Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATTGACAGAATTGTGGCTGGTATGGAAGGGACTGTGATGACAGACGGGAAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatgaatcttcctcttaacagatcttttctcctttgccttgaacattagaatgtgattggtttaattttggtttcgattggtttctcagatatc...

Basic information

species Zea mays
transcript GRMZM2G110408_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110408_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os06g45820.4 (Oryza sativa), 5'ss of exon 3
----CTATTGACAGAATTGTGGCTGGTATGGAAGGGACTGTGATGACAGACGGGAAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatga---atcttcctcttaacagatcttttctcctttgccttgaacattagaatgtgattggtttaattttggtttcgattggtttctcagatatc
    | ||||||||||| ||||||||||||||||| |||||||||||||| ||||||||||||||||||||||||||||||||||| |||||||||||||| ||||||||||| |      |   |  |||| |  ||||| |   || | ||| | || | |||    |     || |  |   |   | ||  ||||  |     
GATTCAATTGACAGAATAGTGGCTGGTATGGAAGGAACTGTGATGACAGATGGGAAGAGCAAAAGTCTTGTTGCTTACCATGAAGTTGGGCATGCAATTTgtgggtaagagataatctgcatatttgctaactgtgcttttgtttattac-ttgcatatcaaaattccgtgcaactattcatatctggaaatgtattctttgtag--

upper sequence: GRMZM2G110408_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os06g45820.1 (Oryza sativa), 5'ss of exon 3
CTATTGACAGAATTGTGGCTGGTATGGAAGGGACTGTGATGACAGACGGGAAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatgaatc---ttcctcttaacagatcttttctcctttgccttgaacattagaatgtgattggtttaattttggtttcgattggtttctcagatatc
| ||||||||||| ||||||||||||||||| |||||||||||||| ||||||||||||||||||||||||||||||||||| |||||||||||||| ||||||||||| |      |   |  |||| |  ||||| |   || | ||| | || | |||    |     || |  |   |   | ||  ||||  |     
CAATTGACAGAATAGTGGCTGGTATGGAAGGAACTGTGATGACAGATGGGAAGAGCAAAAGTCTTGTTGCTTACCATGAAGTTGGGCATGCAATTTGTGGgtaagagataatctgcatatttgctaactgtgcttttgtttattac-ttgcatatcaaaattccgtgcaactattcatatctggaaatgtattctttgtag--

upper sequence: GRMZM2G110408_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os06g45820.3 (Oryza sativa), 5'ss of exon 3
----------------------------------------CTATTGACAGAATTGTGGCTGGTATGGAAGGGACTGTGATGACAGACGGGAAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatgaatc---ttcctcttaacagatcttttctcctttgccttgaacattagaatgtgattggtttaattttggtttcgattg-gtttctcagatatc-------------------------------
                                        | ||||||||||| ||||||||||||||||| |||||||||||||| ||||||||||||||||||||||||||||||||||| |||||||||||||| ||||||||||| |      |   |  |||| |  ||||| |   || | ||| | || | |||    |     || |  |   |   | ||  ||  |   | | |                               
CGTGGTCGGACAGCAATTTCCTCAAAGGAGATTGATGATTCAATTGACAGAATAGTGGCTGGTATGGAAGGAACTGTGATGACAGATGGGAAGAGCAAAAgtcttgttgcttaccatgaagttgggcatgcaatttgtgggtaagagataatctgcatatttgctaactgtgcttttgtttattac-ttgcatatcaaaattccgtgcaactattcatatctggaaatgtattctttgtagaactttgacgcctggccacgaccctgtccaaaag

upper sequence: GRMZM2G110408_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA08G09160.1 (Glycine max), 5'ss of exon 3
CTATTGACAGAATTGTGGCTGGTATGGAAGGGACTGTGATGACAGACGGGAAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatgaatct-------tcctcttaacagatcttttctcctttgccttgaacattagaatgtgattggtttaattttggtttcgattggtttctcagatatc
||||||| || ||||||||||| |||||||| || ||||||||||| ||||||||||||||| | || || || |||||||| || ||||| ||||| |||||||| ||    ||       |    ||||   |   |||     |||| | |||      || ||| || |  |||||  |      ||      || | |||  
CTATTGATAGGATTGTGGCTGGAATGGAAGGAACAGTGATGACAGATGGGAAGAGCAAAAGTTTAGTGGCATATCATGAAGTTGGTCATGCTATTTGTGGgtaagaaatttggctcagtttatgtctttaagtaaatgttttaaggttgcatggaa----gcaaggtgttttgcctaattaggtaaatcatgtaacactta-ata--

upper sequence: GRMZM2G110408_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA09G05820.1 (Glycine max), 5'ss of exon 3
CTATTGACAGAATTGTGGCTGGTATGGAAGGGACTGTGATGACAGACGGGAAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatgaatcttcctcttaacagatcttttctcctttgccttgaacattagaatgtgattggtttaattttggtttcgattggtttctcagatatc--
||||||| || ||||||||||| |||||||| |||||||||||||| || |||||||||||  | || || || |||||||| |||||||| ||||| |||||||  |  ||||    | |       ||||| |   ||    || |  |||  ||||  |      |  | |||  |   ||   ||      | |    
CTATTGATAGGATTGTGGCTGGAATGGAAGGAACTGTGATGACAGATGGAAAGAGCAAAAGCTTAGTGGCATATCATGAAGTTGGGCATGCTATTTGTGGgtaagccaaaaatcagggtgtagttttgtcttt-cgagttaatgtttatgattgcaatggaagcaaggtgttattgcctat-ataaattcacgttacacttg

upper sequence: GRMZM2G110408_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA15G17070.1 (Glycine max), 5'ss of exon 3
CTATTGACAGAATTGTGGCTGGTATGGAAGGGACTGTGATGACAGACGGGAAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatgaatcttcctcttaacagatcttttctcctttgccttgaacattagaatgtgattggtt---taattttggtttcgattggtttctcagat--atc---------------------------------------------------------------------------------------
| ||||| || ||||||||||| |||||||| || || |||||||| || |||||||||||  | || || || |||||||| |||||||| |||||||||||||  |  ||||      | ||    |    | |  |  ||  || | |  |   ||| ||||  |   ||| ||    ||  | | || | | | |   |||                                                                                       
CCATTGATAGGATTGTGGCTGGAATGGAAGGAACCGTAATGACAGATGGAAAGAGCAAAAGCTTAGTGGCATATCATGAAGTTGGGCATGCTATTTGCGGgtaagccaaaaatc----agtaaatgtgtacgatatgatg-gcaatgga-agcaaggtgttattgcctatataaattcatgttacacttgtatataaaagtaatccagaaaaaaacaatggttctcattcagaagctgttttttgtaaacaattccaaaaagttgttcttaaatacctatctgtacttgcag

upper sequence: GRMZM2G110408_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA05G26230.1 (Glycine max), 5'ss of exon 3
CTATTGACAGAATTGTGGCTGGTATGGAAGGGACTGTGATGACAGACGGGAAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatgaatct-tcctcttaacagatcttttctcctttgccttgaacattagaatgtgattggtttaattttggtttcgattggtttctcagatatc
||||||| || ||||||||||| |||||||| || || |||||||| ||||||||||||||  | || || || |||||||| |||||||| ||||| |||||||| ||    || |  | ||      |   |     |||        || | ||| |  ||  ||||  | ||  |  | | |  | |  ||  ||  
CTATTGATAGGATTGTGGCTGGAATGGAAGGAACAGTTATGACAGATGGGAAGAGCAAAAGCTTAGTGGCATATCATGAAGTTGGGCATGCTATTTGTGGgtaagaaatttggctgttgtttttgtgtttaagtaaatgtttcaagattgcaatggaa-gcaatgtgttttgtctttatggctaattatgtaacacttaat

upper sequence: GRMZM2G110408_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT1G06430.1 (Arabidopsis thaliana), 5'ss of exon 3
CTATTGACAGAATTGTGGCTGGTATGGAAGGGACTGTGATGACAGACGGGAAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatgaatcttcctcttaacagatcttttctcctttgccttgaacattagaatgtgattggtttaattttggtttcgattggtttctcagatatc
| |||||||||||||| ||||| |||||||| || || |||||||| ||||||||||||||  | ||||||||||||||||| || ||||| || || |||||||  |  |       ||  |  ||||  | | |   ||  |   ||      ||| | |   ||| | | || |||      |              
CAATTGACAGAATTGTAGCTGGCATGGAAGGAACAGTCATGACAGATGGGAAGAGCAAAAGCTTGGTTGCTTACCATGAAGTTGGCCATGCCATATGTGGgtaagtcagaa-------tcagattagatgatgtgtgtgttatc--aaaagcctaaatttaa---gttcattgttcgttcttgcag--------------

upper sequence: GRMZM2G110408_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT2G30950.1 (Arabidopsis thaliana), 5'ss of exon 3
CTATTGACAGAATTGTGGCTGGTATGGAAGGGACTGTGATGACAGACGGGAAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatgaatcttcctcttaacagatcttttctcctttgccttgaacattagaatgtgattggtttaattttggtttcgattggtttctcagatatc
| ||||| ||||| || ||||| |||||||| || |||||||| || || |||||||||||  | || |||||||||||||| || |||||| | || ||||||| || ||| | |  |   | |   ||| |      || |  | || |    | | | |     | || ||||||||      |             
CCATTGATAGAATCGTTGCTGGCATGGAAGGAACAGTGATGACCGATGGCAAGAGCAAAAGCTTGGTAGCTTACCATGAAGTTGGTCATGCAGTGTGTGGgtaagtga-gaaacatattaaaagcctgtctgtatattattactatcaaaaacttactttaaagttataaactttggttttttacag-------------

upper sequence: GRMZM2G110408_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv12s0028g01600.t01 (Vitis vinifera), 5'ss of exon 3
CTATTGACAGAATTGTGGCTGGTATGGAAGGGACTGTGATGACAGACGGGAAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatga-atcttcctcttaacagatcttttctcctttgccttgaacat-tagaatgtgattggtttaat--tttggtttcga--ttggtttctcagatatc
| ||||| || ||||||||||| |||||||| || || |||||||| || |||||||| ||||| || |||||||||||||| || ||||| || || ||||||| ||  | ||| | |  |         | |   | || ||| ||   || |      ||||  |   |    |||   ||| |   |  ||| |||      
CAATTGATAGGATTGTGGCTGGAATGGAAGGAACAGTTATGACAGATGGAAAGAGCAAGAGTCTGGTGGCTTACCATGAAGTTGGTCATGCCATATGTGGgtaagtgaaaatatcctgccatgtttcttattctggacattcgccatgttgatatccttcttgataaggccagcagttttacttcaaaactaatttttca------

upper sequence: GRMZM2G110408_T01 (Zea mays), 5'ss of exon 3
lower sequence: PP1S156_30V6.1 (Physcomitrella patens), 5'ss of exon 4
CTATTGACAGAATTGTGGCTGGTATGGAAGGGACTGTGATGACAGACGGGAAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatgaatcttcctctta--acagatcttttctcctttgccttgaacattagaatgtgattggttta----attttggtttcgattggtttctcagatatc-----------------
| ||||| ||||| |||||||||||||| ||||| || ||||| || || ||    || |||||||| || || |||||||| || ||||| |||||||||||     |   ||  | ||  |   ||  | |     |  || | |||    |   ||  |  |  | |||       |||   || |  | ||  | | | ||                  
CCATTGATAGAATCGTGGCTGGTATGGAGGGGACAGTCATGACCGATGGCAAAGCAAAGAGTCTTGTCGCATATCATGAAGTTGGCCATGCTATTTGCGGgtactttttctttcaccatccaattgcaattgtacctgcagtttcattgtctctggaaaatttctaaggttacggtgcattgacctctaaggcttattaataaattaattgtgtgaggtgcag

upper sequence: GRMZM2G110408_T01 (Zea mays), 5'ss of exon 3
lower sequence: PP1S118_166V6.1 (Physcomitrella patens), 5'ss of exon 2
CTATTGACAGAATTGTGGCTGGTATGGAAGGGACTGTGATGACAGACGGGAAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatgaatcttcctcttaacagatcttttctcctttgccttgaacattagaatgtgattggtttaattttggtttcgattggtttctcagatatc--------------------------------------------------------------------------------------
| ||||||||||| || || || |||||||| || || ||||| ||||| |||||||| ||||||||||| ||||| |||||||| ||||| || ||||||||||| |    |     ||   |   | | | |    ||||  |   | ||   | | |  |   | || |  ||| ||    |||||  |   |  |                                                                                       
CAATTGACAGAATCGTTGCCGGGATGGAAGGTACCGTCATGACGGACGGCAAGAGCAAGAGTCTTGTTGCATACCACGAAGTCGGCCATGCTATCTGCGGgtaagaaacttgtacaattcgggatgtaccgtatggtttttgt-tcatatat-gcagttttttctatgtagtggtggcttttgctggttctttgtagttggaataactgtgaagtgatatcttcacttaggtcaaaaccatttgatttctgtttgctgaagtgtatgtactgtgtattctgtgcag

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|211130729|gb|FL008630.1|FL008630
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAATCGGGCATGCAATTTGCGG                         AACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
EST: gi|32924261|gb|CF029073.1|CF029073
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGG                         AACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
EST: gi|89248872|gb|DY620658.1|DY620658
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGG                         AACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
EST: gi|37396149|gb|CF635362.1|CF635362
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGG                         AACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
EST: gi|32924520|gb|CF029332.1|CF029332
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGG                         AACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
EST: gi|94472629|gb|EB701587.1|EB701587
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGG                         AACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
EST: gi|67033229|gb|CO461978.1|CO461978
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTTGGGCATGCAATTTGCGG                         AACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
EST: gi|148945969|gb|EC891262.2|EC891262
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGG                         AACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
EST: gi|148955091|gb|EC900605.2|EC900605
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGG                         AACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
EST: gi|32850880|gb|CD990561.1|CD990561
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGG                         AACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
EST: gi|32924145|gb|CF028957.1|CF028957
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGG                         AACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
EST: gi|32850859|gb|CD990540.1|CD990540
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGG                         AACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTATTGACAGAATTGTGGCTGGTATGGAAGGGACTGTGATGACAGACGGGAAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatgaatcttcctcttaacagatcttttctcctttgccttgaacattagaatgtgattggtttaattttggtttcgattggtttctcagatatc

- - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA