgctctagctcgttctctgacatgtccatgcgccgcgcgcgccagCGCGATCAGGCAGGCCGACTGCCTCCGCCGGGACGGCGCCGGCGCCGGCGCGCGCTGCGACGCGCCAGGGACCGTGCTGATGCTGGCGTTCAGCGTGGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG