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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATAGATACCCTGGATAAAGTGTACAATTTGGACTGGAACAGTAGCGCTTCCAAGAATGAGTGCACTGCAGCTATTGGCTTCAAGTGGATGCTAAATCAGgtgcggactaaaacatgcagtatagataatttatttggatgatcctttttcatttatttttccatttagttccagtatgtttcaattattagtatgtgta...

Basic information

species Zea mays
transcript GRMZM2G003530_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G003530_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g27760.1 (Oryza sativa), 5'ss of exon 3
AATAGATACCCTGGATAAAGTGTACAATTTGGACTGGAACAGTAGCGCTTCCAAGAATGAGTGCACTGCAGCTATTGGCTTCAAGTGGATGCTAAATCAGgtgcggactaaaacatgcagtatagataatttatttggatgatcctttttcatttatttttccatttagttccagtatgtttcaattattagt--atgtgta-
|| | | || |||||||| |||||||||||||| ||||| ||||| ||||| |||||||| |||||||| ||| ||||||| || |||||||| ||||||||| | |   ||   || | | ||||| |    ||||  |  |  |  ||||      || || ||   |   ||| ||||    || ||| |  ||  | | 
AACAAAGACACTGGATAAGGTGTACAATTTGGATTGGAATAGTAGTGCTTCTAAGAATGAATGCACTGCTGCTGTTGGCTTAAAATGGATGCTTAATCAGgtgagaa--gaagagtgaaatctagattaacattttgtttttttttaattcaccctccttgcccttcc-tcgaagtttgttattttttttacttgataagcaa

upper sequence: GRMZM2G003530_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA01G39190.1 (Glycine max), 5'ss of exon 3
AATAGATACCCTGGATAAAGTGTACAATTTGGACTGGAACAGTAGCGCTTCCAAGAATGAGTGCACTGCAGCTATTGGCTTCAAGTGGATGCTAAATCAGgtgcggactaaaacatgcagtatagataatttatttggatgatcctttttcatttatttttccatttagttccagtatgtttcaattattagtatgtgta------
  |    ||  | |||||||| |||||||||||||||  || ||| |||||||||||||||||| |||| || | ||| || ||||||||||| |||||||| |      | |       | |   |  | |   | |   |   || |  |   |      |||| | |   | ||    |     | | |  |  | |      
TTTGCTGACTTTAGATAAAGTTTACAATTTGGACTGGTTCAATAGTGCTTCCAAGAATGAGTGCTCTGCTGCAACTGGTTTGAAGTGGATGCTTAATCAGgtac------acatgctttttgttagttttctgagtagtgtactgttgtcaacaaaccaacacattcattaatattaatgcttgtccaatggcttaggaaagttgt

upper sequence: GRMZM2G003530_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA05G16400.1 (Glycine max), 5'ss of exon 2
AATAGATACCCTGGATAAAGTGTACAATTTGGACTGGAACAGTAGCGCTTCCAAGAATGAGTGCACTGCAGCTATTGGCTTCAAGTGGATGCTAAATCAGgtgcggactaaaacatgcagtatagataatttatttg-gatgatccttttt-catttatttttccatttagttccagtatgtttcaattattagtatgtgta
  |  | || ||||| ||||| |||||  ||||||||  |||||| |||||||||||||| ||| | || || ||||| | |||||||||||| ||||||||    |     || ||  |  |   |  || |  ||  |||| | | |||  |||| || |   ||  |     |   | |     || | || |     |
TGTGCAGACTCTGGACAAAGTTTACAACCTGGACTGGCTCAGTAGTGCTTCCAAGAATGAATGCTCAGCTGCAATTGGATCCAAGTGGATGCTTAATCAGgtaaaaatgctcac-tgttgagtccttttttaaagtgtaatgaacttatttatatttgttgtctgatacatacttaacct-tgagtgttttaagaaaagaca

upper sequence: GRMZM2G003530_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA06G04120.1 (Glycine max), 5'ss of exon 3
--------------AATAGATACCCTGGATAAAGTGTACA--ATTTGGACTGGAACAGTAGCGCTTCCAAGAATGAGTGCACTGCAGCTATTGGCTTCAAGTGGATGCTAAATCAGgtgcggactaaaacatgcagtatagataatttatttggatgatcctttttcatttatttttccatttagttccagtatgtttcaattattagtatgtgta
                | || ||  ||||||||||||| |  || | || |||     ||| ||||||||||||||||||||||| ||| |||||||||||| |||||| ||||||||    || || | ||  |    | | || |||  || ||     |   |  ||||| ||    || |     | |    ||  |               
AACGTTTCTTCAATTTTGGAGACAATGGATAAAGTGTATATAATCTTGATTGGTTTTCTAGTGCTTCCAAGAATGAGTGCACTGCGGCTGTTGGCTTCAAgttgatgcttaatcaggtagacaccaatatat-taaagaaaaaaacttaaatgtatttctttaggtactttatgttatttttaatcataaatggaatttta---------------

upper sequence: GRMZM2G003530_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA17G20280.1 (Glycine max), 5'ss of exon 3
AATAGATACCCTGGATAAAGTGTACAATTTGGACTGGAACAGTAGCGCTTCCAAGAATGAGTGCACTGCAGCTATTGGCTTCAAGTGGATGCTAAATCAGgtgcgga----ctaaaacatg-cagtatagataatttatttggatgatcctttttcatttatttttccatttagttccagtatgtttcaattattagtatgtgta
  || | ||  |||| ||||| |||||  ||||||||  ||| || |||||||||||||| ||| | || || ||||| || ||||||||||| ||||||||    |    ||       | |  | |  | |||||| |    ||||   | ||  |    |      ||||    |   |  |||   || | || |      
TGTACAGACTTTGGACAAAGTTTACAACCTGGACTGGCTCAGCAGTGCTTCCAAGAATGAATGCTCAGCTGCAATTGGATTTAAGTGGATGCTTAATCAGgtaaaaatgctctctgttgagtctctgtttaaaatttagtgaactgatttatgtttgtcagatacctactttaaagtcttaaactttgtgttttaagaaa-----

upper sequence: GRMZM2G003530_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA11G06080.1 (Glycine max), 5'ss of exon 3
AATAGATACCCTGGATAAAGTGTACAATTTGGACTGGAACAGTAGCGCTTCCAAGAATGAGTGCACTGCAGCTATTGGCTTCAAGTGGATGCTAAATCAGgtgcggactaaaacatgcagtatagataatttatttgg--atgatcctttttcatttatttttc-catttagttccagtatgtttcaattattagtatgtgta------
  |  ||||  | |||||||| |||||||||||||||  || ||| |||||||||||||||||| |||| || | |||||| ||||||||||| ||||||||||        |||| |  | | | || |||  |  |   ||  |  || |||         | |||| | |   | ||    |     | | |  |  | |      
TTTGCATACTTTAGATAAAGTTTACAATTTGGACTGGTTCAATAGTGCTTCCAAGAATGAGTGCTCTGCTGCAACTGGCTTGAAGTGGATGCTTAATCAGgtgc--------acatacttttt-gttagttttctgagcagtgtactgttgtcaacagcccaacacattcattaatattaatgcttgtccaatggcttaggcaagtttt

upper sequence: GRMZM2G003530_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA14G08870.1 (Glycine max), 5'ss of exon 3
AATAGATACCCTGGATAAAGTGTACAATTTGGACTGGAACAGTAGCGCTTCCAAGAATGAGTGCACTGCAGCTATTGGCTTCAAGTGGATGCTAAATCAGgtgcggactaaaacatgcagtatagataatttatttggatgat--cctttttcatttatttttccatttagttccagtatgtttcaattattagtatgtgta--
  |  | ||  |||||  ||||| |||| | || |||  |||| | |||||||||||||||||  | |||||| | |||| |||||||||||| ||||||||    | |  |   ||    |   || | || |||   | ||  |   | | | || ||| |    ||||||    | | |||   || ||| |  | | |  
TTTGAAGACAATGGATGTAGTGTTCAATCTTGATTGGTTCAGTGGTGCTTCCAAGAATGAGTGTTCCGCAGCTGTGGGCTACAAGTGGATGCTTAATCAGgta---attggagggtgtc-caagaatgagttgtttttttaatggcaaatattaattgtttgtgttgttagttttttttttttttttttgttaatgggaggatt

upper sequence: GRMZM2G003530_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA04G03960.1 (Glycine max), 5'ss of exon 3
AATAGATACCCTGGATAAAGTGTACAATTTGGACTGGAACAGTAGCGCTTCCAAGAATGAGTGCACTGCAGCTATTGGCTTCAAGTGGATGCTAAATCAGgtgcggactaaaacatgcagtatagataatttatttggatgatcctttttcatttatttttccatttagttccagt-atgtttcaattattagtatgtgta
  |||| ||  |||||| |||||| ||| | || |||     ||| ||||||||||||||||||||||||||| ||||||||||||||||||| ||||||||    || ||   |   |    | | || |||  || ||     |   |  |||| | ||   |||| ||  | |  |  ||  |  ||    |  | | 
TTTAGAGACAATGGATAGAGTGTATAATCTTGATTGGTTTTCTAGTGCTTCCAAGAATGAGTGCACTGCAGCTGTTGGCTTCAAGTGGATGCTTAATCAGgtagacaccaatttac-taaaggacaaaacttaaatgtatttctttaggtactttagtgttatttttaattaaaattgtaattttaccatggtaacctatg

upper sequence: GRMZM2G003530_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT4G34420.1 (Arabidopsis thaliana), 5'ss of exon 3
AATAGATACCCTGGATAAAGTGTACAATTTGGACTGGAACAGTAGCGCTTCCAAGAATGAGTGCACTGCAGCTATTGGCTTCAAGTGGATGCTAAATCAGgtgcgg--actaaaacatgcagtatagataatttatttggatgatcctttttcatttatttttccatttagttccagtatgtttcaattattagtatgtgta----
  | || || || || ||||| || ||| | ||||||   ||||| || || ||||| ||||||||| | ||| ||||||||||||||||||| ||||||||   |  | |   |    | |      | |  ||| |   | |  |||| | | | || | |   ||    ||   | |||||| ||| | |||   || |    
TTTCGAGACTCTTGACAAAGTCTATAATCTAGACTGGTTGAGTAGTGCCTCTAAGAACGAGTGCACTTCCGCTGTTGGCTTCAAGTGGATGCTTAATCAGgtaaagtgattgttattcacggacactgtgacatatct---ttagtctttcttactcatatgtt--ttcgactcgtctctgtttccatt-tgagtgcttgaacaaa

upper sequence: GRMZM2G003530_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv07s0031g00880.t01 (Vitis vinifera), 5'ss of exon 4
AATAGATACCCTGGATAAAGTGTACAATTTGGACTGGAACAGTAGCGCTTCCAAGAATGAGTGCACTGCAGCTATTGGCTTCAAGTGGATGCTAAATCAGgtgcggactaaaacatgcagtatagat----aatttatttggatgatcctttttcatttatttttccatttagttccagtatgtttcaattattagtatgtgta----
  |  | || || |||||| | |||||||||||||||  |||||| |||||||||||||||||  | || ||  ||||||||||||||||||| ||||||||    |||    | |  | | ||  |    |  | | ||   ||| | |||| |||   |  ||||||| |     ||||    | || |||   ||| || |    
TGTGAAGACACTAGATAAAATTTACAATTTGGACTGGTTCAGTAGTGCTTCCAAGAATGAGTGTTCAGCTGCAGTTGGCTTCAAGTGGATGCTCAATCAGgtaaatactt--tcttcaaatttaagttccaagctcacttatttgaactttttacatggctgcttccattga---tgagtac---ttaaatatgtatatctgaaaaat

upper sequence: GRMZM2G003530_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv03s0063g00840.t01 (Vitis vinifera), 5'ss of exon 3
AATAGATACCCTGGATAAAGTGTACAATTTGGACTGGAACAGTAGCGCTTCCAAGAATGAGTGCACTGCAGCTATTGGCTTCAAGTGGATGCTAAATCAGgtgcggactaaaacatgcagtatagataatttatttggatgatcctttttcatttattttt--ccatttagttccagtatgtttcaattattagtatgtgta----
 | ||| ||  |||||||| | || ||| | ||||||  |||||| |||||||||||||||||||| || ||  ||||  | ||||||||||| ||||||||  | ||||          ||| | |||||||| |   |  |    ||    | | |||   ||||||||||        |||   ||      |          
CACAGAAACTTTGGATAAAATCTATAATCTAGACTGGCTCAGTAGTGCTTCCAAGAATGAGTGCACAGCTGCCGTTGGGCTGAAGTGGATGCTTAATCAGgttagcactat------tgatatggttaatttatatcattattttccttctggtaaatttaaaccatttagttagtactacttttgtttgacgagagaccccttag

upper sequence: GRMZM2G003530_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv18s0001g11050.t01 (Vitis vinifera), 5'ss of exon 2
AATAGATACCCTGGATAAAGTGTACAATTTGGACTGGAACAGTAGCGCTTCCAAGAATGAGTGCACTGCAGCTATTGGCTTCAAGTGGATGCTAAATCAGgtgcggactaaaacatgcagtatagataatttatttggatgatcctttttcatttatttttccatttagttccagtatgtttcaattattagtatgtgta---------
  |   |||  |||||||||| || ||  ||||||||  |||||| ||||||||||||||||||   || ||  |||||||||| |||||||| ||||||||| | |  | |||| | | |  || | ||  | ||| ||       ||| |   || |    | |  |||    |  | ||| |||||||  ||| |           
TCTGAGTACAATGGATAAAGTATATAACCTGGACTGGTTCAGTAGTGCTTCCAAGAATGAGTGCTTGGCTGCAGTTGGCTTCAAATGGATGCTTAATCAGgtgagtaacataaca-gaatttcagttcatg-acttgaat---ttcatttgaaaaatgtagttaatcggtt---atgcgcttctattattaa-atgggagatcatgttg

upper sequence: GRMZM2G003530_T01 (Zea mays), 5'ss of exon 3
lower sequence: PP1S4_216V6.1 (Physcomitrella patens), 5'ss of exon 3
-AATAGATACCCTGGATAAAGTGTACAATTTGGACTGGAACAGTAGCGCTTCCAAGAATGAGTGCACTGCAGCTATTGGCTTCAAGTGGATGCTAAATCAGgtg-------------cggactaaaacatgcagtatagataatttatttggatgatcctttttcatttatttttccatttagttc-cagtatgtttcaattattagtatgtgta----------------------------
   || | ||  |||| ||||| | |||| |||| |||   |  |||||||| |||||||| |||||||||||| |||| |||||||||||||| || |||||              |  || || || ||   |     |    ||| || || ||   | |  || ||| | |  || | |||  |  |   ||||   |||   ||  ||||                            
TGCTACAAACA-TGGACAAAGTCTTCAATCTGGATTGGCTGAACAGCGCTTCGAAGAATGAATGCACTGCAGCTGTTGGTTTCAAGTGGATGCTCAACCAGgtagatttcatcgaatcctacaaatacttgtgattcgagtgcagtatatgtat-atatatatatatatatatatatatatggttttctttgcttttcttctatctttaactgtacctgtgtcatgtttttgttatgctgcag

upper sequence: GRMZM2G003530_T01 (Zea mays), 5'ss of exon 3
lower sequence: PP1S57_92V6.1 (Physcomitrella patens), 5'ss of exon 4
-AATAGATACCCTGGATAAAGTGTACAATTTGGACTGGAACAGTAGCGCTTCCAAGAATGAGTGCACTGCAGCTATTGGCTTCAAGTGGATGCTAAATCAGgtgcggact------aaaacatgcagtatagataatttatttg----gatgatcctttttcatttatttttccatttagttccagtatgtttcaattatta-gt--atgtgta------------------
   |||| ||  |||| || || | ||| |||||||||   |  || ||||| |||||||| ||||| |||||| | || |||||||||||||||||||||||    | |      |||  |  |  | |   | ||| |  ||     |||| |     |  |||| ||| |   ||  |||||   | ||  ||||  |  ||  ||||||                   
TGCTAGAAACA-TGGACAAGGTCTTCAACTTGGACTGGCTGAACAGTGCTTCGAAGAATGAATGCACCGCAGCTGTGGGTTTCAAGTGGATGCTAAATCAGgtagacatttcattgaaacaactccatgtttttgattcaaatgttgcaatgagcgcaacttttttactttgcttctt--ttccacctttttaaaatttctgtgtcgatgtgtgatgctcgttttgctgcag

upper sequence: GRMZM2G003530_T01 (Zea mays), 5'ss of exon 3
lower sequence: PP1S310_50V6.1 (Physcomitrella patens), 5'ss of exon 7
AATAGATACCCTGGATAAAGTGTACAATTTGGACTGGAACAGTAGCGCTTCCAAGAATGAGTGCACTGCAGCTATTGGCTTCAAGTGGATGCTAAATCAGgtgcggactaaaacatgcagtatagat---aatttatttggatgatccttt-ttcatttatttttccatttagttccagtatgtttcaattattagtatgtgta
   | | ||| |||||||||| ||||| || || |||   | ||| ||| | |||||||| || ||||||||| |||| |||||||||||||| || |||||       | || || |  |   | |   | ||   |  | | || |     |  |||  |||| |  |||||| |||    ||     |   | |  ||   
CGCAAAAACCATGGATAAAGTCTACAACTTAGATTGGCTGAATAGTGCTGCTAAGAATGAATGTACTGCAGCTGTTGGTTTCAAGTGGATGCTCAACCAGgtaaatttcataagatcctatcatgctcttagttccatcaggtcatacacgacttttttcgttttgctgttagtttcagagcattattcct-ccatttcgt---

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|78088532|gb|DV516925.1|DV516925
EST:     CCAAGAATGAGTGCACTGCAGCTATTGGCTTCAAGTGGATGCTAAATCAG                         GGCCTCGTGGCAAACCATGCGGACGTAGTCGACTACTTCAACCGAAGAGGA
genomic: CCAAGAATGAGTGCACTGCAGCTATTGGCTTCAAGTGGATGCTAAATCAGgtgcggacta ... atgttttcagGGCCTCGTGGCAAACCATGCGGACGTAGTCGACTACTTCAACCGAAGAGGA
EST: gi|149076004|gb|EE164574.2|EE164574
EST:     CCAGGAATGAGTGCACTGCAGCTATTGGCTTCAAGTGGATGCTAAATCAG                         GG-CTCGGGGGCAAACCATGCGGACGTAGTCGACTACTTCAACCGAAGAGG
genomic: CCAAGAATGAGTGCACTGCAGCTATTGGCTTCAAGTGGATGCTAAATCAGgtgcggacta ... atgttttcagGGCCTC-GTGGCAAACCATGCGGACGTAGTCGACTACTTCAACCGAAGAGG
EST: gi|78078358|gb|DV506773.1|DV506773
EST:     CCAAGAATGAGTGCACTGCAGCTATTGGCTTCAAGTGGATGCTAAATCAG                         GGCCTCGTGGCAAACCATGCGGACGTAGTCGACTACTTCAACCGAAGAGGA
genomic: CCAAGAATGAGTGCACTGCAGCTATTGGCTTCAAGTGGATGCTAAATCAGgtgcggacta ... atgttttcagGGCCTCGTGGCAAACCATGCGGACGTAGTCGACTACTTCAACCGAAGAGGA
EST: gi|71440142|gb|DR821192.1|DR821192
EST:     CCAAGAATGAGTGCACTGCAGCTATTGGCTTCAAGTGGATGCTAAATCAG                         GGCCTCGTGGCAAACCATGCGGACGTAGTCGACTACTTCAACCGAAGAGGA
genomic: CCAAGAATGAGTGCACTGCAGCTATTGGCTTCAAGTGGATGCTAAATCAGgtgcggacta ... atgttttcagGGCCTCGTGGCAAACCATGCGGACGTAGTCGACTACTTCAACCGAAGAGGA

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), 49 (downstream exon)
Score: 45

AATAGATACCCTGGATAAAGTGTACAATTTGGACTGGAACAGTAGCGCTTCCAAGAATGAGTGCACTGCAGCTATTGGCTTCAAGTGGATGCTAAATCAGgtgcggacta ... atgttttcagGGCCTCGTGGCAAACCATGCGGACGTAGTCGACTACTTCAACCGAAGAGGAGTCTCTGCGATATTTCTTTTCAGAAGGAACCTGCTCCGCCAGTTGGTAT


Block sizes: 20 (upstream exon), 49 (downstream exon)
Score: 10

AATAGATACCCTGGATAAAGTGTACAATTTGGACTGGAACAGTAGCGCTTCCAAGAATGAGTGCACTGCAGCTATTGGCTTCAAGTGGATGCTAAATCAGgtgcggacta ... atgttttcagGGCCTCGTGGCAAACCATGCGGACGTAGTCGACTACTTCAACCGAAGAGGAGTCTCTGCGATATTTCTTTTCAGAAGGAACCTGCTCCGCCAGTTGGTAT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 22

AATAGATACCCTGGATAAAGTGTACAATTTGGACTGGAACAGTAGCGCTTCCAAGAATGAGTGCACTGCAGCTATTGGCTTCAAGTGGATGCTAAATCAGgtgcggacta ... atgttttcagGGCCTCGTGGCAAACCATGCGGACGTAGTCGACTACTTCAACCGAAGAGGAGTCTCTGCGATATTTCTTTTCAGAAGGAACCTGCTCCGCCAGTTGGTAT


Block sizes: 33 (upstream exon), 48 (downstream exon)
Score: 24

AATAGATACCCTGGATAAAGTGTACAATTTGGACTGGAACAGTAGCGCTTCCAAGAATGAGTGCACTGCAGCTATTGGCTTCAAGTGGATGCTAAATCAGgtgcggacta ... atgttttcagGGCCTCGTGGCAAACCATGCGGACGTAGTCGACTACTTCAACCGAAGAGGAGTCTCTGCGATATTTCTTTTCAGAAGGAACCTGCTCCGCCAGTTGGTAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATAGATACCCTGGATAAAGTGTACAATTTGGACTGGAACAGTAGCGCTTCCAAGAATGAGTGCACTGCAGCTATTGGCTTCAAGTGGATGCTAAATCAGgtgcggactaaaacatgcagtatagataatttatttggatgatcctttttcatttatttttccatttagttccagtatgtttcaattattagtatgtgta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA