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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAGCCACGGAAGACTGAAATCACCGAAAAGCTACGCCAAGAAATCAATAAGgttttgattttttttttcagctaactttttttagttttataggcagtatcaaattttatataatcatgtaagaatcttcacctgattttaaattttacatggtgaaag

Basic information

species Zea mays
transcript GRMZM2G032267_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G032267_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os07g08170.1 (Oryza sativa), 5'ss of exon 6
CCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAGCCACGGAAGACTGAAATCACCGAAAAGCTACGCCAAGAAATCAATAAGgt-tttgattttttttttcagctaactttttttagttttataggcagtatcaaattttatataatcatgtaagaatcttcacctgat-tttaaattttacatggtgaaag-----
 || |||||||| |||||||||||||||||||||||||| |||||||||||||||||||| ||||||||||| || |||||||| ||||||||||||||||| ||  | |||    |  |||  |    |  |  ||||| | |  | | || |||| ||| |  ||||| || ||   ||  |||| |||||  | || |  ||          
TCAACCACAAGGAGGCCAAGATATTTTGTCCCTTATGGGACAGATGATGAAGCCACGGAAAACTGAAATCACTGAGAAGCTACGACAAGAAATCAATAAGgtattcaaatttcccatgtagc--agcactgctgcttttaaaagtgg-accacatttaataaa--catgtcaggattggcatatgatctttaacatctatactgtatgttgctag

upper sequence: GRMZM2G032267_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g62040.1 (Oryza sativa), 5'ss of exon 6
CCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAGCCACGGAAGACTGAAATCACCGAAAAGCTACGCCAAGAAATCAATAAGgttttgattttttttttcagctaactttttttagttttataggcagtatcaaattttatataatcatgtaagaatcttcacctgat-tttaaattttacatggtgaaag-----
 || |||||||| |||||||||||||||||||||||||| || |||||||||||||| |||||||||||||| || ||||| || ||||||||||||||||||||   |   ||| | |   | |       | | ||  |  | | || |||||| ||  |  |||   || |||      |||| |||||  |||| || |           
TCAACCACAAGGAGGCCAAGATATTTTGTCCCTTATGGGGCAAATGATGAAGCCACGAAAGACTGAAATCACTGACAAGCTTCGGCAAGAAATCAATAAGgtttt---tcagtttctgattgagcggcacccattctttgaaactggattaaatttaatgaa--cattccaggatcgatgtatgatctttaatctttatattgcattttagtag

upper sequence: GRMZM2G032267_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA08G21830.1 (Glycine max), 5'ss of exon 6
CCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAGCCACGGAAGACTGAAATCACCGAAAAGCTACGCCAAGAAATCAATAAGgttttgattttttttttcagctaacttt----ttttagttttataggcagtatcaaattttatataatcatgtaagaatcttcacctgattttaaattttacatggtgaaag
 |  || ||||| || ||||||||| |||| || ||||| ||||||||||||||  |||| || |||||||| || ||| |  | ||||| || || ||||| ||    |   |||| |   || |||    |||    ||||| || |  || ||   |   | | | | |      ||||  |    | || ||||              
ACGACCTCAAGGGGGACAAGATATTCTGTCTCTGATGGGTCAGATGATGAAGCCCAGGAAAACAGAAATCACTGACAAGTTGAGGCAAGAGATTAACAAGgtattttaataacttttgatacaagtttgtagtttcttatttatgggaaaaattaagggtcgaaaagtga-gcttttgtcttagcaatttgttcaattgct-----------

upper sequence: GRMZM2G032267_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA07G02170.1 (Glycine max), 5'ss of exon 6
CCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAGCCACGGAAGACTGAAATCACCGAAAAGCTACGCCAAGAAATCAATAAGgttttgattttttttttcagctaactttttttagttttataggcagtatcaaattttatataatcatgtaagaatcttcacctgattttaaattttacatggtgaaag--
 |  || ||||| || ||||||||| |||| |||||||| ||||||||||||||  |||| || || ||||| || ||| |  | |||||||| || ||||| ||    |   |||| |   || ||| |  ||||| ||    |  || |    ||||      |  ||||  |||  |    | |     |||| | | |  |     
ACGACCTCAAGGGGGACAAGATATTCTGTCTCTTATGGGTCAGATGATGAAGCCTAGGAAAACAGAGATCACTGACAAGTTGAGGCAAGAAATTAACAAGgtattttcataacttttgatacaagtttgt--agtttcatcttta--attag---ttatggggaaaattaagggtctaaa---aaatgagcttttttcttagcaatttct

upper sequence: GRMZM2G032267_T02 (Zea mays), 5'ss of exon 6
lower sequence: AT5G22330.1 (Arabidopsis thaliana), 5'ss of exon 6
CCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAGCCACGGAAGACTGAAATCACCGAAAAGCTACGCCAAGAAATCAATAAGgttttgattttttttttcagctaactttttttagttttataggcagtatcaaattttatataatcatgtaaga-atcttcacctgattttaaattttacatggtgaaag
 |  || ||||||||||| |||||  | ||  | |||||||| |||||||| || ||||||||||| ||||| || ||||| || |||||||| || ||||   |||||||   |   ||   || |   | | |||| || ||| | | |  || | | |    | ||   | || || |  ||   ||  |                
TCGACCTCAAGGTGGCCAGGATATACTTTCTTTGATGGGCCAAATGATGAAACCGCGGAAGACTGAGATCACTGATAAGCTTCGGCAAGAAATTAACAAGg---tgattttcgct---agt--acatgggtgatttttttaagca-tcttactttctcttttgcaaggtctaatatttttatatgccattgtag---------------

upper sequence: GRMZM2G032267_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv06s0004g02910.t01 (Vitis vinifera), 5'ss of exon 6
CCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAGCCACGGAAGACTGAAATCACCGAAAAGCTACGCCAAGAAATCAATAAGgttttgattttttttttcagctaactttttttagttttataggcagtatcaaatttta----tataatcatgtaagaatcttcacctgattttaaattttacatggtgaaag
 | ||| |||||||| |||||||| |||||||| ||||| ||||||||||||||  |||| || |||||||| || ||| |||| || ||||| || ||||| |   ||| |   |       | |    |   |||| |      | |  || | ||    | || | ||  ||  |  || |   |     ||  |||            
ACGGCCTCAAGGTGGACAAGATATATTGTCCCTAATGGGTCAGATGATGAAGCCCAGGAAAACAGAAATCACTGATAAGTTACGACAGGAAATTAACAAGgtatcattttctggatgggagatattaacctatattttttcatttcttttgaactctaaatctgtagttatacaaacaggttaattggggaacaatcttt------------

upper sequence: GRMZM2G032267_T02 (Zea mays), 5'ss of exon 6
lower sequence: PP1S4_73V6.1 (Physcomitrella patens), 5'ss of exon 7
CCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAGCCACGGAAGACTGAAATCACCGAAAAGCTACGCCAAGAAATCAATAAGgt-------tttgattttttttttcagctaactttttttagttttata---ggcagtatca-aattttatataatcatgtaagaatcttcacctgattttaaattttacatggtgaaag--------------------------
 |  || ||||| ||||||||||| |||||| | ||||||||||||||||| || || ||||||||||| || || ||  |||| ||||| || || |||||        ||||   | |  |     ||         |   |  ||    |  || |   ||  |||||| || |   ||||       |    |   ||     ||  | |  |                            
TCGCCCTCAAGGAGGCCAAGATATATTGTCCATGATGGGCCAGATGATGAAACCTCGTAAGACTGAAATTACTGATAAATTACGACAAGAGATTAACAAGgtaatttttcttgacgctgtgctgtgagtatggacaagaaacctcgtacaaagtcgtgttgtaacattatattattaatcaagaggtaatgctgagtcagaagggcaacgagtttgagatggtttctcgttcatttgtggtgcag

upper sequence: GRMZM2G032267_T02 (Zea mays), 5'ss of exon 6
lower sequence: EFJ33466 (Selaginella moellendorffii), 5'ss of exon 6
CCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAGCCACGGAAGACTGAAATCACCGAAAAGCTACGCCAAGAAATCAATAAGgttttgattttttttttcagctaactttttttagttttataggcagtatcaaattttatataatcatgtaaga-atcttcacctgattttaaattttacatggtgaaag
 |  || |||||||| ||||||||| | ||| | ||||| ||||||||||||||    |||||||| ||||| || ||||| || || |||||||| ||||||   |       ||   |  | || |  |  ||||   |||   |   |   | || |  || ||||  |  || ||      |                       
GCGTCCTCAAGGTGGACAAGATATTCTTTCCATGATGGGACAGATGATGAAGCCGAAAAAGACTGAGATCACTGATAAGCTGCGGCAGGAAATCAACAAGgttagcagccggcgttc--gtcagctctcct--gtttcg-aggattttctattgtctaaaggattatgtgtggcatgtttgtggcag----------------------

upper sequence: GRMZM2G032267_T02 (Zea mays), 5'ss of exon 6
lower sequence: EFJ27201 (Selaginella moellendorffii), 5'ss of exon 6
CCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAGCCACGGAAGACTGAAATCACCGAAAAGCTACGCCAAGAAATCAATAAGgttttgattttttttttcagctaactttttttagttttataggcagtatcaaattttatataatcatgta-agaatcttcacctgattttaaattttacatggtgaaag
 |  || |||||||| ||||||||| | ||| | ||||| ||||||||||||||    |||||||| ||||| || || ||||| ||||||||||| ||||||  |    | ||  ||||||  | | ||||        |||   |   |   | || |  || ||||   | |||||      |                       
GCGTCCTCAAGGTGGACAAGATATTCTTTCCATGATGGGACAGATGATGAAGCCGAAAAAGACTGAGATCACTGATAAACTACGGCAAGAAATCAACAAGgtta-gccggtgttcgtcagctctcctgttttg-------aggattttctattgtctagaggattatgtgtgggatctttgtggcag----------------------

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|60342617|gb|DN209590.1|DN209590
EST:     AGCCACGGAAGACTGAAATCACCGAAAAGCTACGCCAAGAAATCAATAAG                         GTGGTAAACAGATATATCGACGAAGGAATCGCAGAGCTTGTACCTGGTGTT
genomic: AGCCACGGAAGACTGAAATCACCGAAAAGCTACGCCAAGAAATCAATAAGgttttgattt ... atggtgaaagGTGGTAAACAGATATATCGACGAAGGAATCGCAGAGCTTGTACCTGGTGTT
EST: gi|32933015|gb|CF037827.1|CF037827
EST:     AGCCACGGAAGACTGAAATCACCGAAAAGCTACGCCAAGAAATCAATAAG                         GTGGTAAACAGATATATCGACGAAGGAATCGCAGAGCTTGTA
genomic: AGCCACGGAAGACTGAAATCACCGAAAAGCTACGCCAAGAAATCAATAAGgttttgattt ... atggtgaaagGTGGTAAACAGATATATCGACGAAGGAATCGCAGAGCTTGTA
EST: gi|32933753|gb|CF038565.1|CF038565
EST:     AGCCACGGAAGACTGAAATCACCGNNNNNNNNCGCCAAGAAATCAATAAG                         GTGGTAAACAGATATATCGACGAAGGAATCGCAGAGCTTGT
genomic: AGCCACGGAAGACTGAAATCACCGAAAAGCTACGCCAAGAAATCAATAAGgttttgattt ... atggtgaaagGTGGTAAACAGATATATCGACGAAGGAATCGCAGAGCTTGT
EST: gi|74241474|gb|DT649388.1|DT649388
EST:     AGCCACGGAAGACTGAAATCACCGAAAAGCTACGCCAAGAAATCAATAAG                         GTGGTAAACAGATATATCGACGAAGGAATCGCAGAGCTTGTACCTGGTGTT
genomic: AGCCACGGAAGACTGAAATCACCGAAAAGCTACGCCAAGAAATCAATAAGgttttgattt ... atggtgaaagGTGGTAAACAGATATATCGACGAAGGAATCGCAGAGCTTGTACCTGGTGTT
EST: gi|87157723|gb|DY402512.1|DY402512
EST:     GAAATCAATAAG                         GTGGTAAACAGATATATCGACGAAGGAATCGCAGAGCTTGTACCTGGTGTT
genomic: GAAATCAATAAGgttttgattt ... atggtgaaagGTGGTAAACAGATATATCGACGAAGGAATCGCAGAGCTTGTACCTGGTGTT
EST: gi|26559755|gb|CA831990.1|CA831990
EST:     CCAAGAAATCAATAAG                         G-GGTAAACAGATATATCGACGAAGGAATCGCAGAGCTTGTACCTGNG-GT
genomic: CCAAGAAATCAATAAGgttttgattt ... atggtgaaagGTGGTAAACAGATATATCGACGAAGGAATCGCAGAGCTTGTACCTG-GTGT
EST: gi|60356915|gb|DN223888.1|DN223888
EST:     AGCCACGGAAGACTGAAATCACCGAAAAGCTACGCCAAGAAATCAATAAG                         GTGGTAAACAGATATATCGACGAAGGAATCGCAGAGCTTGTACCTGGTGTT
genomic: AGCCACGGAAGACTGAAATCACCGAAAAGCTACGCCAAGAAATCAATAAGgttttgattt ... atggtgaaagGTGGTAAACAGATATATCGACGAAGGAATCGCAGAGCTTGTACCTGGTGTT
EST: gi|78103432|gb|DV521860.1|DV521860
EST:     AGCCACGGAAGACTGAAATCACCGAAAAGCTACGCCAAGAAATCAATAAG                         GTGGTAAACAGATATATCGACGAAGGAATCGCAGAGCTTGTACCTGGTGTT
genomic: AGCCACGGAAGACTGAAATCACCGAAAAGCTACGCCAAGAAATCAATAAGgttttgattt ... atggtgaaagGTGGTAAACAGATATATCGACGAAGGAATCGCAGAGCTTGTACCTGGTGTT

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), 49 (downstream exon)
Score: 269

CCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAGCCACGGAAGACTGAAATCACCGAAAAGCTACGCCAAGAAATCAATAAGgttttgattt ... atggtgaaagGTGGTAAACAGATATATCGACGAAGGAATCGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 124

CCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAGCCACGGAAGACTGAAATCACCGAAAAGCTACGCCAAGAAATCAATAAGgttttgattt ... atggtgaaagGTGGTAAACAGATATATCGACGAAGGAATCGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 108

CCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAGCCACGGAAGACTGAAATCACCGAAAAGCTACGCCAAGAAATCAATAAGgttttgattt ... atggtgaaagGTGGTAAACAGATATATCGACGAAGGAATCGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 112

CCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAGCCACGGAAGACTGAAATCACCGAAAAGCTACGCCAAGAAATCAATAAGgttttgattt ... atggtgaaagGTGGTAAACAGATATATCGACGAAGGAATCGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAGCCACGGAAGACTGAAATCACCGAAAAGCTACGCCAAGAAATCAATAAGgttttgattttttttttcagctaactttttttagttttataggcagtatcaaattttatataatcatgtaagaatcttcacctgattttaaattttacatggtgaaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA