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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGAAGAGCGTATGACACTATGCAACATGGTTATTGAAGCTGGTGGAAAGAACGGTGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaagtagtcccttgaaatgctcataataaagttgggccaatgtgcttttctttcataacgttccaataactttgagatagagagtgctcttgtactaagaccaatttgcaaaaatgagcttctactatttagtttgtacgataattctgacgtcattgccgttgtgttggtatactgcag

Basic information

species Zea mays
transcript GRMZM2G133988_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133988_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g03260.1 (Oryza sativa), 5'ss of exon 8
ATGGAAGAGCGTATGACACTATGCAACATGGTTATTGAAGCTGGTGGAAAGAACGGTGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaagtagtcccttgaaatgctca-taataaagttgggccaatgtgcttttctttcataacgttccaataactttgagatagagagtgctcttgtactaagaccaatttgcaaaaatgagcttctactatttagtttgtacgataattctgacgtcattgccgttgtgttggtatactgcag
||||||||||| |||||||| |||||||||||||||||||||||||| ||||| |||||||||||||| ||| ||||||||||||| || ||||||||||   | | | || || |||||||   ||||||| | | || |   |  | | |    | |||   |||| | | || || |         ||   ||  ||||   |||| ||| ||  |  |||||   ||||  |  |  ||||||| ||||  |||  | ||  |  ||||| |||||||
ATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAGAATGGTGTTGTGCCTGCCGATCAAACTACATTTAACTATCTTGAGgtactttaatgg-cctttaaaatgcttggtaataaaat-gagcgatatttttatgcaaataaaacaacccaacatccttaagct---------tcgaataagaagaaatatttacaagaacaaatttctaacttttacataat--gataattatgactccatatcggtcatcctggta-actgcag

upper sequence: GRMZM2G133988_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA20G34160.1 (Glycine max), 5'ss of exon 10
ATGGAAGAGCGTATGACACTATGCAACATGGTTATTGAAGCTGGTGGAAAGAACGGTGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaagtagtcccttgaaatgctcataataaagttgggccaatgtgcttttctttcataacgttccaataactttgagatagagagtgctcttgtactaagaccaatttgcaaaaatgagcttctactatttagtttgtacgataattctgacgtcattgccgttgtgttggtatactgcag
||||||||  | |||||||| |||||||||||||| |||||||| || || |||||| ||||  ||||||||  ||| ||||  ||||||||||||||                          |  | ||||||  | |  |  ||||   ||  |  | || || |   | |    |   |  ||  |||| |   | ||  ||     |   |||  ||  |                                                        
ATGGAAGAAAGGATGACACTGTGCAACATGGTTATAGAAGCTGGAGGGAAAAACGGTATTGTTGCTGCTGATAGAACCACATACAAATACCTTGAGgt--------------------------tgttgaagttgaac-agcgccctttatgtttttctcatttcactgtttctctcttcatgtatgtgcttgcatatatac--atgcaagatgctgaattttca--------------------------------------------------------

upper sequence: GRMZM2G133988_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA14G40570.1 (Glycine max), 5'ss of exon 9
ATGGAAGAGCGTATGACACTATGCAACATGGTTATTGAAGCTGGTGGAAAGAACGGTGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaagtagtcccttgaaatgctcataataaagttgggccaatgtgcttttctttcataacgttccaataactttgagatagagagtgctcttgtactaagaccaatttgcaaaaatgagcttctactatttagtttgtacgataattctgacgtcattgccgttgtgttggtatactgcag
|||||||| || |||||| | |||||||||||| ||||||||||||||||||| |||||||| ||||||||    |||||||||||||| ||||||||        | |   | ||    || | | | |  ||  |||  |    || | | |  | |  |   ||  | ||    |||     || |  | | |||                                                                                   
ATGGAAGAACGGATGACATTGTGCAACATGGTTGTTGAAGCTGGTGGAAAGAATGGTGTTGTTCCTGCTGACAGCACTACATTTAAATATCTTGAGgtttgtgca-actgagtagatgcactgaaattgatattttgcctctaaagttatatgttgtcat-tggtaaagatttcataatatct--tgattgtatcctaga---------------------------------------------------------------------------------

upper sequence: GRMZM2G133988_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA17G37540.1 (Glycine max), 5'ss of exon 9
-ATGGAAGAGCGTATGACACTATGCAACATGGTTATTGAAGCTGGTGGAAAGAACGGTGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaagtagtcccttgaaatgctcataataaagttgggccaatgtgcttttctttcataacgttccaataactttgagatagagagtgctcttgtactaagaccaatttgcaaaaatgagcttctactatttagtttgtacgataattctgacgtcattgccgttgtgttggtatactgcag
 |||||||| || |||||| | |||||||||||| ||||||||||||||||||| |||||||| ||||||||    |||||||||||||| ||||||||       | || |     | |      | | || ||||     ||  || |    | |||   |  || |  ||||       |  |   | ||    |||||  |  ||| |                                                                      
GATGGAAGAACGGATGACATTGTGCAACATGGTTGTTGAAGCTGGTGGAAAGAATGGTGTTGTTCCTGCTGACAGCACTACATTTAAATATCTTGAggt-------ttgtgcaactgagtagatgcactgaaattggtatcttgc-ctctaaagttatatgttctcattggcttt----ctcaatggattttt----taagagaagattgta----------------------------------------------------------------------

upper sequence: GRMZM2G133988_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv08s0056g01640.t01 (Vitis vinifera), 5'ss of exon 9
ATGGAAGAGCGTATGACACTATGCAACATGGTTATTGAAGCTGGTGGAAAGAACGGTGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaagtagtcccttgaaatgctcataataaagttgggccaatgtgcttttctttcataacgttccaataactttgagatagagagtgctcttgtactaagaccaatttgcaaaaatgagcttctactatttagtttgtacgataattctgacgtcattgccgttgtgttggtatactgcag
||||||||  | |||||| |||||||||||||| |||||||||| |||||||| |||||||| |||||||||   ||||||  ||| ||||||||||| |  ||  | ||  ||    |     |||||    || || | ||   |   |    | ||      || ||  ||    |      ||  ||| |  |   || | ||||      |  ||||     | ||  |||| ||                                         
ATGGAAGAAAGGATGACATTATGCAACATGGTTGTTGAAGCTGGAGGAAAGAATGGTGTTGTTCCTGCTGATAGTACTACACATAAGTACCTTGAGgt-cggaataaatcagtttctctttctctaatatttgtgtgctattga--taaacgaaaaaaaaaaaggaacaaaattt--gttctttttgtgcttatcatgcaactattttgt-----ttggcttaagtcagtttctttgcacag---------------------------------------

upper sequence: GRMZM2G133988_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv05s0049g01980.t01 (Vitis vinifera), 5'ss of exon 9
ATGGAAGAGCGTATGACACTATGCAACATGGTTATTGAAGCTGGTGGAAAGAACGGTGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaagtagtcccttgaaatgctcataataaagttgggccaatgtgcttttctttcataacgttccaataactttgagatagagagtgctcttgtactaagaccaatttgcaaaaatgagcttctactatttagtttgtacgataattctgacgtcattgccgttgtgttggtatactgcag
||||||||  | |||||| ||||||||||||||||||||||||| |||||||| |||||||| |||||||||   ||||||  ||| |||||||||||  | ||| | ||  |                           || |   | ||| ||  |   || | ||  |    | |  | || |  | || |  | |  |  ||| |   || |    |||| ||   ||  |  |  | |  ||   ||                             
ATGGAAGAAAGAATGACATTATGCAACATGGTTATTGAAGCTGGGGGAAAGAATGGTGTTGTCCCTGCTGATAGTACTACACATAAGTACCTTGAGgt-tagaagaaatcattc--------------------------atctctctctctctctcatgcttgctattgcc--aaaagggtgattttttttctctttatgcttatt-gtgcaact--ctttcttctggctaagtcat-tgtttctttgcacag---------------------------

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|211485260|gb|FL406758.1|FL406758
EST:     GAAACTACATTTAAATACCTTGAG                         GGTAAGACATCAGTCGATTATGAACCTGTCTACAGNGATGCTCAAGCCAG
genomic: GAAACTACATTTAAATACCTTGAGgtacaaaagt ... tatactgcagGGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG
EST: gi|211297290|gb|FL430291.1|FL430291
EST:     TGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG                         GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG
genomic: TGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaagt ... tatactgcagGGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG
EST: gi|13382157|gb|BG458832.1|BG458832
EST:     GAAAGAACGGTGTTGTGCCTGCTGATGAAACTACATTTATATACCTTGAG                         GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG
genomic: GAAAGAACGGTGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaagt ... tatactgcagGGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG
EST: gi|211084567|gb|FL380768.1|FL380768
EST:     TGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG                         GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG
genomic: TGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaagt ... tatactgcagGGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG
EST: gi|211445219|gb|FL371640.1|FL371640
EST:     TGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG                         GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG
genomic: TGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaagt ... tatactgcagGGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG
EST: gi|211476197|gb|FL374877.1|FL374877
EST:     TGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG                         GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG
genomic: TGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaagt ... tatactgcagGGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG
EST: gi|211199607|gb|FL408270.1|FL408270
EST:     TGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG                         GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG
genomic: TGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaagt ... tatactgcagGGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG
EST: gi|211413964|gb|FL425524.1|FL425524
EST:     TGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG                         GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG
genomic: TGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaagt ... tatactgcagGGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG
EST: gi|211201683|gb|FL384209.1|FL384209
EST:     TGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG                         GGTAAGACATCAGTCGATTATGAACCTGTCTACAGNGATGCTCAAGCCAG
genomic: TGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaagt ... tatactgcagGGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG
EST: gi|32849674|gb|CD989355.1|CD989355
EST:     GAAAGAACGGTGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG                         GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCCCAAGCCAG
genomic: GAAAGAACGGTGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaagt ... tatactgcagGGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG
EST: gi|211150179|gb|FL390454.1|FL390454
EST:     TGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG                         GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG
genomic: TGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaagt ... tatactgcagGGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG
EST: gi|31356659|gb|CD441016.1|CD441016
EST:     GAAAGAACGGTGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG                         GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG
genomic: GAAAGAACGGTGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaagt ... tatactgcagGGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG
EST: gi|33100114|gb|CF060074.1|CF060074
EST:     GAAAGAACGGTGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG                         GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG
genomic: GAAAGAACGGTGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaagt ... tatactgcagGGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG
EST: gi|211282426|gb|FL393385.1|FL393385
EST:     TGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG                         GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG
genomic: TGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaagt ... tatactgcagGGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG
EST: gi|211228096|gb|FL409262.1|FL409262
EST:     TGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG                         GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG
genomic: TGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaagt ... tatactgcagGGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG
EST: gi|166431623|gb|EG098503.1|EG098503
EST:     ATTTAAATACCTTGAG                         GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG
genomic: ATTTAAATACCTTGAGgtacaaaagt ... tatactgcagGGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG

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: 40 (upstream exon), 48 (downstream exon)
Score: 27

ATGGAAGAGCGTATGACACTATGCAACATGGTTATTGAAGCTGGTGGAAAGAACGGTGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaagt ... tatactgcagGGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 120

ATGGAAGAGCGTATGACACTATGCAACATGGTTATTGAAGCTGGTGGAAAGAACGGTGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaagt ... tatactgcagGGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 78

ATGGAAGAGCGTATGACACTATGCAACATGGTTATTGAAGCTGGTGGAAAGAACGGTGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaagt ... tatactgcagGGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG


Block sizes: 41 (upstream exon), 47 (downstream exon)
Score: 43

ATGGAAGAGCGTATGACACTATGCAACATGGTTATTGAAGCTGGTGGAAAGAACGGTGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaagt ... tatactgcagGGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGAAGAGCGTATGACACTATGCAACATGGTTATTGAAGCTGGTGGAAAGAACGGTGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaagtagtcccttgaaatgctcataataaagttgggccaatgtgcttttctttcataacgttccaataactttgagatagagagtgctcttgtactaagaccaatttgcaaaaatgagcttctactatttagtttgtacgataattctgacgtcattgccgttgtgttggtatactgcag

- - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT