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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccagtagtgattgctaataaaatacatgtaggtgtagcttacatatccaagcttcgttaatagaagtcataaaaccggtgaaaatataatgcagGAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTGGAGGGGCCCAAGGACAGGAGACTGATCTTGAGATTCAG

Basic information

species Zea mays
transcript GRMZM2G121456_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G121456_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g19510.1 (Oryza sativa), 3'ss of exon 7
gtaccagtagtgattgctaataaaatacatgtaggtgtagcttacatatccaagcttcgttaatagaagtcataaaaccggtgaaaatataatgcagGAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTGGAGGGGCCCAAGGACAGGAGACTGATCTTGAGATTCAG
|||   | |||||||| ||||  ||    |  |  | |     |  ||  |     |   |  | |||   |    ||  |||||  | |||  |||| ||||||||||||||||| |||||||| |||||||||||||||||||| ||||| ||||||||||| ||||||||||||||||| |||
gtaattg-agtgattgttaatgcaagtactacatttattctacaactagactgatctgaatccttgaa--tactgtacttgtgaa--tgtaacacagGGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAG

upper sequence: GRMZM2G121456_T03 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA10G01550.2 (Glycine max), 3'ss of exon 7
---------------------------------gtaccagtagtgattgctaataaaatacatgtaggtgtagcttacatatccaagcttcg-ttaatagaagtcataaaaccggtgaaaatataatgc---agGAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTGGAGGGGCCCAAGGACAGGAGACTGATCTTGAGATTCAG
                                    ||     |  ||| | || ||   ||| |     |  |||  | ||   |     | ||  |   |    || | ||  |     |  | | |   ||||||| |||||||||| ||||| |||||||||||||| |||||||| ||||| || || ||||||  | | |||||  | || ||||||
gtattcttttaacatgcaatcgctgtatctatccccccctctttctttgttgatgaatgccatttccactt--cttgaaaattagaataatgcttctttctaactttatatcccttcctccttcacttctgaagGAAAGAGATACAGCTTGCCAAATTCAAGGATAATGATTCATCAACCGCTTGGTGGTGCTCAAGGAGGGCAAACTGACATAGATATTCAG

upper sequence: GRMZM2G121456_T03 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA02G01510.2 (Glycine max), 3'ss of exon 7
------------------------------------------gtaccagtagtgattgctaataaaatacatgtaggtgtagcttacatatccaagcttcgttaatagaagtcataaaaccggtgaaaatataatgc---agGAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTGGAGGGGCCCAAGGACAGGAGACTGATCTTGAGATTCAG
                                             |      |  ||| | || ||   ||| |     |  |  | |||   ||  | | |   |  || |  || | ||  |     |  | | |   ||||||| |||||||||| ||||| |||||||||||||| |||||||| ||||| || || ||||||  | | |||||  | || ||||||
gtattcttttaacatgcaatcagtgtatccatccccctatcccctctctctttctttgttgatgaatgtcattttcacctctcgaaaataagaaaaatgcttctttctaactt-tatatcccttcctctttcacttctgaagGAAAGAGATACAGCTTGCCAAATTCAAGGATAATGATTCATCAACCGCTTGGTGGTGCTCAAGGAGGGCAAACTGACATAGATATTCAG

upper sequence: GRMZM2G121456_T03 (Zea mays), 3'ss of exon 7
lower sequence: AT1G02560.1 (Arabidopsis thaliana), 3'ss of exon 7
--------gtaccagtagtgattgctaataaaatacatgtaggtgtagcttacatatccaagcttcgttaatagaagtcataaaaccggtgaaaatataatgcagGAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTGGAGGGGCCCAAGGACAGGAGACTGATCTTGAGATTCAG
         ||    |    ||   || |||||  | | |||      ||||   ||   |  ||   | ||   ||||||         | |||   | || ||||||  |||||||  |||||||||||||||||||||||||||| || ||||| || || |||||     | || ||  |||| ||||||
gtagtctcttaatcctttcaatcattagtaaaaatcttttagtgaagtcttatgaatttca-tttttctgatgtgagtcatgctttattcgtaaa---actgtagGAAAAAGATACAGTCTACCAAACTCAAGGATAATGATCCATCAGCCGCTTGGTGGAGCTCAAGGTGGCCAAACCGACATTGACATTCAG

upper sequence: GRMZM2G121456_T03 (Zea mays), 3'ss of exon 7
lower sequence: Vv07s0005g01530.t01 (Vitis vinifera), 3'ss of exon 7
----------------gtaccagtagtgattgctaataaaatacatgtaggtgtagcttacatatccaagctt-cgttaatagaagtcataaaaccggtgaaaatataatgcagGAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTGGAGGGGCCCAAGGACAGGAGACTGATCTTGAGATTCAG
                |     || || | || |    |  | ||  |    || || ||    |    |  | | || | |   ||| |   |||  |     |  | || ||||||  |||| ||||| |||||||||||||| ||||||||||| ||||| || || || |||||   | | |||||  | || ||||||
gtaagtaatttcctaggcttttgttgttagtggtttggagttccactt---cgtggcatatgctttttggtgtgctttgacatgtgtc-tgtcacc--tccctcttaactgaagGAAAAAGATATAGCTTGCCAAACTCAAGGATCATGATCCATCAGCCTCTCGGTGGAGCTCAAGGTGGGCAAACTGACATAGATATTCAG

upper sequence: GRMZM2G121456_T03 (Zea mays), 3'ss of exon 7
lower sequence: PP1S49_191V6.1 (Physcomitrella patens), 3'ss of exon 7
------gtaccagtagtgat-tgctaataaaatacatgtaggtgtagcttacatatccaagcttcgttaatagaagtcataaaaccggtgaaaatataatgcagGAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTGGAGGGGCCCAAGGACAGGAGACTGATCTTGAGATTCAG
      | |      ||| |     || | ||| | |||||   |  ||    || |      |  ||  |||||           |||     |  |   |||| || ||||||||  ||||||| ||  | || ||||| ||||||||||| ||||| || ||||||||| |||||||| |||| ||||||
agctgtggattcaacgtgctgcagcaagagaatgc-tgtagacatttctcgtttacctctaactgattt-tagaaactgcct--ttggttttcttccatcccagGTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAG

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|19769319|gb|BQ034040.1|BQ034040
EST:     CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG                         GAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTG
genomic: CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAGgtaccagtag ... tataatgcagGAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTG
EST: gi|149088220|gb|EE287341.2|EE287341
EST:     CATGGGAACTTTTCTACTTAGTGCTGGGACCAAAG                         GAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTG
genomic: CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAGgtaccagtag ... tataatgcagGAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTG
EST: gi|88752492|gb|DY536633.1|DY536633
EST:     CATGGGAGCTTTTCTATTTAGTGCTGGGACCAAAG                         GAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTG
genomic: CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAGgtaccagtag ... tataatgcagGAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTG
EST: gi|20208074|gb|BQ134163.1|BQ134163
EST:     CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG                         GAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTG
genomic: CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAGgtaccagtag ... tataatgcagGAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTG
EST: gi|32942454|gb|CF047273.1|CF047273
EST:     CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG                         GAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTG
genomic: CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAGgtaccagtag ... tataatgcagGAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTG
EST: gi|71307771|gb|DR790104.1|DR790104
EST:     CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG                         GAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTG
genomic: CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAGgtaccagtag ... tataatgcagGAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTG
EST: gi|76281084|gb|DV020652.1|DV020652
EST:     TAGCTGCAAGCATGGGAGCTTTTCTACTTAGTGCTGGGGCCAAAG                         GAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTG
genomic: TAGCTGCAAGCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAGgtaccagtag ... tataatgcagGAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTG
EST: gi|149043157|gb|EE047302.2|EE047302
EST:     CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG                         GAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTG
genomic: CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAGgtaccagtag ... tataatgcagGAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTG
EST: gi|74237087|gb|DT645001.1|DT645001
EST:     CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG                         GAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTG
genomic: CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAGgtaccagtag ... tataatgcagGAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTG
EST: gi|76012849|gb|DT940019.1|DT940019
EST:     CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG                         GAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTG
genomic: CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAGgtaccagtag ... tataatgcagGAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTG

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: 44 (upstream exon), 49 (downstream exon)
Score: 311

CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAGgtaccagtag ... tataatgcagGAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTGGAGGGGCCCAAGGACAGGAGACTGATCTTGAGATTCAG


Block sizes: 35 (upstream exon), 49 (downstream exon)
Score: 331

CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAGgtaccagtag ... tataatgcagGAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTGGAGGGGCCCAAGGACAGGAGACTGATCTTGAGATTCAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 159

CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAGgtaccagtag ... tataatgcagGAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTGGAGGGGCCCAAGGACAGGAGACTGATCTTGAGATTCAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 190

CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAGgtaccagtag ... tataatgcagGAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTGGAGGGGCCCAAGGACAGGAGACTGATCTTGAGATTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacatatccaagcttcgttaatagaagtcataaaaccggtgaaaatataatgcagGAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTGGAGGGGCCCAAGGACAGGAGACTGATCTTGAGATTCAG
                                       tgaaaatataat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccagtagtgattgctaataaaatacatgtaggtgtagcttacatatccaagcttcgttaatagaagtcataaaaccggtgaaaatataatgcagGAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTGGAGGGGCCCAAGGACAGGAGACTGATCTTGAGATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA