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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATTAAGGCCTGGCTTTATGACAATATGGGATCTAGGGTGGACTACGATGCTCCTGGCAAGTGGTGTACTACTATGCTATATAGTGCTGATGGAACTAGgtaagaatagttaggttggctcttatttttatcaccaaagttagttctagttttcaatttttactgaggaaacaatttgccttttcttcatgtgaag

Basic information

species Zea mays
transcript GRMZM2G316967_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G316967_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os01g15020.2 (Oryza sativa), 5'ss of exon 14
AAATTAAGGCCTGGCTTTATGACAATATGGGATCTAGGGTGGACTACGATGCTCCTGGCAAGTGGTGTACTACTATGCTATATAGTGCTGATGGAACTAGgtaagaatagttaggttggctcttatttttatcaccaaagttagttctagttttcaatttttactgaggaaacaatttgccttttcttcatgtgaag
|||||||||| |||||||||||  |||||||||| ||||| || || |||||||| || || ||||||||||||||||| ||||| ||||||||||||||||||| | || ||         ||| |||  |  | ||||||       || || | || ||  ||  | |  ||||| | | || ||||| |||||
AAATTAAGGCATGGCTTTATGATCATATGGGATCCAGGGTAGATTATGATGCTCCAGGAAAATGGTGTACTACTATGCTTTATAGCGCTGATGGAACTAGgtaagcagaggta---------ttactttcgtaccgaaagtt-------gtctttagttattgttgttgtactaatttacttgtttttcatatgaag

upper sequence: GRMZM2G316967_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA10G29090.1 (Glycine max), 5'ss of exon 15
AAATTAAGGCCTGGCTTTATGACAATATGGGATCTAGGGTGGACTACGATGCTCCTGGCAAGTGGTGTACTACTATGCTATATAGTGCTGATGGAACTAGgtaagaatagttaggttggctcttatt-tttatcaccaaagttagttctagttttcaatttttactgaggaaacaatttgccttttcttcatgtgaag----------------------
|||| ||||| ||||| || || || ||||| |||||||| ||||| ||||| |||||  | ||||| ||||| ||||| || ||||||||||||||||||||||     |  || ||    | ||| ||  |   ||   | |    | ||  |   |      | | ||   | | |        ||| | |||                        
AAATAAAGGCATGGCTATACGATAACATGGGTTCTAGGGTTGACTATGATGCCCCTGGTCACTGGTGCACTACAATGCTTTACAGTGCTGATGGAACTAGgtaagttggatatggatgagggtaattattcctttacagtatcatgcttggtgcttggtggacgtttaagatgtattatattaaagtttcttatgacattttccaaaatattttctccag

upper sequence: GRMZM2G316967_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA03G39290.1 (Glycine max), 5'ss of exon 15
AAATTAAGGCCTGGCTTTATGACAATATGGGATCTAGGGTGGACTACGATGCTCCTGGCAAGTGGTGTACTACTATGCTATATAGTGCTGATGGAACTAGgtaagaatagttaggttggc--------tcttatttttatcaccaaagttagttctagttttcaatttttactgaggaaacaatttgccttttcttcatgtgaag--------------
|||| || |||||| | || || |||||||| |||||||| || || ||||| || ||  | ||||||||||| ||||| || ||||||||||||| ||||||||||   || || ||          | | | ||| ||   ||| |     |  | |||   || | |       || |   ||  | | ||||| | |  |               
AAATAAAAGCCTGGTTATACGATAATATGGGTTCTAGGGTTGATTATGATGCCCCAGGTCATTGGTGTACTACAATGCTTTACAGTGCTGATGGAAGTAGgtaagaaggatttgggtgcggataagtatttaagtttcatgttcaatggataattgaatttgagatgtattaaataaaaccgtattaacatgtcttcctatttatcattatttctatag

upper sequence: GRMZM2G316967_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA19G41840.2 (Glycine max), 5'ss of exon 14
AAATTAAGGCCTGGCTTTATGACAATATGGGATCTAGGGTGGACTACGATGCTCCTGGCAAGTGGTGTACTACTATGCTATATAGTGCTGATGGAACTAGgtaagaatagttaggttggc--------tcttatttttatcaccaa-agttagttctagttt-tcaatttttactgaggaaaca-atttgccttttcttcatgtgaag---------
|||| || |||||| | ||||| |||||||| |||||||| || || ||||| || ||  | ||||||||||| ||||| || ||||||||||||| ||||||||||   || || ||          | | | ||| ||   |||  | || ||    | | | || |   || |    ||||  | | ||| ||  || |               
AAATAAAAGCCTGGTTATATGATAATATGGGTTCTAGGGTTGATTATGATGCCCCAGGTCATTGGTGTACTACAATGCTTTACAGTGCTGATGGAAGTAGgtaagaaggatttgggtgcggataagtatttaagtttcatgttcaatggataattaagatgtattaaataaaaccgtattaacatgtcttcctatttgtcttccattatttctatag

upper sequence: GRMZM2G316967_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA20G38230.1 (Glycine max), 5'ss of exon 15
AAATTAAGGCCTGGCTTTATGACAATATGGGATCTAGGGTGGACTACGATGCTCCTGGCAAGTGGTGTACTACTATGCTATATAGTGCTGATGGAACTAGgtaagaatagttaggttggctcttatt-tttatcaccaaagttagttctagttttcaatttttactgaggaaac--aatttgccttttcttcatgtgaag-------------
|||| ||||| ||| | || || || ||||| |||||||| ||||| ||||| |||||  | ||||| ||||| ||||| || ||||| |||||||||||||||||    || || ||    | ||| ||      ||   | |     | |    ||||   |   |  | |   || || | | |    | |   ||              
AAATAAAGGCATGGTTATACGATAACATGGGTTCTAGGGTTGACTATGATGCCCCTGGTCACTGGTGCACTACAATGCTTTACAGTGCAGATGGAACTAGgtaagatggatttggatgagggtaattattcggttacagtatcatgctcaatggataattaagatgtattatattaaagtttcttatgacactttccaaaatattttctccag

upper sequence: GRMZM2G316967_T01 (Zea mays), 5'ss of exon 14
lower sequence: AT5G27030.2 (Arabidopsis thaliana), 5'ss of exon 13
AAATTAAGGCCTGGCTTTATGACAATATGGGATCTAGGGTGGACTACGATGCTCCTGGCAAGTGGTGTACTACTATGCTATATAGTGCTGATGGAACTAGgtaagaatagttaggttggctcttatttttatcaccaaagttagttctagttttcaatttttactgaggaaacaatttg---ccttttcttca-tgtgaag------------------------------------------------------------------------------------------
|||| || |||||||||||||| ||| |||| || || || ||||| |||||||| || || |||||||| |  ||||| || ||||||||||| |||||||||||    |||   |       ||||   ||  | |      || |  | |||| |  | | |    |||   ||      ||||| || | |  | ||                                                                                          
AAATAAAAGCCTGGCTTTATGATAATCTGGGTTCCAGAGTTGACTATGATGCTCCCGGTAAATGGTGTACGAGGATGCTTTACAGTGCTGATGGTACTAGgtaagatc--ttaaactcataaacatttccctcttctataccgcttgt--tcttcactcctcagtttccaaaatcttcagattcttttgtttactccggaggatactgagttgtgtccttgagtttctaatcttatctttctgttttaagtttaccttttcagtgctttctgatgttttttcccccttcag

upper sequence: GRMZM2G316967_T01 (Zea mays), 5'ss of exon 14
lower sequence: Vv14s0060g01680.t01 (Vitis vinifera), 5'ss of exon 14
AAATTAAGGCCTGGCTTTATGACAATATGGGATCTAGGGTGGACTACGATGCTCCTGGCAAGTGGTGTACTACTATGCTATATAGTGCTGATGGAACTAGgtaagaatagttaggttggctcttatttttatcaccaaagttagttctagttttcaatttttactgaggaaacaattt--gccttttcttcatgtgaag-------------------------------------------------------------------------------------------------------
||||||| |||||| | |||||||| || || || || || ||||| |||||||||||    ||||| ||||| ||||| || ||||||||||||| ||||||||| | || |  ||  |  ||       | |  ||| ||  || || |||||  ||||| || |    | |||||   | |||   | ||||                                                                                                           
AAATTAAAGCCTGGTTGTATGACAACATTGGGTCCAGAGTTGACTATGATGCTCCTGGGCTATGGTGCACTACAATGCTTTACAGTGCTGATGGAAGTAGgtaagattggtgaaattcacaattccagacctaataaaattttattttatttttc--tttttgctcaatttaaaatttcaacttttctgtaatgttgttatagttgtcttttcataccatactgtgctacttttgatcaaatatatctgacagaacatttgtaactaatttgtgactttttttttcctcttcttcttttcag

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|6021011|gb|AW065939.1|AW065939
EST:     GCTCCCGGCAAGTGGTGTACTACTATGCTATATAGTGCTGATGGGACTAG                         GTTGTTCTCATGTGGAACTAGCAAAGAGGGAGACTCCTATTTGGTTGAGTG
genomic: GCTCCTGGCAAGTGGTGTACTACTATGCTATATAGTGCTGATGGAACTAGgtaagaatag ... tcatgtgaagGTTGTTCTCATGTGGAACTAGCAAAGAGGGAGACTCCTATTTGGTTGAGTG
EST: gi|32865226|gb|CF004908.1|CF004908
EST:     GCTCCCGGCAAGTGGTGTACTACTATGCTATATAGTGCTGATGGGACTAG                         GTTGTTCTCATGTGGAACTAGCAAAGAGGGAGACTCCTATTTGGTTGAGTG
genomic: GCTCCTGGCAAGTGGTGTACTACTATGCTATATAGTGCTGATGGAACTAGgtaagaatag ... tcatgtgaagGTTGTTCTCATGTGGAACTAGCAAAGAGGGAGACTCCTATTTGGTTGAGTG

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: 47 (upstream exon), 48 (downstream exon)
Score: 167

AAATTAAGGCCTGGCTTTATGACAATATGGGATCTAGGGTGGACTACGATGCTCCTGGCAAGTGGTGTACTACTATGCTATATAGTGCTGATGGAACTAGgtaagaatag ... tcatgtgaagGTTGTTCTCATGTGGAACTAGCAAAGAGGGAGACTCCTATTTGGTTGAGTGGAATGAAAGTGAAGGATCTATCAAGAGGACATATTCTGGATTCCGTAAA


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 140

AAATTAAGGCCTGGCTTTATGACAATATGGGATCTAGGGTGGACTACGATGCTCCTGGCAAGTGGTGTACTACTATGCTATATAGTGCTGATGGAACTAGgtaagaatag ... tcatgtgaagGTTGTTCTCATGTGGAACTAGCAAAGAGGGAGACTCCTATTTGGTTGAGTGGAATGAAAGTGAAGGATCTATCAAGAGGACATATTCTGGATTCCGTAAA


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 192

AAATTAAGGCCTGGCTTTATGACAATATGGGATCTAGGGTGGACTACGATGCTCCTGGCAAGTGGTGTACTACTATGCTATATAGTGCTGATGGAACTAGgtaagaatag ... tcatgtgaagGTTGTTCTCATGTGGAACTAGCAAAGAGGGAGACTCCTATTTGGTTGAGTGGAATGAAAGTGAAGGATCTATCAAGAGGACATATTCTGGATTCCGTAAA


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 99

AAATTAAGGCCTGGCTTTATGACAATATGGGATCTAGGGTGGACTACGATGCTCCTGGCAAGTGGTGTACTACTATGCTATATAGTGCTGATGGAACTAGgtaagaatag ... tcatgtgaagGTTGTTCTCATGTGGAACTAGCAAAGAGGGAGACTCCTATTTGGTTGAGTGGAATGAAAGTGAAGGATCTATCAAGAGGACATATTCTGGATTCCGTAAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAATTAAGGCCTGGCTTTATGACAATATGGGATCTAGGGTGGACTACGATGCTCCTGGCAAGTGGTGTACTACTATGCTATATAGTGCTGATGGAACTAGgtaagaatagttaggttggctcttatttttatcaccaaagttagttctagttttcaatttttactgaggaaacaatttgccttttcttcatgtgaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA