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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATTATACTCATTAGAGATATTCCTGATGCAAAGGAAAGCGGTTTATTTCACTTATGCGAATTCATAGAAGATTGTGAATTCACCTATTTGTCCACTCAGgtaatcaattaatcattctgcaagcatgtaatttggaaaatacctgtaagatatcaatttaattatctttttttttgtctaaatggtatttttcttttgt...

Basic information

species Zea mays
transcript GRMZM2G036034_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G036034_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os07g10150.1 (Oryza sativa), 5'ss of exon 10
TATTATACTCATTAGAGATATTCCTGATGCAAAGGAAAGCGGTTTATTTCACTTATGCGAATTCATAGAAGATTGTGAATTCACCTATTTGTCCACTCAGgtaat---caattaatcattctgcaagcatgtaatttggaaaatacctgtaagatatcaatttaattatctttttttttgtctaaatggtatttttcttttgt
||| ||||||||||||||||||||||||||||| ||||| |||||||||||||| || |||||||| ||||||||||| ||||| ||| |||| |||||||||||   ||||  |||||| |  ||   |||| |||| ||   ||  || |  |   || |||      | |   ||  |    |   | |  | |||    
TATCATACTCATTAGAGATATTCCTGATGCAAAAGAAAGTGGTTTATTTCACTTGTGTGAATTCATTGAAGATTGTGAGTTCACTTATATGTCTACTCAGgtaatggccaatctatcattttataaatgtgtattttgcaagtcactagttatttccgaacttaggaggttgtaacttaattgcgacaatgtcatgcttg---

upper sequence: GRMZM2G036034_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA06G01520.1 (Glycine max), 5'ss of exon 10
TATTATACTCATTAGAGATATTCCTGATGCAAAGGAAAGCGGTTTATTTCACTTATGCGAATTCATAGAAGATTGTGAATTCACCTATTTGTCCACTCAGgtaatcaattaatcat-tctgcaagcatgtaat-ttggaaaatacctgtaagatatcaatttaattatctttttttttgtctaaatggtatttttctt-ttgt--
| | || |||||||||||||| |||||||||||||||   || ||  ||||  | || || ||||| ||||||||||| ||||| ||||||||||| |||||| |   |  | | | |     |  ||  | | || |   ||  || |    |   | | ||   |||||  || ||  | |  | ||     |  |  |||  
TGTGATTCTCATTAGAGATATCCCTGATGCAAAGGAAGTGGGGTTGCTTCATCTTTGTGAGTTCATTGAAGATTGTGAGTTCACTTATTTGTCCACGCAGgtattacttccagcttgtgcttcattattcactgtttgtgcatttcttttgtctggaattcta--catcttggttgttaaccattttgttccccttgtactgtag

upper sequence: GRMZM2G036034_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA04G01470.1 (Glycine max), 5'ss of exon 10
TATTATACTCATTAGAGATATTCCTGATGCAAAGGAAAGCGGTTTATTTCACTTATGCGAATTCATAGAAGATTGTGAATTCACCTATTTGTCCACTCAGgtaatcaattaatcattctgcaagcatgtaatt-tggaaaatacctgtaagatatcaatttaattatctttttttttgtc-taaatggtatt-tttcttttgt-------
| | || |||||||||||||| ||| |||||||||||   || ||  ||||  | || || ||||||||||||||||| ||||| ||||||||||| |||||| | | ||     || |||  |    | ||| |  |   |   || |     |   | |     |||   | || ||  | || | | || || |  ||||       
TGTGATTCTCATTAGAGATATCCCTAATGCAAAGGAAGCTGGGTTGCTTCATCTTTGTGAGTTCATAGAAGATTGTGAGTTCACTTATTTGTCCACACAGgta-ttacttccgacttgtgcttgtgcttcattattcactgtttgtgcatttcttttgtctggaattctacatcttggttgttaacgattttgttccccttgtactgtag

upper sequence: GRMZM2G036034_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA11G12610.1 (Glycine max), 5'ss of exon 10
TATTATACTCATTAGAGATATTCCTGATGCAAAGGAAAGCGGTTTATTTCACTTATGCGAATTCATAGAAGATTGTGAATTCACCTATTTGTCCACTCAGgtaatcaattaatcattctgca--agcatgtaatttggaaaatacctgtaagatatcaatttaattatctttttttttgtctaaatggtatttttcttttgt
| | || || ||||||||||| |||||||| |||||||| || ||  ||||| | || || || || ||||||||||||||||| ||||||||||| |||||| | | ||     || | |     ||| || ||||     | |  |     ||||  |||  | || ||| | | | ||     |               
TGTGATTCTTATTAGAGATATCCCTGATGCTAAGGAAAGTGGGTTGCTTCACCTTTGTGAGTTTATTGAAGATTGTGAATTCACTTATTTGTCCACACAGgtagtaattttggttttgtcctttgccatttactttgtgtgcttctggatttttatct-tttggtaatttttctctctatcccttag---------------

upper sequence: GRMZM2G036034_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA12G04820.1 (Glycine max), 5'ss of exon 10
TATTATACTCATTAGAGATATTCCTGATGCAAAGGAAAGCGGTTTATTTCACTTATGCGAATTCATAGAAGATTGTGAATTCACCTATTTGTCCACTCAGgtaatcaattaatcattctgca--agcatgtaatttggaaaatacctgtaagatatcaatttaattatctttttttttgtctaaatggtatttttcttttgt
| | || || ||||||||||| |||||||| |||||||| || ||  ||||  | || || || || ||||||||||||||||| ||||||||||| |||||| | | ||     || | |     ||| || ||||     | |  |     ||||  ||||||| |   ||||| | ||||     ||            
TGTGATTCTTATTAGAGATATCCCTGATGCTAAGGAAAGTGGGTTGCTTCATCTTTGTGAGTTTATTGAAGATTGTGAATTCACTTATTTGTCCACACAGgtagtaattttggttttgtcctttgccatttactttgtgcgcttctggatttttatc--tttaattgttaatttttctctctatcccttag-----------

upper sequence: GRMZM2G036034_T01 (Zea mays), 5'ss of exon 10
lower sequence: AT4G34450.1 (Arabidopsis thaliana), 5'ss of exon 9
TATTATACTCATTAGAGATATTCCTGATGCAAAGGAAAGCGGTTTATTTCACTTATGCGAATTCATAGAAGATTGTGAATTCACCTATTTGTCCACTCAGgtaatcaattaatcattc-tgcaagcatgtaatttggaaaatacctgtaagatatcaatttaattatctttttttttgtctaaatggtatttttcttttgt
| | |   | || ||||||||||| |||||||||||||| ||  |  ||||  |||| |||||||| ||||||||||||||||| ||| | || || |||||||| | |  ||||| | |    |  ||  |||    ||| || | |  | |||  |  |  ||||  |                               
TGTGACCATTATCAGAGATATTCCGGATGCAAAGGAAAGTGGACTGCTTCATCTATGTGAATTCATTGAAGATTGTGAATTCACATATCTTTCAACACAGgtaattattccatcatccatctggggttgctatt----aaaaacttatgtgttattgaaatgtttattctcgcacag------------------------

upper sequence: GRMZM2G036034_T01 (Zea mays), 5'ss of exon 10
lower sequence: Vv03s0063g02450.t01 (Vitis vinifera), 5'ss of exon 10
TATTATACTCATTAGAGATATTCCTGATGCAAAGGAAAGCGGTTTATTTCACTTATGCGAATTCATAGAAGATTGTGAATTCACCTATTTGTCCACTCAGgtaatcaattaatcattctgcaagcatgtaatttggaaaatacctgtaagatatcaatttaattatctttttttttgtctaaatggtatttttcttttgt
  | || ||||| |||||||||||||||||||| |||||||| ||  ||||  | || ||||| || ||||||||||| ||||||||| | || || ||||||     ||  ||  | |   | | |  | |   |   ||     | |  ||    ||| | |||   |  | |  || |  |  | |  ||  ||   
CGTGATCCTCATAAGAGATATTCCTGATGCAAAAGAAAGCGGGTTGCTTCATCTGTGTGAATTTATTGAAGATTGTGAGTTCACCTATCTTTCAACACAGgtagcatttttctccatttaatatctttaattcaagctcatggtgtttatttacttctttgactatagatagtctactcaattttatttccttaattcag

upper sequence: GRMZM2G036034_T01 (Zea mays), 5'ss of exon 10
lower sequence: PP1S15_298V6.2 (Physcomitrella patens), 5'ss of exon 9
TATTATACTCATTAGAGATATTCCTGATGCAAAGGAAAGCGGTTTATTTCACTTATGCGAATTCATAGAAGATTGTGAATTCACCTATTTGTCCACTCAGgtaatcaattaat--------cattctgcaagcatgtaatttgg-aaaatacct---gtaa-gatatcaatttaattatctt--tttttttgtctaaatggtattt--ttcttttgt----------------------------------------------
  |||| |||||| | || ||||||||||| |||||||||||  | | |||| | |||||||| || |||||||| ||||| |||||  ||||||| ||||| |  ||  | |          || |||     |  |||  |  || | | ||    ||| || |   ||   |  |  ||  ||||| | | ||||| | ||    | |  | |                                               
CCTTATCCTCATTCGTGAGATTCCTGATGCCAAGGAAAGCGGGCTGTCTCACCTTTGCGAATTTATTGAAGATTGCGAATTTACCTACCTGTCCACCCAGgttagtaacgactgcatattgtgttatgccgttgttcaatccgataagacatcttgtataacgagagtcatgagagcactttgttttttctttttaaattggatgaagtgccctggaatatttctcaaccattagtgtgagcatttcattttgttctgtgcag

upper sequence: GRMZM2G036034_T01 (Zea mays), 5'ss of exon 10
lower sequence: PP1S276_96V6.1 (Physcomitrella patens), 5'ss of exon 10
TATTATACTCATTAGAGATATTCCTGATGCAAAGGAAAGCGGTTTATTTCACTTATGCGAATTCATAGAAGATTGTGAATTCACCTATTTGTCCACTCAGgtaatcaattaat-cattctgcaagcatgtaatttggaaaatacctgtaagatatcaatttaattatctttttttttgt---ctaaatggtatttttcttttgt-------------------------------------------------------------------------------------
| | || |||||  | || ||||||||||| |||||||||||  | | |||| | ||||| |||||||||||||| |||||||||||  |||| || ||||| |  ||| | | | |  ||      |||      | | |   |  | | || | |  ||    | |  | || | |    |    |||| ||||  |||| |                                                                                     
TCTCATCCTCATCCGTGAGATTCCTGATGCTAAGGAAAGCGGACTGTCTCACCTTTGCGAGTTCATAGAAGATTGCGAATTCACCTACCTGTCTACGCAGgttagtaatcactgcgtgttgtg---ttgtgcggcagtacacttccatgatattttaccttgtacaacggtgttgtagagaaccctctggttttttctttttattaatagaaatgacgactttgccggaacactaaaacatcagtccagcgtgagaaagtcatattttactaaccctttttgattgcag

upper sequence: GRMZM2G036034_T01 (Zea mays), 5'ss of exon 10
lower sequence: PP1S41_154V6.1 (Physcomitrella patens), 5'ss of exon 10
TATTATACTCATTAGAGATATTCCTGATGCAAAGGAAAGCGGTTTATTTCACTTATGCGAATTCATAGAAGATTGTGAATTCACCTATTTGTCCACTCAGgtaatcaattaatcatt-ctgcaag---catgtaatttggaaaatacc-tgtaagatatcaatttaattatctttttttttgtctaaatggtatttttcttttgt
  |||| |||||| | || |||||||| || |||||||| ||  | | |||  | ||||||||||||||||| || |||||||||||  |||| |||||||| | |||| | | ||| |||  |    | |   ||  | |  | |   | | |  |      || | |         ||| |   |||  ||    | |     
ACTTATCCTCATTCGTGAGATTCCTGACGCTAAGGAAAGTGGACTCTCTCATCTCTGCGAATTCATAGAAGACTGCGAATTCACCTACCTGTCTACTCAGgttagcaatcactgattgctgtgaaatccctcccatccgaaggagattgtctcaattgatttcttgagttagagacagtttattataataataacacttt-----

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|89106351|gb|DY576568.1|DY576568
EST:     ACTTATGCGAATTCATAGAAGACTGTGAATTCACCTATTTGTCCACTCAG                         ATACTTCACTTTTTGGGAAATGAAGGCCCCAAAACATCAGATCCCAGTAAA
genomic: ACTTATGCGAATTCATAGAAGATTGTGAATTCACCTATTTGTCCACTCAGgtaatcaatt ... cctgcggcagATACTTCACTTTTTGGGAAATGAAGGCCCAAAAACATCAGATCCCAGTAAA
EST: gi|18963611|gb|BM660532.1|BM660532
EST:     ACTTATGCGAATTCATAGAAGACTGTGAATTCACCTATTTGTCCACTCAG                         ATACTTCACTTTTTGGGAAATGAAGGCCCCAAAACATCAGATCCCAGTAAA
genomic: ACTTATGCGAATTCATAGAAGATTGTGAATTCACCTATTTGTCCACTCAGgtaatcaatt ... cctgcggcagATACTTCACTTTTTGGGAAATGAAGGCCCAAAAACATCAGATCCCAGTAAA

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), 49 (downstream exon)
Score: 243

TATTATACTCATTAGAGATATTCCTGATGCAAAGGAAAGCGGTTTATTTCACTTATGCGAATTCATAGAAGATTGTGAATTCACCTATTTGTCCACTCAGgtaatcaatt ... cctgcggcagATACTTCACTTTTTGGGAAATGAAGGCCCAAAAACATCAGATCCCAGTAAATACATACGCTATATATACAATAGGGTGATACTTGAAAATGCTACAGTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 258

TATTATACTCATTAGAGATATTCCTGATGCAAAGGAAAGCGGTTTATTTCACTTATGCGAATTCATAGAAGATTGTGAATTCACCTATTTGTCCACTCAGgtaatcaatt ... cctgcggcagATACTTCACTTTTTGGGAAATGAAGGCCCAAAAACATCAGATCCCAGTAAATACATACGCTATATATACAATAGGGTGATACTTGAAAATGCTACAGTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 219

TATTATACTCATTAGAGATATTCCTGATGCAAAGGAAAGCGGTTTATTTCACTTATGCGAATTCATAGAAGATTGTGAATTCACCTATTTGTCCACTCAGgtaatcaatt ... cctgcggcagATACTTCACTTTTTGGGAAATGAAGGCCCAAAAACATCAGATCCCAGTAAATACATACGCTATATATACAATAGGGTGATACTTGAAAATGCTACAGTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 311

TATTATACTCATTAGAGATATTCCTGATGCAAAGGAAAGCGGTTTATTTCACTTATGCGAATTCATAGAAGATTGTGAATTCACCTATTTGTCCACTCAGgtaatcaatt ... cctgcggcagATACTTCACTTTTTGGGAAATGAAGGCCCAAAAACATCAGATCCCAGTAAATACATACGCTATATATACAATAGGGTGATACTTGAAAATGCTACAGTTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATTATACTCATTAGAGATATTCCTGATGCAAAGGAAAGCGGTTTATTTCACTTATGCGAATTCATAGAAGATTGTGAATTCACCTATTTGTCCACTCAGgtaatcaattaatcattctgcaagcatgtaatttggaaaatacctgtaagatatcaatttaattatctttttttttgtctaaatggtatttttcttttgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaaaata