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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAAGACACAGCTCTCCCATCCCCTGAATGGTCATCAGATCACATAGCACTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAGgtatgttacaaaggaaatcagtgttgtcatattgcttctattgcaactgaatgttgtttttttgttgacatgaatgatgttggattgtgttagagtaaat...

Basic information

species Zea mays
transcript GRMZM2G118467_T03
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118467_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os10g27230.3 (Oryza sativa), 5'ss of exon 12
GAAAAGACACAGCTCTCCCATCCCCTGAATGGTCATCAGATCACATAGCACTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAGgtatgttacaaaggaaatcagtgttgtcatattgcttctattgcaactgaatgttgtttttttgttgacatgaatgatgt-tggattgtgttagagtaaat-
|||||||||| || || || || ||||||||||| || ||||| ||||||||||| || || |||||||||||||| ||||||||||| |||||| |||||||||| | || || |   |      |  || |  | || | | |      || | |  ||||| |      ||       ||| |   || ||| |   | 
GAAAAGACACGGCCCTTCCTTCTCCTGAATGGTCTTCGGATCATATAGCACTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAGgtatgtcataagggca--taaccacattttaattatactgtaggactgcggtgctctgattttgctagtgcaaacagcacatggctcaagtaagatttggtg

upper sequence: GRMZM2G118467_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA02G26620.2 (Glycine max), 5'ss of exon 11
GAAAAGACACAGCTCTCCCATCCCCTGAATGGTCATCAGATCACATAGCACTCTTAGCTGAGTTCCGGTGC---AAGCCAAGAATCAGACGTTGACACATTAGgtatgttacaaaggaaatcagt--gttgtcatattgcttctattgcaactgaatgttgtttttttgttgacatgaatgatgttggattgtgttagagtaaat
   | |||||||| || || || ||||||||||| |||||||||||||| |||||||| || || || |||   |||   | |   || ||||||||  | ||||| |   ||     || |          ||||| |||| | |||  | | | | |||        |  ||   | |||  ||   ||  ||    ||   |
---AGGACACAGCACTTCCTTCACCTGAATGGTCCTCAGATCACATAGCTCTCTTAGCCGAATTTCGCTGCTGCAAGAATAAATCTAGGCGTTGACAGTTAAGgtaggcaccatcctcaacccccccacccacatatagcttgt-ttgagaattattattggaaaag-atcaacggaagtgaactttcttttggtgctggttcct

upper sequence: GRMZM2G118467_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA09G15980.2 (Glycine max), 5'ss of exon 11
GAAAAGACACAGCTCTCCCATCCCCTGAATGGTCATCAGATCACATAGCACTCTTAGCTGAGTTCCGGTGC---AAGCCAAGAATCAGACGTTGACACATTAGgtatgttacaaaggaaatcagt-gttgtcatattgcttctattgcaactgaatgttgtttttttgttgacatgaatgatgttggattgtgttagagtaaat-
   | |||||||| || || || ||||||||||| ||||||||||| || |||||||||||||| || |||   |||   | |   || ||||||||  | ||||| |   ||     || |         ||||| |||| | ||| || | | | |||        |  ||   | || | ||   ||  ||     |   | 
---AGGACACAGCACTTCCTTCACCTGAATGGTCCTCAGATCACATTGCTCTCTTAGCTGAGTTTCGCTGCTGCAAGAATAAATCTAGGCGTTGACAGTTAAGgtaggcaccatcctcaaccccccacccacatatagcttgt-ttgaaaattattattggaaaag-atcaacggcagtggtctttcttttggtgctgattcctt

upper sequence: GRMZM2G118467_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA19G39210.3 (Glycine max), 5'ss of exon 11
GAAAAGACACAGCTCTCCCATCCCCTGAATGGTCATCAGATCACATAGCACTCTTAGCTGAGTTCCGGTGC---AAGCCAAGAATCAGACGTTGACACATTAGgtatgttacaaaggaaatcagtgttgtcatattgcttctattgcaactgaatgttgtttttttgttgacatgaatgat-gttggattgtgttagagtaaat-------------
   |||||||||| || || || ||||||||||| || ||||| ||||| || |||||||||||||| |||   |||   |||   || || |||| ||| |||||             ||||    |||| | || | | |||  ||| |     ||  |  ||  ||    ||| || |  |||  || ||  |   | ||              
---AAGACACAGCACTTCCTTCTCCTGAATGGTCCTCTGATCATATAGCTCTGTTAGCTGAGTTCCGCTGCTGCAAGAATAGATCTAGGCGCTGACTCATAAGgtacc-----------atcatctctgtcct-ttccctttat--caattattattttatgcttaatttgtgtgagtggttattgttttatggaaagatcaaggctcttggcattt

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|6194468|gb|AW146572.1|AW146572
EST:     CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAGCTCTCCAG                  
genomic: CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACAC---A--T-T--AGgtatgttaca ... agc
EST: gi|33092350|gb|CF052344.1|CF052344
EST:     CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAGCTCTCCAG                  
genomic: CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACAC---A--T-T--AGgtatgttaca ... agc
EST: gi|149111795|gb|EE190948.2|EE190948
EST:     CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAG                         C
genomic: CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAGgtatgttaca ... agctctccag-
EST: gi|149111795|gb|EE190948.2|EE190948
EST:     CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAG                         C
genomic: CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAGgtatgttaca ... agctctccag-
EST: gi|149111795|gb|EE190948.2|EE190948
EST:     CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAG                         C
genomic: CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAGgtatgttaca ... agctctccag-
EST: gi|149111795|gb|EE190948.2|EE190948
EST:     CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAG                         C
genomic: CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAGgtatgttaca ... agctctccag-
EST: gi|149111795|gb|EE190948.2|EE190948
EST:     CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAG                         C
genomic: CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAGgtatgttaca ... agctctccag-
EST: gi|149111795|gb|EE190948.2|EE190948
EST:     CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAG                         C
genomic: CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAGgtatgttaca ... agctctccag-
EST: gi|149111795|gb|EE190948.2|EE190948
EST:     CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAG                         C
genomic: CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAGgtatgttaca ... agctctccag-
EST: gi|149111795|gb|EE190948.2|EE190948
EST:     CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAG                         C
genomic: CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAGgtatgttaca ... agctctccag-
EST: gi|211013492|gb|FL469772.1|FL469772
EST:     CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAG                         GTCTTGTAGAAAAGGTCATTGTCATCATCCTTGGTGGTGGAACACCGTTCC
genomic: CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAGgtatgttaca ... agctctccagGTCTTGTAGAAAAGGTCATTGTCATCATCCTTGGTGGTGGAACACCGTTCC
EST: gi|148934305|gb|EC878331.2|EC878331
EST:     CTTTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAG                         GTTTTGTAGAAAAGGTCATTGTCATCATCCTTGGTGGTGGAACACCGTTCC
genomic: CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAGgtatgttaca ... agctctccagGTCTTGTAGAAAAGGTCATTGTCATCATCCTTGGTGGTGGAACACCGTTCC
EST: gi|60343893|gb|DN210866.1|DN210866
EST:     CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAG                         C
genomic: CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAGgtatgttaca ... agctctccag-
EST: gi|60343893|gb|DN210866.1|DN210866
EST:     CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAG                         C
genomic: CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAGgtatgttaca ... agctctccag-
EST: gi|60343893|gb|DN210866.1|DN210866
EST:     CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAG                         C
genomic: CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAGgtatgttaca ... agctctccag-
EST: gi|60343893|gb|DN210866.1|DN210866
EST:     CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAG                         C
genomic: CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAGgtatgttaca ... agctctccag-
EST: gi|60343893|gb|DN210866.1|DN210866
EST:     CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAG                         C
genomic: CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAGgtatgttaca ... agctctccag-
EST: gi|60343893|gb|DN210866.1|DN210866
EST:     CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAG                         C
genomic: CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAGgtatgttaca ... agctctccag-
EST: gi|60343893|gb|DN210866.1|DN210866
EST:     CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAG                         C
genomic: CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAGgtatgttaca ... agctctccag-
EST: gi|60343893|gb|DN210866.1|DN210866
EST:     CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAG                         C
genomic: CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAGgtatgttaca ... agctctccag-
EST: gi|211427750|gb|FL230782.1|FL230782
EST:     CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAGCTCTCCAG                  
genomic: CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACAC---A--T-T--AGgtatgttaca ... agc
EST: gi|211241666|gb|FL441721.1|FL441721
EST:     CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAG                         GTCTTGTAGAAAAGGTCATTGTCATCATCCTTGGTGGTGGAACACCGTTCC
genomic: CTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAGgtatgttaca ... agctctccagGTCTTGTAGAAAAGGTCATTGTCATCATCCTTGGTGGTGGAACACCGTTCC

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: 44

GAAAAGACACAGCTCTCCCATCCCCTGAATGGTCATCAGATCACATAGCACTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAGgtatgttaca ... agctctccagGTCTTGTAGAAAAGGTCATTGTCATCATCCTTGGTGGTGGAACACCGTTCCATGTGGGAACTTGAGGCAGGGCGGGAACGCGGGCTCTCGGGGAAGCAAA


Block sizes: 41 (upstream exon), 42 (downstream exon)
Score: 18

GAAAAGACACAGCTCTCCCATCCCCTGAATGGTCATCAGATCACATAGCACTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAGgtatgttaca ... agctctccagGTCTTGTAGAAAAGGTCATTGTCATCATCCTTGGTGGTGGAACACCGTTCCATGTGGGAACTTGAGGCAGGGCGGGAACGCGGGCTCTCGGGGAAGCAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 46

GAAAAGACACAGCTCTCCCATCCCCTGAATGGTCATCAGATCACATAGCACTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAGgtatgttaca ... agctctccagGTCTTGTAGAAAAGGTCATTGTCATCATCCTTGGTGGTGGAACACCGTTCCATGTGGGAACTTGAGGCAGGGCGGGAACGCGGGCTCTCGGGGAAGCAAA


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 23

GAAAAGACACAGCTCTCCCATCCCCTGAATGGTCATCAGATCACATAGCACTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAGgtatgttaca ... agctctccagGTCTTGTAGAAAAGGTCATTGTCATCATCCTTGGTGGTGGAACACCGTTCCATGTGGGAACTTGAGGCAGGGCGGGAACGCGGGCTCTCGGGGAAGCAAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAAAGACACAGCTCTCCCATCCCCTGAATGGTCATCAGATCACATAGCACTCTTAGCTGAGTTCCGGTGCAAGCCAAGAATCAGACGTTGACACATTAGgtatgttacaaaggaaatcagtgttgtcatattgcttctattgcaactgaatgttgtttttttgttgacatgaatgatgttggattgtgttagagtaaat

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA