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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgccgatgtgtgtcatgcttcctgctcaccccctatcctcaaccttttggagtgctattaatttttcccttgtgaccagttattttccttctctgcagATATAATCCTTTCAGGCTTATTGGTGTTGGCTTGTTAGTGTGGACTATCGCAACAGCTGGTTGTGGGGTATCATTTGATTTCTGGTCAATTACTATATGC

Basic information

species Zea mays
transcript GRMZM2G164743_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164743_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g44430.1 (Oryza sativa), 3'ss of exon 2
---gttgccgatgtgtgtcatgctt-cctgctcaccccctatcctcaaccttttggagtgctattaatttttcccttgtgaccagttattttccttctctgcagATATAATCCTTTCAGGCTTATTGGTGTTGGCTTGTTAGTGTGGACTATCGCAACAGCTGGTTGTGGGGTATCATTTGATTTCTGGTCAATTACTATATGC
    ||  || | ||    | |||  | |      |    |     ||||||||  ||||  ||    || |  |   |||    || ||  |||||| | |||| | |||||||||||||||||||||||||| || ||||| |||||||| ||||||||||||||||||   ||||||||||||||||||||||||||||||
atacttcacgttctgctggaggctaacataggtttctgaaacatcaaaccttttatagtgtaatg---ttctgacgcatgatagtttgttccccttcttt-cagACACAATCCTTTCAGGCTTATTGGTGTTGGATTATTAGTCTGGACTATTGCAACAGCTGGTTGTGGGTGCTCATTTGATTTCTGGTCAATTACTATATGC
















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|149078499|gb|EE167282.2|EE167282
EST:     ATGGTTGGACTGTTGGTGTCTTCGCTGATATTTGCATGCCTTGTAAAAAG                         ATATAATCCTTTCAGGCTTATTGGTGTTGGCTTGTTAGTGTGGACTATCGC
genomic: ATGGTTGGACTGTTGGTGTCTTCGCTGATATTTGCATGCCTTGTAAAAAGgttagctctc ... ttctctgcagATATAATCCTTTCAGGCTTATTGGTGTTGGCTTGTTAGTGTGGACTATCGC
EST: gi|148961886|gb|EE012673.2|EE012673
EST:     ATGGTTGGACTGTTGGTGTCTTCGCTGATATTTGCATGCCTTGTAAAAAG                         ATATAATCCTTTCAGGCTTATTGGTGTTGGCTTGTTAGTGTGGACTATCGC
genomic: ATGGTTGGACTGTTGGTGTCTTCGCTGATATTTGCATGCCTTGTAAAAAGgttagctctc ... ttctctgcagATATAATCCTTTCAGGCTTATTGGTGTTGGCTTGTTAGTGTGGACTATCGC
EST: gi|91051856|gb|EB162274.1|EB162274
EST:     ATGGTTGGACTGTTGGTGTCTTCGCTGATATTTGCATGCCTTGTAAAAAG                         ATATAATCCTTTCAGGCTTATTGGTGTTGGCTTGTTAGTGTGGACTATCGC
genomic: ATGGTTGGACTGTTGGTGTCTTCGCTGATATTTGCATGCCTTGTAAAAAGgttagctctc ... ttctctgcagATATAATCCTTTCAGGCTTATTGGTGTTGGCTTGTTAGTGTGGACTATCGC
EST: gi|148952110|gb|EC897902.2|EC897902
EST:     ATGGTTGGACTGTTGGTGTCTTCGCTGATATTTGCATGCCTTGTAAAAAG                         ATATAATCCTTTCAGGCTTATTGGTGTTGGCTTGTTAGTGTGGACTATCGC
genomic: ATGGTTGGACTGTTGGTGTCTTCGCTGATATTTGCATGCCTTGTAAAAAGgttagctctc ... ttctctgcagATATAATCCTTTCAGGCTTATTGGTGTTGGCTTGTTAGTGTGGACTATCGC
EST: gi|74232781|gb|DT640695.1|DT640695
EST:     ATGGTTGGACTGTTGGTGTCTTCGCTGATATTTGCATGCCTTGTAAAAAG                         ATATAATCCTTTCAGGCTTATTGGTGTTGGCTTGTTAGTGTGGACTATCGC
genomic: ATGGTTGGACTGTTGGTGTCTTCGCTGATATTTGCATGCCTTGTAAAAAGgttagctctc ... ttctctgcagATATAATCCTTTCAGGCTTATTGGTGTTGGCTTGTTAGTGTGGACTATCGC
EST: gi|148990916|gb|EE032339.2|EE032339
EST:     ATGGTTGGACTGTTGGTGTCTTCGCTGATATTTGCATGCCTTGTAAAAAG                         ATATAATCCTTTCAGGCTTATTGGTGTTGGCTTGTTAGTGTGGACTATCGC
genomic: ATGGTTGGACTGTTGGTGTCTTCGCTGATATTTGCATGCCTTGTAAAAAGgttagctctc ... ttctctgcagATATAATCCTTTCAGGCTTATTGGTGTTGGCTTGTTAGTGTGGACTATCGC
EST: gi|101385012|gb|EB814551.1|EB814551
EST:     ATGGTTGGACTGTTGGTGTCTTCGCTGATATTTGCATGCCTTGTAAAAAG                         ATATAATCCTTTCAGGCTTATTGGCGTTGGCTTGTTAGTGTGGACTATCGC
genomic: ATGGTTGGACTGTTGGTGTCTTCGCTGATATTTGCATGCCTTGTAAAAAGgttagctctc ... ttctctgcagATATAATCCTTTCAGGCTTATTGGTGTTGGCTTGTTAGTGTGGACTATCGC

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: 41 (upstream exon), 48 (downstream exon)
Score: 73

GGGACTTCGATCTTAATAATCTTGAAGATGGTACATTGTCCTCAGCATTTATGGTTGGACTGTTGGTGTCTTCGCTGATATTTGCATGCCTTGTAAAAAGgttagctctc ... ttctctgcagATATAATCCTTTCAGGCTTATTGGTGTTGGCTTGTTAGTGTGGACTATCGCAACAGCTGGTTGTGGGGTATCATTTGATTTCTGGTCAATTACTATATGC


Block sizes: 41 (upstream exon), 48 (downstream exon)
Score: 175

GGGACTTCGATCTTAATAATCTTGAAGATGGTACATTGTCCTCAGCATTTATGGTTGGACTGTTGGTGTCTTCGCTGATATTTGCATGCCTTGTAAAAAGgttagctctc ... ttctctgcagATATAATCCTTTCAGGCTTATTGGTGTTGGCTTGTTAGTGTGGACTATCGCAACAGCTGGTTGTGGGGTATCATTTGATTTCTGGTCAATTACTATATGC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 143

GGGACTTCGATCTTAATAATCTTGAAGATGGTACATTGTCCTCAGCATTTATGGTTGGACTGTTGGTGTCTTCGCTGATATTTGCATGCCTTGTAAAAAGgttagctctc ... ttctctgcagATATAATCCTTTCAGGCTTATTGGTGTTGGCTTGTTAGTGTGGACTATCGCAACAGCTGGTTGTGGGGTATCATTTGATTTCTGGTCAATTACTATATGC


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

GGGACTTCGATCTTAATAATCTTGAAGATGGTACATTGTCCTCAGCATTTATGGTTGGACTGTTGGTGTCTTCGCTGATATTTGCATGCCTTGTAAAAAGgttagctctc ... ttctctgcagATATAATCCTTTCAGGCTTATTGGTGTTGGCTTGTTAGTGTGGACTATCGCAACAGCTGGTTGTGGGGTATCATTTGATTTCTGGTCAATTACTATATGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttggagtgctattaatttttcccttgtgaccagttattttccttctctgcagATATAATCCTTTCAGGCTTATTGGTGTTGGCTTGTTAGTGTGGACTATCGCAACAGCTGGTTGTGGGGTATCATTTGATTTCTGGTCAATTACTATATGC
            tattaat  putative branch site (score: 121)
                                    ttattttccttctctg  putative PPT
         tgctattaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgccgatgtgtgtcatgcttcctgctcaccccctatcctcaaccttttggagtgctattaatttttcccttgtgaccagttattttccttctctgcagATATAATCCTTTCAGGCTTATTGGTGTTGGCTTGTTAGTGTGGACTATCGCAACAGCTGGTTGTGGGGTATCATTTGATTTCTGGTCAATTACTATATGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
gttgccg
- - - - - - - - -tgcttcc
- - - - - - - - - - - - - - caccccc