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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attactaagttggacatccataagtgcaaaaatattgtcgaaactagaggctcatgtggacttttggtgctattttcttatagaatgtcttcattgacagGTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCTGCTACCTTTAAG

Basic information

species Zea mays
transcript GRMZM2G351417_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G351417_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g39630.1 (Oryza sativa), 3'ss of exon 4
--attactaagttggacatccataagtgcaaaaatattgtcgaaactagaggctcatgtggacttttggtgctattttcttatagaatgtcttcattgacagGTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCTGCTACCTTTAAG
  | ||   | |  |   | |||||     |||||| ||| |||| ||||   || ||| |   |  ||||||  ||| |  | | |  | |||| | ||||||| ||||||||||| || || |||||||||||||| ||||||||||| ||||||||||||||||| || || ||||||||||| |||||||||
caactaaggattctgttttacataaaccataaaatactgtagaaattagaaattcctgtcggaat--ggtgcttatttatcttggtaaatgttcactcacagGTACGTTTTAGAGTCTGACCACATGAAGAAGTTCTTTGACTATATACAACTTCCAAATTTTGACATTGCATCAGATGCTTCTGCGACCTTTAAG

upper sequence: GRMZM2G351417_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA15G12220.2 (Glycine max), 3'ss of exon 2
--attacta-agttggacatccataagtg-caaaaatattgtcgaaactagaggctcatgtggacttttggtgctattttcttatagaatgtcttcattgacagGTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCTGCTACCTTTAAG
  |  |||| | || || |     || || |  |  | || |  ||  |     | |||    ||| ||| || |  | |  |     |||  ||  |   ||| |||||  |  | ||    | |||||||||||| || |||||||| || ||||||||||||||||| ||| | |||||| | || |||||||||
tgaacactagaattagaaaagggaaaatggcctaggtcttat--aatttttttccccatcataactattg-tgttgctgtaattcttcatggttttgt-atcagATATGTGCTGAACTCACCTCGTATGAAGAAGTTTTTTGACTATATCCAACTTCCAAATTTTGACATTGCTGCGGATGCTGCAGCAACCTTTAAG

upper sequence: GRMZM2G351417_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA14G00940.1 (Glycine max), 3'ss of exon 4
-attactaagttggacatccataagtgcaaaaatattgtcgaaactagaggctcatgtggacttttggtgctattttcttatagaatgtcttcattgacagGTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCTGCTACCTTTAAG
 |  |  ||  | | ||  |||   ||||    |    | | || |  |   || |||     |||  |    | |   ||    |  |  |  ||   ||| || |||| || || || || ||||||||||| || |||||||| ||||| ||||||||||| ||||| || ||||||  ||| || ||||| 
aaaaaaaaatgtagccaagcatct-tgcatggctgactttggaattttactttcttgttcctcttttttaaattctgactagcttaatttatggtttttagGCATATTTTGGAATCAGAGCACATGAAGAAGTTTTTTGACTATATTCAGCTACCAAATTTTGAAATAGCATCAGATGCTGTTGCAACTTTTAAA

upper sequence: GRMZM2G351417_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G47710.1 (Glycine max), 3'ss of exon 4
----------------------------------------------------------------------------attactaagttggacatccataagt---gcaaaaatattgtcgaaactagaggctcatgtggacttttggtgctattttcttatagaatgtcttcattgacagGTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCTGCTACCTTTAAG
                                                                            ||||  ||       | | |    |   ||     |    | |||| |  |   || |||  | ||||  |    | |   ||    |  |  |  ||   ||| ||||||| || || || || ||||||||||| || |||||||| ||||| ||||| ||||| ||||| || ||||||  ||| || ||||| 
gtacgcaatttaaatcatctcttaattaattattcatgtcaacatagatctcatacttaattgttaactttcggagattaaaaaaaaatgtagcaaaggatcttgcgtggctgactttgaaattttactttcttgttcattttttctaaattctgactagtttaatttatgttttttagGCATGTTTTGGAATCAGAGCACATGAAGAAGTTTTTTGACTATATTCAGCTACCAAACTTTGAAATAGCATCAGATGCTGTTGCAACTTTTAAA

upper sequence: GRMZM2G351417_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA09G01370.2 (Glycine max), 3'ss of exon 4
attactaagttggacatccataagtgcaaaaatattgtcgaaactagaggctcatgtggacttttggtgctattttcttatagaatgtcttcatt----gacagGTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCTGCTACCTTTAAG
    || |       |   | ||  |  |||||    | |    || |   |  |    |   |   |  | | ||  | ||     || | |||      ||| |||||  |  | ||    | |||||||||||| || |||||||| || ||||||||||||||||| ||| | |||||| | || |||||||||
----ctgaacactggaattagaaaagggaaaatgacctaggtcttataatttttttcccatcataactaatgtgttgctgtaattcttcatgattttgtatcagATATGTCCTGAACTCACCTCGTATGAAGAAGTTTTTTGACTATATCCAACTTCCAAATTTTGACATTGCTGCAGATGCTGCAGCAACCTTTAAG

upper sequence: GRMZM2G351417_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA17G01180.1 (Glycine max), 3'ss of exon 3
attactaagttggacatc-cataagtgcaaaaatattgtcgaaactagaggctcatgtg----gacttttggtgctatt-ttcttatagaatgtcttcattgacagGTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCTGCTACCTTTAAG
 ||    | |   | |   | || ||   |   |  | || |   | ||   |  || |    ||||| || |||| |  || ||||    || ||| ||   ||| |||||| | || ||    |||||||||||||| || ||||| || |||||||||||||||||||||||| | |||||  | || || ||||||
gttgtagaataaaagacagcctaggtatgatctttctttctagtat-gacttttgtgagttgtgacttgtgatgctgtaattattat----tggctttat-atcagATATGTTCTGGACTCACCTCATATGAAGAAGTTTTTTGACTACATTCAGCTTCCAAATTTTGACATAGCTGCAGATGCCGCAGCAACTTTTAAG

upper sequence: GRMZM2G351417_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT5G47540.1 (Arabidopsis thaliana), 3'ss of exon 4
atta-ctaa--gttggacatccataagtgcaaaaatattgtcgaaactagaggctcatgtggacttttggtgctatttt--cttatagaatgtcttcattgacagGTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCTGCTACCTTTAAG
 | | | ||  |||  |  | | | | |  |  |    ||  | || ||  |  ||| | | |     |    | | ||  || |   ||| ||||      ||| |||||||| ||||| || ||| ||||||| ||||| || || ||||||||||||||||| ||||| ||| | |||||| ||||||| ||||||
gtgagccaatcgtttcattttcttcattttacgacctatggagtaattatggattca-gagaataacggaaaatgtgtttactaacttaatttctttggattcagATATGTTTTGGAGTCTGACCATGTGAAGAAATTCTTTGATTACATACAGCTTCCAAATTTCGACATTGCTGCCGATGCTGCTGCTACTTTTAAG

upper sequence: GRMZM2G351417_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv10s0405g00020.t01 (Vitis vinifera), 3'ss of exon 4
attactaagttggacatccataa-gtgcaaaaatattgtcgaaactagaggctcatgtggactt---ttggtgctattttcttat--agaatgtcttcattgacagGTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCTGCTACCTTTAAG
  |    |   | |  |  | ||  |     | |||| |    | ||     | || |||  ||   |  ||   ||||||| ||  |   | | ||   ||||||||| ||  | || || |  || ||||||||||| || || ||||| || ||||||||||||||||| ||| | |||||| |||| || ||||||
-ctgtccaaaggcagtttgacaatatcttttattattattattatta-----ttatatgggtttaactgagttgaattttctaatttatggtttttttcctgacagGTACGTCCTGGAATCAGCGCACATGAAGAAGTTTTTTGATTATATTCAACTTCCAAATTTTGACATTGCTGCAGATGCTGCTGCAACTTTTAAG

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|60349070|gb|DN216043.1|DN216043
EST:     CATTATGGTGCTATGTTGAGGGAATGTATTCGCCACCAAAGCATTGCAAG                         GTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCT
genomic: CATTATGGTGCTATGTTGAGGGAATGTATTCGCCACCAAAGCATTGCAAGgtgatactac ... tcattgacagGTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCT
EST: gi|60401041|gb|DN233848.1|DN233848
EST:     CATTATGGTGCTATGTTGAGGGAATGTATTCGCCACCAAAGCATTGCAAG                         GTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCT
genomic: CATTATGGTGCTATGTTGAGGGAATGTATTCGCCACCAAAGCATTGCAAGgtgatactac ... tcattgacagGTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCT
EST: gi|148951718|gb|EC897471.2|EC897471
EST:     ATTATGGTGCTATGTTGAGGGAATGTATTCGCCACCAAAGCATTTGCA-G                         GTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGC
genomic: ATTATGGTGCTATGTTGAGGGAATGTATTCGCCACCAAAGCATT-GCAAGgtgatactac ... tcattgacagGTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGC
EST: gi|5895978|gb|AW037224.1|AW037224
EST:     CATTATGGTGCTATGTTGAGGGAATGTATTCGCCACCAAAGCATTGCAAG                         GTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCT
genomic: CATTATGGTGCTATGTTGAGGGAATGTATTCGCCACCAAAGCATTGCAAGgtgatactac ... tcattgacagGTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCT
EST: gi|60359357|gb|DN226330.1|DN226330
EST:     CATTATGGTGCTATGTTGAGGGAATGTATTCGCCACCAAAGCATTGCAAG                         GTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCT
genomic: CATTATGGTGCTATGTTGAGGGAATGTATTCGCCACCAAAGCATTGCAAGgtgatactac ... tcattgacagGTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCT
EST: gi|6194551|gb|AW146655.1|AW146655
EST:     CATTATGGCGCTATGCTGAGGGAATGTATTCGCCACCAAAGCATTGCAAG                         GTATGTTTTAGAGTCCGAACATATGAAGAAGGTCTTCGACTATATACAGCT
genomic: CATTATGGTGCTATGTTGAGGGAATGTATTCGCCACCAAAGCATTGCAAGgtgatactac ... tcattgacagGTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCT
EST: gi|60352002|gb|DN218975.1|DN218975
EST:     CATTATGGTGCTATGTTGAGGGAATGTATTCGCCACCAAAGCATTGCAAG                         GTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCT
genomic: CATTATGGTGCTATGTTGAGGGAATGTATTCGCCACCAAAGCATTGCAAGgtgatactac ... tcattgacagGTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCT
EST: gi|149081164|gb|EE170272.2|EE170272
EST:     CATTATGGTGCTATGTTGAGGGAATGTATTCGCCACCAAAGCATTGCAAG                         GTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATAC
genomic: CATTATGGTGCTATGTTGAGGGAATGTATTCGCCACCAAAGCATTGCAAGgtgatactac ... tcattgacagGTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaggctcatgtggacttttggtgctattttcttatagaatgtcttcattgacagGTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCTGCTACCTTTAAG
                                          tcttcatt  CT-rich tract
                         tattttcttatagaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attactaagttggacatccataagtgcaaaaatattgtcgaaactagaggctcatgtggacttttggtgctattttcttatagaatgtcttcattgacagGTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCTGCTACCTTTAAG

- - - - - - -acatcca
- - - - - - - - - - - - - -aaaaata
- - - - - - - - - - - - - - - - - - - - - - - - -gctcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttttggt