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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtctctgctcattttcatgtttgtccttgtttctggaggggtcaatctaaccattttacattatgccagGCTCTTCCTCGCTTGAGGTTTAATAAAGAAGGCAATCTTCTTGCTGTTACTACAGCAGACAATGGTTTTAAGATACTTGCAAATGCTGATGGACTTAGAA

Basic information

species Zea mays
transcript GRMZM2G316967_T01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 15
gttagtctctgctcattttcatgtttgtc-cttgtttctggaggggtcaatctaaccattttacattatgccagGCTCTTCCTCGCTTGAGGTTTAATAAAGAAGGCAATCTTCTTGCTGTTACTACAGCAGACAATGGTTTTAAGATACTTGCAAATGCTGATGGACTTAGAA
|||||||| || ||  |    ||||   |  || |||||     |||      || |  | |||||| |  |||| |||||| || |||||||| ||||||||||||||||||||||||||||||||||  |||||||| ||||||||||||||||||||||||||||| ||||
gttagtctatgttccctactgtgttaaacatttttttctcttttggtagtctaaaactgtgtacattctatcagGGTCTTCCACGGTTGAGGTTCAATAAAGAAGGCAATCTTCTTGCTGTTACTACAGTGGACAATGGGTTTAAGATACTTGCAAATGCTGATGGACTCAGAA

upper sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA20G38230.1 (Glycine max), 3'ss of exon 16
-------------gttagtctctgctcattttcatg---tttgtccttgtttctggaggggtca---atctaaccattttacattatgccagGCTCTTCCTCGCTTGAGGTTTAATAAAGAAGGCAATCTTCTTGCTGTTACTACAGCAGACAATGGTTTTAAGATACTTGCAAATGCTGATGGACTTAGAA
             ||||  || |  | | | |  ||   | |  |     |||   |    ||    || |||   | | |  || |  |||   ||||| |||||||| || || || ||||| ||| |||||||||||||||| |  ||||||||||| ||||||||||| ||||||  ||| |||||| 
gttgttatttatggttaa-ctattttaagtcttgtggaatataactacacttcataaaacatcctgtatataattgtatgaatttgt-tcagAGCCTTCCACGCTTGAGATTCAACAAGGAAGGTAATATTCTTGCTGTTACTACCGTGGACAATGGTTTCAAGATACTTGCTAATGCTTCTGGTCTTAGAT

upper sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 16
-----gttag--tctctgctcattttcatgtttgtcct-tgtttctggaggggtcaatctaaccattttac--attatgccagGCTCTTCCTCGCTTGAGGTTTAATAAAGAAGGCAATCTTCTTGCTGTTACTACAGCAGACAATGGTTTTAAGATACTTGCAAATGCTGATGGACTTAGAA
     ||||   | | |     ||||    | |  | |    ||    ||   |   |   |  ||| ||   ||     ||| | ||||| | |||||| || || || ||||| |||||||||||||||||||| |||||||| || || || || ||||| |||||| |||| |||||| 
gtggagttaacttttttatgtcttttggaatatagcttacactttataagacattccttatataattgtatgaatctattcagACCCTTCCACACTTGAGATTCAACAAGGAAGGAAATCTTCTTGCTGTTACTACTGCAGACAAGGGATTCAAAATTCTTGCTAATGCTAATGGTCTTAGAT

upper sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA19G41840.3 (Glycine max), 3'ss of exon 15
-----gttagtctctgc---tcattttcatgtttgtccttgtttctggaggggtcaatctaaccattttac--attatgccagGCTCTTCCTCGCTTGAGGTTTAATAAAGAAGGCAATCTTCTTGCTGTTACTACAGCAGACAATGGTTTTAAGATACTTGCAAATGCTGATGGACTTAGAA
     | ||   | |     || |||  |   | |       ||    ||   |   ||  |  ||| ||   ||     ||||| ||||| | |||||| || || || ||||| ||| | |||||||||||||| ||||||||||| || || || ||||| |||||  |||| |||||| 
gtggagataacttttttaagtcttttggaatatagcttacactttataagacattcctcatataattgtatgaatctattcagGCCCTTCCGCACTTGAGATTCAACAAGGAAGGAAATGTGCTTGCTGTTACTACTGCAGACAATGGATTCAAAATTCTTGCTAATGCCAATGGTCTTAGAT

upper sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA10G29090.1 (Glycine max), 3'ss of exon 16
-------------gttagtctctgctcattttcatg---tttgtccttgtttc-tggaggggtcaatcta-accattttacattatgccagGCTCTTCCTCGCTTGAGGTTTAATAAAGAAGGCAATCTTCTTGCTGTTACTACAGCAGACAATGGTTTTAAGATACTTGCAAATGCTGATGGACTTAGAA
             ||||  || |  | | | |  ||   | |  |     ||| |  |     |  | || |    | |  |||    |||   ||||| |||||||| || || || ||||| ||| ||||||||||||||||    ||||||||||| ||||||||||| ||||||  ||| |||||| 
gttggtatttatggttaa-ctattttaagtcttgtggaatataactacacttcataaaatatcctgtatatatttgtatgaatttgttcagAGCCTTCCACGCTTGAGATTCAACAAGGAAGGAAATATTCTTGCTGTTACTACCATGGACAATGGTTTCAAGATACTTGCCAATGCTTCTGGTCTTAGAT

upper sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 15
lower sequence: AT5G27030.2 (Arabidopsis thaliana), 3'ss of exon 14
-------------gttagtctctgctcattttcatgtttg--tccttgtttctggaggggtcaatctaaccattttacattatgccagGCTCTTCCTCGCTTGAGGTTTAATAAAGAAGGCAATCTTCTTGCTGTTACTACAGCAGACAATGGTTTTAAGATACTTGCAAATGCTGATGGACTTAGAA
              ||  | |   |     ||  || |||  |  | || | |  |||  |  || ||||   ||  |   |   ||||||||||| |  ||||| ||||| || || ||||||||||| || |||||||| ||||| || || |||||||| || || ||| | | |||  |  || 
gtaagtcccaaagattctttttcccatggcttgttgcttggatgttcgtctttttaggtttgcatataac---ttgtcccaacttcagGCTCTTCCCCATTTGAGATTTAACAAGGACGGCAATCTTCTAGCCGTTACTACGGCAGATAACGGATTTAAGATCCTAGCTAATCCAGCTGGTTTCCGAT

upper sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 15
lower sequence: AT3G16830.1 (Arabidopsis thaliana), 3'ss of exon 15
-------------------------gttagtctctgctcattttcatgtttgtccttgtttctggaggggtcaatctaaccattttacat------tatgccagGCTCTTCCTCGCTTGAGGTTTAATAAAGAAGGCAATCTTCTTGCTGTTACTACAGCAGACAATGGTTTTAAGATACTTGCAAATGCTGATGGACTTAGAA
                           |  |  || ||  | |  |   |  |   | ||   |     || | | ||   ||  ||  |      |||  |||  ||| || || ||||| || || || || || ||||||||||| |||||||||||||| ||||| || ||||| ||||||||| ||||||| || ||||
gtatgacattcttgcccaaaatactcctcttggctacttgtatataaaatcttttgtattctcgagcctgttactttactgatgctatgtaccgtttatttcagAATCTACCCCGATTGAGATTCAACAAGGATGGGAATCTTCTTGCAGTTACTACAGCAGATAATGGATTCAAGATCCTTGCAAATACTGATGGTCTCAGAA

upper sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 15
lower sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 15
---------------gttagtctctgctcattttcatgtttgtccttgtttctggaggggtcaatctaaccattttacattatg----ccagGCTCTTCCTCGCTTGAGGTTTAATAAAGAAGGCAATCTTCTTGCTGTTACTACAGCAGACAATGGTTTTAAGATACTTGCAAATGCTGATGGACTTAGAA
                | | ||| |  |  || |      | ||    |   || |   |   | || || |  | ||||||      ||||  | ||||||||||||| || || || ||||| |||||||||||||||||||| ||||||||||| |||||||||||||||| ||||| ||| || ||| 
gtcagtattgcaggaataaatcttttattcttatgcgaaatatctgcatgattgaatcag--gaactgacaacatcacattaaatgctccagAGTGTTCCTCGCTTGAGATTCAACAAGGAAGGAAATCTTCTTGCTGTTACTACTGCAGACAATGGATTTAAGATACTTGCAACTGCTGCTGGTCTCAGAT

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|67029310|gb|CO458059.1|CO458059
EST:     TTGACAATAATAACATGCTGATCTGCACCGATGCTGAAGGAGGCCTCCCA                         GCTCTTCCTCGCTTGAGGTTTAATAAAGAAGGCAATCTTCTTGCTGTTACT
genomic: TTGACAATAATAACATGCTGATCTGCACCGATGCTGAAGGAGGCCTCCCAgttagtctct ... attatgccagGCTCTTCCTCGCTTGAGGTTTAATAAAGAAGGCAATCTTCTTGCTGTTACT
EST: gi|6021011|gb|AW065939.1|AW065939
EST:     TTGACAATAATAACATGCTGATCTGCACCGATGCTGAAGGAGGCCTCCCA                         GCTCTTCCTCGCTTGAGGTTTAATAAAGAAGGCAATCTTCTTGCTGTTACT
genomic: TTGACAATAATAACATGCTGATCTGCACCGATGCTGAAGGAGGCCTCCCAgttagtctct ... attatgccagGCTCTTCCTCGCTTGAGGTTTAATAAAGAAGGCAATCTTCTTGCTGTTACT
EST: gi|32865226|gb|CF004908.1|CF004908
EST:     TTGACAATAATAACATGCTGATCTGCACCGATGCTGAAGGAGGCCTCCCA                         GCTCTTCCTCGCTTGAGGTTTAATAAAGAAGGCAATCTTCTTGCTGTTACT
genomic: TTGACAATAATAACATGCTGATCTGCACCGATGCTGAAGGAGGCCTCCCAgttagtctct ... attatgccagGCTCTTCCTCGCTTGAGGTTTAATAAAGAAGGCAATCTTCTTGCTGTTACT

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: 149

GAATCACATTCTGGCTGCTGGTGAAGATAACCATATTAAATTTTGGGATGTTGACAATAATAACATGCTGATCTGCACCGATGCTGAAGGAGGCCTCCCAgttagtctct ... attatgccagGCTCTTCCTCGCTTGAGGTTTAATAAAGAAGGCAATCTTCTTGCTGTTACTACAGCAGACAATGGTTTTAAGATACTTGCAAATGCTGATGGACTTAGAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 171

GAATCACATTCTGGCTGCTGGTGAAGATAACCATATTAAATTTTGGGATGTTGACAATAATAACATGCTGATCTGCACCGATGCTGAAGGAGGCCTCCCAgttagtctct ... attatgccagGCTCTTCCTCGCTTGAGGTTTAATAAAGAAGGCAATCTTCTTGCTGTTACTACAGCAGACAATGGTTTTAAGATACTTGCAAATGCTGATGGACTTAGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 204

GAATCACATTCTGGCTGCTGGTGAAGATAACCATATTAAATTTTGGGATGTTGACAATAATAACATGCTGATCTGCACCGATGCTGAAGGAGGCCTCCCAgttagtctct ... attatgccagGCTCTTCCTCGCTTGAGGTTTAATAAAGAAGGCAATCTTCTTGCTGTTACTACAGCAGACAATGGTTTTAAGATACTTGCAAATGCTGATGGACTTAGAA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 91

GAATCACATTCTGGCTGCTGGTGAAGATAACCATATTAAATTTTGGGATGTTGACAATAATAACATGCTGATCTGCACCGATGCTGAAGGAGGCCTCCCAgttagtctct ... attatgccagGCTCTTCCTCGCTTGAGGTTTAATAAAGAAGGCAATCTTCTTGCTGTTACTACAGCAGACAATGGTTTTAAGATACTTGCAAATGCTGATGGACTTAGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatgtttgtccttgtttctggaggggtcaatctaaccattttacattatgccagGCTCTTCCTCGCTTGAGGTTTAATAAAGAAGGCAATCTTCTTGCTGTTACTACAGCAGACAATGGTTTTAAGATACTTGCAAATGCTGATGGACTTAGAA
                              atctaac  putative branch site (score: 91)
                                      attttacattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtctctgctcattttcatgtttgtccttgtttctggaggggtcaatctaaccattttacattatgccagGCTCTTCCTCGCTTGAGGTTTAATAAAGAAGGCAATCTTCTTGCTGTTACTACAGCAGACAATGGTTTTAAGATACTTGCAAATGCTGATGGACTTAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA