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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGCTTGTAGAACAAATTAATAAGTCTCTCTCAGTTGGCAAGCGTCGAACTGGGAGATCTATCAGTATTCTTGATATCTATGGCTTTGAATCATTTGATgtaatataccttttttacctaaagttgtcatatattagaagggcaggcctgttgcgatggtgagaattgtctcactaagttaccaggtagcgggttcgaa...

Basic information

species Zea mays
transcript GRMZM2G139583_T02
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139583_T02 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os10g34710.1 (Oryza sativa), 5'ss of exon 13
ATGGCTTGTAGAACAAATTAATAAGTCTCTCTCAGTTGGCAAGCGTCGAACTGGGAGATCTATCAGTATTCTTGATATCTATGGCTTTGAATCATTTGATgtaatatacctt--ttttacctaaagttgtcatatattagaagggcaggcctgttgcgatggtgagaattgtctcactaagttaccaggtagcgggttcgaa
 |||||||| ||||||||||| |||||||| ||||||||||||||||||||||||||||| ||||| ||||||||||||||||||||||||||||| |||||||| ||| |   ||| || |   ||  |||||| ||| |  ||||      ||   |||       |  |  ||| || || |                 
GTGGCTTGTTGAACAAATTAACAAGTCTCTTTCAGTTGGCAAGCGTCGAACTGGGAGATCAATCAGCATTCTTGATATCTATGGCTTTGAATCATTCGATgtaatgtacttccatttgacatgctgtcatcatatttta-attggcaaatggtttctcatg-------tcataacacaaaattgcag---------------

upper sequence: GRMZM2G139583_T02 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA09G42180.1 (Glycine max), 5'ss of exon 12
ATGGCTTGTAGAACAAATTAATAAGTCTCTCTCAGTTGGCAAGCGTCGAACTGGGAGATCTATCAGTATTCTTGATATCTATGGCTTTGAATCATTTGATgta-atatacctt---ttttacctaaagttgtc-atatattagaagggcaggcctgttgcgatggtgagaattg-tctcactaagttaccaggtagcgggttcgaa-----------------
 ||| | || ||||| || ||||| || ||  | ||||||||  | || || || ||||| ||||||||||| |||||||||||||||||||| ||  |||||  | ||  ||    |||| ||| |  | || |||||||  | |      |         |  |     ||| | | |  |  ||         | | | | |                  
TTGGTTGGTTGAACAGATAAATAAATCACTTGCTGTTGGCAAAAGACGTACCGGCAGATCAATCAGTATTCTAGATATCTATGGCTTTGAATCTTTCAATgtatgtttatattaaactttatctacatctttctatatattt-atgatttatctcaccatcttcatcctgtttgatattaaaatattttggctctactgatgctatgcattttatgcctgcag

upper sequence: GRMZM2G139583_T02 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA10G43230.1 (Glycine max), 5'ss of exon 12
ATGGCTTGTAGAACAAATTAATAAGTCTCTCTCAGTTGGCAAGCGTCGAACTGGGAGATCTATCAGTATTCTTGATATCTATGGCTTTGAATCATTTGATgtaatataccttttttacctaaagttgtcatatat-tagaagggcaggcctgttgcgatggtgag---aattgtctcactaagttaccaggtagcgggttcgaa-------------------
 ||| | || |||||||| || || || ||| | ||||||||  | |||||||| ||||| ||||| ||||| ||||| ||||||||||| |||||  |||||   ||  || | |  | | |  | | |||| | |    | |      | |  | ||  | |    | ||   |   |||  |    | |     ||  |                     
TTGGTTGGTTGAACAAATAAACAAATCCCTCGCGGTTGGCAAAAGACGAACTGGCAGATCAATCAGCATTCTAGATATTTATGGCTTTGAGTCATTCAATgtatgttatattatatgac-agatcttttatatgtgtgtgtgtgtgtatttatcactatccttatcctatttaattttttaaaatgtttgctctgttgtatgcggtggattttatgcatgcag

upper sequence: GRMZM2G139583_T02 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA20G00320.1 (Glycine max), 5'ss of exon 14
ATGGCTTGTAGAACAAATTAATAAGTCTCTCTCAGTTGGCAAGCGTCGAACTGGGAGATCTATCAGTATTCTTGATATCTATGGCTTTGAATCATTTGATgta-atatacctt---ttttacctaaagttgtcat-atattagaagggcaggcc-----tgttgcgatggtgagaattgtctcactaa-gttaccaggtagcgggttcgaa---
 ||| | || ||||| || ||||| || ||  | ||||||||  | || || || ||||| ||||||||||| |||||||| ||||||||||| ||  |||||  | ||  ||    |||| |||    | || | |||||        |   |       |     || |    ||| |  | |||  | | | | | |     | |      
TTGGTTGGTTGAACAGATAAATAAATCACTTGCTGTTGGCAAAAGACGTACCGGCAGATCAATCAGTATTCTAGATATCTACGGCTTTGAATCTTTCAATgtatgtttatattaaactttatctacctctttctttatatttatgatttatctcaccatcttcatcctgtttgatattttgcctctactgatgctatgcattttatccctgcag

upper sequence: GRMZM2G139583_T02 (Zea mays), 5'ss of exon 13
lower sequence: AT3G19960.1 (Arabidopsis thaliana), 5'ss of exon 14
ATGGCTTGTAGAACAAATTAATAAGTCTCTCTCAGTTGGCAAGCGTCGAACTGGGAGATCTATCAGTATTCTTGATATCTATGGCTTTGAATCATTTGATgtaatatacctttttta-----cctaaagttgtcatatattagaagggcaggcctgtt----gcgatggtgagaattgt--ctcactaagttaccaggtagcg--ggttcgaa--------------------------------------------------------------------------------------
 ||||| || ||||| || || || |||||  | || || ||| | |||||||| |||||||||||||||||||||||||| ||||||||||||||||||||| | | ||| || |      |    || | ||   |   | |||   |    || |    || ||  | |||  |     |  | | | |||||   || |     | | |                                                                                      
CTGGCTGGTTGAACAGATCAACAAATCTCTTGCTGTGGGAAAGAGGCGAACTGGCAGATCTATCAGTATTCTTGATATCTACGGCTTTGAATCATTTGATgta-tgttcctgttctctggctctctgagctttctcctga-aaaagattacaattgctaccagctatcattagaccttcagtttgcaatgataccaaacagtgccaaatagtagaactctatatctatgtgcttttgtgtttccatttcttgatttatgtgtcttattgatttgctatacgactttcattcctctgcag

upper sequence: GRMZM2G139583_T02 (Zea mays), 5'ss of exon 13
lower sequence: AT1G50360.1 (Arabidopsis thaliana), 5'ss of exon 14
ATGGCTTGTAGAACAAATTAATAAGTCTCTCTCAGTTGGCAAGCGTCGAACTGGGAGATCTATCAGTATTCTTGATATCTATGGCTTTGAATCATTTGATgtaatataccttttttacctaaagttgtcatatattagaagggcaggcctgttgcgatggtgagaattgtctca-ctaagttac--caggtagcgggttcgaa----------------------------------
 ||||| || ||||| ||||| || |||||  | || || ||| |  ||||||| ||||| ||||| |||||||||||||||||||||||||||||  ||||| |     |||||   ||    |||   | || |  | |  |   | |   || ||  ||   |||   ||  ||  |||||     ||| |    |  |                                   
CTGGCTAGTTGAACAGATTAACAAATCTCTTGCGGTGGGAAAGAGGAGAACTGGCAGATCCATCAGCATTCTTGATATCTATGGCTTTGAATCATTCAATgta-tgctggtttttagtctccctttgcgttttactgcatgaacttacataa-gctatc-tgcacattacatcttctgtgttacattttgtaccaatgttaatttggtttgctgaataaatactatacatgttgcag

upper sequence: GRMZM2G139583_T02 (Zea mays), 5'ss of exon 13
lower sequence: Vv10s0071g00210.t01 (Vitis vinifera), 5'ss of exon 13
ATGGCTTGTAGAACAAATTAATAAGTCTCTCTCAGTTGGCAAGCGTCGAACTGGGAGATCTATCAGTATTCTTGATATCTATGGCTTTGAATCATTTGATgtaatataccttttttacctaaagttgtcatatattagaagggcaggcctgttgcgatggtgagaattgtctcactaagttaccaggtagcgggttcgaa--------
 ||||| || |||||||| || ||||| ||  | || || || || || ||||| ||||| || || ||||||||||||||||| ||||||||||| ||||||  |||  || ||||  |   | ||| |   |||       |   ||  |  | || ||     |    | | ||| |   || ||  |   |||           
CTGGCTGGTCGAACAAATCAACAAGTCACTTGCTGTAGGAAAACGGCGTACTGGCAGATCCATTAGCATTCTTGATATCTATGGATTTGAATCATTCGATgtatgata--ttatttagtttctgctgtaaataatttttcattccccccattccccattgtccccctaaattta-taaatattcatgttacatattctgtttttccag

upper sequence: GRMZM2G139583_T02 (Zea mays), 5'ss of exon 13
lower sequence: PP1S104_215V6.1 (Physcomitrella patens), 5'ss of exon 13
ATGGCTTGTAGAACAAATTAATAAGTCTCTCTCAGTTGGCAAGCGTCGAACTGGGAGATCTATCAGTATTCTTGATATCTATGGCTTTGAATCATTTGATgtaatataccttttttacctaaagttgtcatatattagaagggcaggcctgttgcgatggtgagaattgtctcactaagttaccaggtagcgggttcgaa
 ||||| || ||||   | || || || ||   || |||||||   |||||||| ||||| ||||| ||||| ||||||||||| |||||| | ||  | ||||| |  |||   | | |  | |      | | |   |   ||  | | | ||  | |||  | | || |  | |      |      ||| ||    
TTGGCTGGTTGAACGTGTAAACAAATCACTGGAAGCTGGCAAGTTGCGAACTGGAAGATCAATCAGCATTCTGGATATCTATGGATTTGAAACTTTCAAGgtaatttttcttcgctccttccaatgcattcaaaattctaacacaaccatttggcattagtgtcattggtgtttcgaccccgacttcccacggtttgctg

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|211511074|gb|FL380238.1|FL380238
EST:     CTGGGAGATCTATCAGTATTCTTGATATCTATGGCTTTGAATCNTTTGAT                         AAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAG
genomic: CTGGGAGATCTATCAGTATTCTTGATATCTATGGCTTTGAATCATTTGATgtaatatacc ... acatttgcagAAGAACAGTTTTGAACAGTTCTGCATCAATTATGCTAATGAAAGGTTGCAA




















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: 240

ATGGCTTGTAGAACAAATTAATAAGTCTCTCTCAGTTGGCAAGCGTCGAACTGGGAGATCTATCAGTATTCTTGATATCTATGGCTTTGAATCATTTGATgtaatatacc ... acatttgcagAAGAACAGTTTTGAACAGTTCTGCATCAATTATGCTAATGAAAGGTTGCAACAACATTTCAATCGTCATTTATTTAAGCTTGAGCAAGAG


Block sizes: 36 (upstream exon), 47 (downstream exon)
Score: 33

ATGGCTTGTAGAACAAATTAATAAGTCTCTCTCAGTTGGCAAGCGTCGAACTGGGAGATCTATCAGTATTCTTGATATCTATGGCTTTGAATCATTTGATgtaatatacc ... acatttgcagAAGAACAGTTTTGAACAGTTCTGCATCAATTATGCTAATGAAAGGTTGCAACAACATTTCAATCGTCATTTATTTAAGCTTGAGCAAGAG


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 36

ATGGCTTGTAGAACAAATTAATAAGTCTCTCTCAGTTGGCAAGCGTCGAACTGGGAGATCTATCAGTATTCTTGATATCTATGGCTTTGAATCATTTGATgtaatatacc ... acatttgcagAAGAACAGTTTTGAACAGTTCTGCATCAATTATGCTAATGAAAGGTTGCAACAACATTTCAATCGTCATTTATTTAAGCTTGAGCAAGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 120

ATGGCTTGTAGAACAAATTAATAAGTCTCTCTCAGTTGGCAAGCGTCGAACTGGGAGATCTATCAGTATTCTTGATATCTATGGCTTTGAATCATTTGATgtaatatacc ... acatttgcagAAGAACAGTTTTGAACAGTTCTGCATCAATTATGCTAATGAAAGGTTGCAACAACATTTCAATCGTCATTTATTTAAGCTTGAGCAAGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGCTTGTAGAACAAATTAATAAGTCTCTCTCAGTTGGCAAGCGTCGAACTGGGAGATCTATCAGTATTCTTGATATCTATGGCTTTGAATCATTTGATgtaatataccttttttacctaaagttgtcatatattagaagggcaggcctgttgcgatggtgagaattgtctcactaagttaccaggtagcgggttcgaa

- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC