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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctcattcgtcctcacatgctacatctcttacatacatccagttgtggtttttgagaagtgtggttccttgattcttgctcttgtttgtagCTACTCGAGATTTTGTCAGAATTCACCCCTGAGCAGCAGCATGCGTTCTGCCAGTTTGTAACCGGTGCTCCTCGGCTTCCACATGGTGGATTGGCTGCCC

Basic information

species Zea mays
transcript GRMZM2G374574_T02
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G374574_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os02g01170.1 (Oryza sativa), 3'ss of exon 7
gtaagctcattcgtcctcacatgctacatctcttacatacatccagttgtggtttttgagaagtgtggttccttgattcttgctcttgtttgtagCTACTCGAGATTTTGTCAGAATTCACCCCTGAGCAGCAGCATGCGTTCTGCCAGTTTGTAACCGGTGCTCCTCGGCTTCCACATGGTGGATTGGCTGCCC
                      |||| ||   || || | |||    | |||  ||    |||| | ||| ||| |||  |   | ||||||||||||||||||||  || | ||||||||||| ||||| || ||||| ||||||||||||||||| ||||||||||||||||| | |||||| || |||||||
--------------gtaagtgcgctatatgcatttca-atatctgaat-tggccttctgtaagtttagttacttaattgctctacatgtttgtagCTACTCGAGATCATGGCTGAATTCACCCCAGAGCAACAACATGCATTCTGCCAGTTTGTAACTGGTGCTCCTCGGCTTCCGCCTGGTGGTTTAGCTGCCC

upper sequence: GRMZM2G374574_T01 (Zea mays), 3'ss of exon 14
lower sequence: Vv04s0023g03830.t01 (Vitis vinifera), 3'ss of exon 14
gtaagctcattcgtcctcacatgctacatctcttacat-----aca---tccagttgtggtttttgagaagtg------tggttccttgattct--tgctcttg-tttgtagCTACTCGAGATTTTGTCAGAATTCACCCCTGAGCAGCAGCATGCGTTCTGCCAGTTTGTAACCGGTGCTCCTCGGCTTCCACATGGTGGATTGGCTGCCC
||||| |  ||| |        |  |  |   ||   |     |||   |  | |  |   | ||    | ||      || ||  || ||| |  |||  ||| ||| ||| |||| || ||  ||  ||||||||| ||||||||||||||||| |||||||| ||  | || ||||| ||| ||||||| | ||| ||  ||||     
gtaagattcttcctatatttggggcatttggatttagtgggaaacagggtgtaatgataactcttatatattgactgcatgatttgtttattgtaatgcctttgctttctagTTACTTGAAATCATGGGAGAATTCACTCCTGAGCAGCAGCATGCATTCTGCCAATTCATTACTGGTGCACCTAGGCTTCCTCCTGGAGGTCTGGCAATGT
















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|37379576|gb|CF626532.1|CF626532
EST:     AAAAGTCCTGCGATCGTGAAT                         CTACTCGAGA-TTTGTCAGAATTTCACCCNTGAGCAGCAGCATGCGTTCTG
genomic: AAAAGTCCTGCGATCGTGAATgtaagctcat ... ttgtttgtagCTACTCGAGATTTTGTCAGAA-TTCACCCCTGAGCAGCAGCATGCGTTCTG
EST: gi|26558996|gb|CA831231.1|CA831231
EST:     ACATAAAATTTGATCATGGATACACTGCTAAAAGTCCTGCGATCGTGAAT                         CTACTCGAGATTTTGTCAGAATTCACCCCTGAGCAGCAGCATGC
genomic: ACATAAAATTTGATCATGGATATACTGCTAAAAGTCCTGCGATCGTGAATgtaagctcat ... ttgtttgtagCTACTCGAGATTTTGTCAGAATTCACCCCTGAGCAGCAGCATGC
EST: gi|87157724|gb|DY402513.1|DY402513
EST:     ACATAAAATTTGATCATGGATATACTGCTAAAAGTCCTGCGATCGTGAAT                         CTACTCGAGATTTTGTCAGAATTCACCCCTGAGCAGCAGCATGCGTTCTGC
genomic: ACATAAAATTTGATCATGGATATACTGCTAAAAGTCCTGCGATCGTGAATgtaagctcat ... ttgtttgtagCTACTCGAGATTTTGTCAGAATTCACCCCTGAGCAGCAGCATGCGTTCTGC
EST: gi|211367974|gb|FL128469.1|FL128469
EST:     ACATAAAATTTGATCATGGATATACTGCTAAAAGTCCTGCGATCGTGAAT                         CTACTCGAGATTTTGTCAGAATTCACCCCTGAGCAGCAGCATGCGTTCTGC
genomic: ACATAAAATTTGATCATGGATATACTGCTAAAAGTCCTGCGATCGTGAATgtaagctcat ... ttgtttgtagCTACTCGAGATTTTGTCAGAATTCACCCCTGAGCAGCAGCATGCGTTCTGC
EST: gi|31558796|gb|CD528008.1|CD528008
EST:     GGATATACTGCTAAAAGTCCTGCGATCGTGAAT                         CTACTCGAGATTTTGTCAGAATTCACCCCTGAGCAGCAGCATGCGTTCTGC
genomic: GGATATACTGCTAAAAGTCCTGCGATCGTGAATgtaagctcat ... ttgtttgtagCTACTCGAGATTTTGTCAGAATTCACCCCTGAGCAGCAGCATGCGTTCTGC

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), 47 (downstream exon)
Score: 45

TCGGAATCCCTGGTGGATAACATAAAATTTGATCATGGATATACTGCTAAAAGTCCTGCGATCGTGAATgtaagctcat ... ttgtttgtagCTACTCGAGATTTTGTCAGAATTCACCCCTGAGCAGCAGCATGCGTTCTGCCAGTTTGTAACCGGTGCTCCTCGGCTTCCACATGGTGGATTGGCTGCCC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 50

TCGGAATCCCTGGTGGATAACATAAAATTTGATCATGGATATACTGCTAAAAGTCCTGCGATCGTGAATgtaagctcat ... ttgtttgtagCTACTCGAGATTTTGTCAGAATTCACCCCTGAGCAGCAGCATGCGTTCTGCCAGTTTGTAACCGGTGCTCCTCGGCTTCCACATGGTGGATTGGCTGCCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 23

TCGGAATCCCTGGTGGATAACATAAAATTTGATCATGGATATACTGCTAAAAGTCCTGCGATCGTGAATgtaagctcat ... ttgtttgtagCTACTCGAGATTTTGTCAGAATTCACCCCTGAGCAGCAGCATGCGTTCTGCCAGTTTGTAACCGGTGCTCCTCGGCTTCCACATGGTGGATTGGCTGCCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 51

TCGGAATCCCTGGTGGATAACATAAAATTTGATCATGGATATACTGCTAAAAGTCCTGCGATCGTGAATgtaagctcat ... ttgtttgtagCTACTCGAGATTTTGTCAGAATTCACCCCTGAGCAGCAGCATGCGTTCTGCCAGTTTGTAACCGGTGCTCCTCGGCTTCCACATGGTGGATTGGCTGCCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atccagttgtggtttttgagaagtgtggttccttgattcttgctcttgtttgtagCTACTCGAGATTTTGTCAGAATTCACCCCTGAGCAGCAGCATGCGTTCTGCCAGTTTGTAACCGGTGCTCCTCGGCTTCCACATGGTGGATTGGCTGCCC
                              ccttgat  putative branch site (score: 51)
                                    ttcttgctcttgttt  CT-rich tract
            tttttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctcattcgtcctcacatgctacatctcttacatacatccagttgtggtttttgagaagtgtggttccttgattcttgctcttgtttgtagCTACTCGAGATTTTGTCAGAATTCACCCCTGAGCAGCAGCATGCGTTCTGCCAGTTTGTAACCGGTGCTCCTCGGCTTCCACATGGTGGATTGGCTGCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA