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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctcatacatattacataaacgttttatctgggcttgataaatattttcctttctacag

Basic information

species Zea mays
transcript GRMZM2G148323_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 5'ss of exon 10
TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctcatacata-ttacataaacgtttta------tctgggcttgataaatattttcctttctacag-------------------------------------------------------------------------------
|||||| ||||||||||||||||| |||||||||||||||||||| |||||||||||| |||||||||||||||||||||||||||||||||||||||||||| ||| ||| | ||| | | ||||| | ||| | ||| | | | | |
TTTCTATGAGGAGCAATTGCACCGGATGGAGTGCATGGCACAAGAACCTGTGCTTTTTGAGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagcatcttggacagaattattgatgcattttaggcctgtttggaacagtggaatgtcagcatgttgaggaattgcaccatttaatgcaaaattcctgtgttccaaacaagtccttaaactgaatttgataaatcttttcttttccacag

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA03G41180.1 (Glycine max), 5'ss of exon 10
TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctcatacatattacataaacgttttatctgggcttgataaatatt--ttcctttctacag---------------------------------
||| || |||||||||||||| ||||||||||||||||| ||||| |||||||||||| ||| ||| | |||||||| ||||| ||||||||||| ||||| | | | | || | || || | || |||| || || | |||
TTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAAGAACCTGTGCTTTTTGAGGATATACTGTGCCAGATTATTGACATGATTGGACCTGAGgtttgtctttcaattttttttttctactgattgtttgcccttgtattatgttgatgagaagtcacattagctggaatatgatattctaatctagtcagta

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA20G35090.1 (Glycine max), 5'ss of exon 10
TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctcatacatattacataaacgttttatctgggcttgataaatattttcctttctacag--------------------------------
|| || |||||||| ||||| || |||||||||||||| |||||||||||||| ||| || ||||| || ||||| | |||||||||||||||||||| | | | | | || | | | | |||| | || ||| |||
CTTTTATGAGGAGCAGTTGCATCGGATGGAGTGCATGGCCCAAGAGCCTGTGCTGTTTGAAGATATATTGTGTCAGATTGTGGATATGATTGGACCAGAGgtttttctttgttcttgttcttgcgtcttgattcttttacttgtttttgtttcattcctctgcagtatagcaagtggtaactgtcctacgtttgcag

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA19G43790.1 (Glycine max), 5'ss of exon 10
TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctcatacatattacataaacgtt--------ttatctgggcttgataaatattttcctttctacag---------------------------
||| || |||||||||||||| ||||||||||||||||| ||||| |||||||||||| ||| ||| | |||||||| ||||| ||||||||||| ||||| | | | | || || || || | | | ||||| | | | | || |
TTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAAGAACCTGTGCTTTTTGAGGATATACTGTGCCAGATTATTGACATGATTGGACCTGAGgtttgtctttcaatgttttttttatttattgtttgcccttgtattgtgttgatgagaagtcacattagttggaatatgatatgctaatctagtctgtagt

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA20G36530.1 (Glycine max), 5'ss of exon 10
TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctcatacat-----------attacataaacgttttatc-tgggcttgataaatattttcctttctacag-----------------------
||| || ||||| |||||||| || |||||||||||||| |||||||||||||||||| ||||||||| || ||||| ||||| |||||| ||| ||||| | | | ||| | | | |||| || | | ||| | | | ||||| |
TTTTTATGAGGAACAATTGCATCGGATGGAGTGCATGGCCCAAGAGCCTGTGCTTTTTGAGGACATATTGTGTCAGATAATTGACATGATTAAACCTGAGgtttgcctttccatctttcttttgatgattgtttgatctttttttcattgtgttgttgtgaaataacctttgcctggaaaagaaagtacaactctagtga

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA10G32500.1 (Glycine max), 5'ss of exon 10
TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctcatacatattacataaacgttttatctgggcttgataaatattttcctttctacag--------------------------------
|| || |||||||| ||||| || |||||||||||||| |||||||||||||| ||| || ||||| || ||||| | |||||||||||||||||||| | | | | | || | | | | |||| | ||| | ||| |||
CTTTTATGAGGAGCAGTTGCATCGGATGGAGTGCATGGCCCAAGAGCCTGTGCTGTTTGAAGATATATTGTGTCAGATTGTGGATATGATTGGACCAGAGgtttttctttgttcttgttcttgcgtcttgattcttttacttgtttttgttttactcctctgcagtatagcaagtggtaactgtcctacgtttgcag

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA10G30930.1 (Glycine max), 5'ss of exon 10
TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtaga--ttctcatacatattac-ataaacgttttatctgggcttgata-aatatttt----cctttctacag---------------------------
||| || |||||||||||||| || ||||| |||||||| |||||||||||||| ||| ||||||||| || ||||| ||||| |||||| ||| ||||| || |||| | || || | |||| |||| | | | || | || |||
TTTTTATGAGGAGCAATTGCATCGGATGGAATGCATGGCCCAAGAGCCTGTGCTCTTTGAGGACATATTGTGTCAGATAATTGACATGATTAAACCTGAGgtttgcctttccatatttcttttgatgattgtttgatcttctatcattgtggtgttgtaaaattgttggacaagtgacctcaataatttaaggggggggg

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 10
lower sequence: AT5G28850.1 (Arabidopsis thaliana), 5'ss of exon 9
TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctcatacatattacataaacgttttatctgggcttgataa-atattttcctttctacag---------------------------------------------------------------------------------
|| || || ||||| ||||| |||||||||||||||| |||||| |||| ||||| ||| || ||||| ||||||||||||||||| ||||| ||||| | || | || | || | ||| | || |||| | | || ||||
CTTTTATGAAGAGCAGTTGCATAGAATGGAGTGCATGGCGCAAGAGGCTGTTCTTTTCGAGGATATCTTATGTCAGATGATTGATATGATCGGACCTGAGgttcaacaatatgtctcttgttt---ttttctttctatattaaggaagatatatgacagtc-acagaagtagtttgggttcccagtttttctttctgactcttgcgattttgtcttgtgtttgattgttttttatttccttccacag

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 10
lower sequence: AT5G28900.1 (Arabidopsis thaliana), 5'ss of exon 10
TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctcatacatattacataaacgttt---tatctgggcttg----ataaatattttcctttctacag-------------------------------------------------------------
|| || || ||||| ||||| |||||||||||||||| |||||| |||| ||||| ||| || ||||| ||||||||||||||||| ||||| ||||| | ||| | || | ||| ||| | | | | | || || ||| ||| |||
CTTTTATGAAGAGCAGTTGCATAGAATGGAGTGCATGGCGCAAGAGGCTGTTCTTTTCGAGGATATCTTATGTCAGATGATTGATATGATCGGACCTGAGgttcaacaatatatctcttgttttcttctttctatatttagtatagtcacagaagtagtttgtgttcc-cagttttctttctgagtcttgtgattttgttttgtgtttgattgttttttatttccttccacag

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 10
lower sequence: Vv07s0005g03730.t01 (Vitis vinifera), 5'ss of exon 11
TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgt-agattctcatacatattacataaacgttttatctgggcttgataaatattttcctttctacag--------------------
|| || |||||||||||||| |||||||| |||||||| ||||||||||| || ||| ||| || ||||| ||||| |||| ||||||| ||||||||| | | | | || | | | | | | | | | | | | |||
CTTTTATGAGGAGCAATTGCATCGAATGGAATGCATGGCCCAAGAGCCTGTACTATTTGAGGATATCTTATGTCAGATAGTTGACATGATTGCACCAGAGgtcacggcttttttcgtacccagatcatctcccgtgttctagtagttagcaataactcattttcagggcatgatttttgcttgcag

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 10
lower sequence: PP1S7_163V6.1 (Physcomitrella patens), 5'ss of exon 10
TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctcataca-----tattacataaac-gttttatc--tgggcttgataaatattt--tcctttctacag--------------------------------------------------
||| |||||||||||| | || || |||||||||||||| || |||||||| |||||| ||| || | || || |||| |||||||| ||||| | ||| | | | ||||| | || | | | || || | | | | || || |
TTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGACAGATATGATCGGACCTGCTgtaagcgtttgagtagtctcttctacattggttgcttcactattcgactaaatgggtctcgcattcatttcactgctagttaatgtgaagttttcactgaaacttatcctctactctggctgcag

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|23199690|gb|BU582255.1|BU582255
EST:     TATGATTGGACCAGAG                         AATGAGAGCTATTTAACTCTACGGGACTTAAAACGG-GTAAACTCTCAGGA
genomic: TATGATTGGACCAGAGgtagattctc ... ctttctacagAATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGA
EST: gi|87156079|gb|DY400868.1|DY400868
EST:     TGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAT                         AATGAGAGCTATTTAATTCTACAGGACTT
genomic: TGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctc ... ctttctacagAATGAGAGCTATTTAACTCTACGGGACTT
EST: gi|83279222|gb|DV943230.1|DV943230
EST:     TATGCCAGATGATTGATATGATTGGACCAGAG                         AATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGA
genomic: TATGCCAGATGATTGATATGATTGGACCAGAGgtagattctc ... ctttctacagAATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGA
EST: gi|23199745|gb|BU582310.1|BU582310
EST:     TGCTTTTTCTGGACATATTATGCCAGATGATTGCTATGATTGGACCAGAG                         AATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGA
genomic: TGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctc ... ctttctacagAATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGA
EST: gi|211505069|gb|FK974737.1|FK974737
EST:     TGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAG                         AATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGA
genomic: TGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctc ... ctttctacagAATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGA
EST: gi|26560172|gb|CA832407.1|CA832407
EST:     TGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAG                         AATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGA
genomic: TGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctc ... ctttctacagAATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGA

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: 48 (upstream exon), 48 (downstream exon)
Score: 323

TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctc ... ctttctacagAATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 224

TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctc ... ctttctacagAATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 211

TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctc ... ctttctacagAATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 247

TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctc ... ctttctacagAATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctcatacatattacataaacgttttatctgggcttgataaatattttcctttctacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG