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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_T02
intron # 3
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|149103428|gb|EE288821.2|EE288821
EST:     CATTATGGTGCTATGTTGAGGGAATGTATTCGCCACCAAAGCATTGCAAG                         GTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCT
genomic: CATTATGGTGCTATGTTGAGGGAATGTATTCGCCACCAAAGCATTGCAAGgtgatactac ... tcattgacagGTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCT




















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), 47 (downstream exon)
Score: 182

GTATGAGAATATGGACATTGCTTTACATTATGGTGCTATGTTGAGGGAATGTATTCGCCACCAAAGCATTGCAAGgtgatactac ... tcattgacagGTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCTGCTACCTTTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 307

GTATGAGAATATGGACATTGCTTTACATTATGGTGCTATGTTGAGGGAATGTATTCGCCACCAAAGCATTGCAAGgtgatactac ... tcattgacagGTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCTGCTACCTTTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 232

GTATGAGAATATGGACATTGCTTTACATTATGGTGCTATGTTGAGGGAATGTATTCGCCACCAAAGCATTGCAAGgtgatactac ... tcattgacagGTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCTGCTACCTTTAAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 237

GTATGAGAATATGGACATTGCTTTACATTATGGTGCTATGTTGAGGGAATGTATTCGCCACCAAAGCATTGCAAGgtgatactac ... tcattgacagGTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCTGCTACCTTTAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaggctcatgtggacttttggtgctattttcttatagaatgtcttcattgacagGTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCTGCTACCTTTAAG
                                          tcttcatt  CT-rich tract
                         tattttcttatagaat  TA-rich tract