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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgtatattagtagtgttagatatgttgggcgtttgaaaacttcaattgtagattattttgatgtactatggtcatgatccccaatttattctttgcagCCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATAT

Basic information

species Zea mays
transcript GRMZM2G052403_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 21
-----tttgtatattagtagtgttagatatgttgggcgtttgaaaacttcaattgtagattattttgatgtactatggtcatgatccccaatttattctttgcagCCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATAT
     |||    |    | | ||   |||||||||     | |     || |||  ||     | | |   | |       || |    ||| | ||  |||||||||||||||||||||||||| || ||||||||||| ||||||||||| |||||||| || |||||||||||||||||||||||||| ||||| || ||||
ctatattttgggacggatggagtattatatgttggctacctaattttctctatttaagtcctatcttaaaaattgc--ctctggta---aatctgttacttgcagCCTTGCAAGGGAATATTGCTGTTTGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATAT

upper sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 17
--------tttgtatattagtagtgttagatatgttgggcgtttgaaaacttcaattgtagattattttgatgtactatggtcatgatccccaatttattctttgcagCCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATAT
        |||  || ||||| || ||| ||   |||   |   ||||   |  |  |||||| ||    ||||     |  | | ||    | |   ||   |  |||||||||| |||||||||||||| || ||||||||||| || ||||| |||||||| || || |||||||||||||| || || ||||| || || || |
gtgaaagattttcattttagttgt-ttaaatgacttg--tgaaagaaattgttga--gtagatcatgcc-atgtgtgtagcacctaattgtaattactttgggtatagCCTTGCAAAGGAATATTGCTTTTTGGCCCTCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTTATTAACATTT

upper sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 20
-tttgtatattagtagtgttagatatgttgggcgt----ttgaaaacttcaatt-gtagattattttgatgtactatggtcatgatccccaatttatt-ctttg----cagCCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATAT
 || ||| |||  |  | |||| |   ||    |     | ||| || |   || |||||| || || || |  | ||   |  | | |    | ||| |||||     ||||||||||||||||||||||||| || || |||||||| || ||||| |||||||| || || |||||||||||||| || || |||||||| || || |
gttggtagattt-tctttttagttgctttaaatgacaagtggaacacattttttagtagatgatattcatatcatgtgtgtagcacctcattgtaattactttggatatagCCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTT

upper sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 17
----------tttgtatattagtagtgttagatatgttgggcgtttgaaaacttcaattgtagattattttgatgtactatggtcatgatccccaatttattctttgcagCCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATAT
          |||  || ||||| || ||| ||   |||   |   || |   | ||  |||||| ||    |||      |  | | ||    | |   ||   |  ||||||||||||||||||||||||| || || |||||||| || ||||| |||||||| || || || ||||||||||| || || ||||| || || || |
gtgaaaaatattttcattttagttgt-ttaaatgacttg--tgaaagacattgttaa--gtagatcatgcc-atgcgtgtagcacctaattgtaattactttgggtatagCCTTGCAAGGGAATATTGCTTTTTGGCCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTGGCAACTGAAGCTGGAGCAAATTTTATTAACATTT

upper sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 16
---------tttgtatattagtagtgttagatatgttgggcgtttgaaaacttcaatt-gtagattattttgatgtactatggtcatgatccccaatttatt-ctttg----cagCCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATAT
         |||   | ||||| |  ||| ||   ||| |     ||| || |   || |||||| || ||    |  | ||   |  | | |    | ||| |||||     ||||||||||||||||||||||||| || || |||||||| || ||||| |||||||| || || |||||||||||||| || || |||||||| || || |
gttgatagattttctttttagttgctttaaatgacttgtg-----gaacacattttttagtagatcatattcgaatcatgtgtgtagcacctcattgtaattactttggatatagCCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTT

upper sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 12
lower sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 20
tttgtatattagtagtgttagatatgttgggcgtttgaaaact-tcaattgtagattattttgatgtactatggtcatgatccccaatttattctttgcagCCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATAT
   |||  ||  || || || |    ||     ||||  |  | | | |  || || | |   |   |  ||     ||||    |||         |||||||   || || ||| || | || ||||||||||| ||||| || || ||||| || ||||||||||||||||| || || || |||||||||||||| |
---gtaccttt-tattgctatacggatt---tatttgttagttgttactcctacataactgaaaccaaacatatatttgatgtttaat---------gcagCCTACGAAAGGTATACTGTTGTTTGGACCTCCTGGTACTGGAAAGACGATGCTGGCAAAAGCAGTAGCAACTGAGGCTGGCGCAAATTTCATCAATATCT

upper sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 12
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 20
-----------------------------------------tttgtatattagtagtgttagatatgttgggcgtttgaa-----aacttcaattgtagattattttgatgtactatggtcatgatcc---ccaatttatt-ctttgcagCCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATAT
                                         | | |||||     || |  | |    |   | ||||||      |  | | || ||  | |||      |  ||||   || |||      |  ||| |  ||| |||||||||||||||||  | || || || |||||||| ||||| ||||| |||||||| || || || |||||||| |||||||| ||||| ||||| ||||
gttaggtgtttcacatgttttatttctttattgtgtatgtatatatatatattgtgtatctggtggaattttcttttgaattatggaagtaagttttatctaattcatgccttgtatgtctatcatctgaatgaggttactatttttcagCCTTGCAAGGGAATTCTTCTATTTGGGCCTCCTGGGACTGGAAAAACAATGCTTGCGAAGGCGGTTGCAACTGAGGCAGGTGCAAATTTTATCAACATAT

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|22490580|gb|BU050503.1|BU050503
EST:     TGCTCCCTTTACAAAGACCTGAATTGTTCTGCAAAGGGCAGCTAACAAAG                         CCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATG
genomic: TGCTCCCTTTACAAAGACCTGAATTGTTCTGCAAAGGGCAGCTAACAAAGgtagcatcat ... ttctttgcagCCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATG
EST: gi|67025653|gb|CO454402.1|CO454402
EST:     TGCTCCCTTTACAAAGACCTGAATTGTTCTGCAAAGGGCAGCTAACAAAG                         CCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATG
genomic: TGCTCCCTTTACAAAGACCTGAATTGTTCTGCAAAGGGCAGCTAACAAAGgtagcatcat ... ttctttgcagCCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATG
EST: gi|87153787|gb|DY398576.1|DY398576
EST:     TGCTCCCTTTACAAAGACCTGAATTGTTCTGCAAAGGGCAGCTAACAAAG                         CCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATG
genomic: TGCTCCCTTTACAAAGACCTGAATTGTTCTGCAAAGGGCAGCTAACAAAGgtagcatcat ... ttctttgcagCCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATG
EST: gi|67034427|gb|CO462977.1|CO462977
EST:     TGCTCCCTTTACAAAGACCTGAATTGTTCTGCAAAGGGCAGCTAACAAAG                         CCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATG
genomic: TGCTCCCTTTACAAAGACCTGAATTGTTCTGCAAAGGGCAGCTAACAAAGgtagcatcat ... ttctttgcagCCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATG
EST: gi|22490811|gb|BU050734.1|BU050734
EST:     TGCTCCCTTTACAAAGACCTGAATTGTTCTGCAAAGGGCAGCTAACAAAG                         CCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATG
genomic: TGCTCCCTTTACAAAGACCTGAATTGTTCTGCAAAGGGCAGCTAACAAAGgtagcatcat ... ttctttgcagCCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATG
EST: gi|60399121|gb|DN231935.1|DN231935
EST:     TGCTCCCTTTACAAAGACCTGAATTGTTCTGCAAAGGGCAGCTAACAAAG                         CCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATG
genomic: TGCTCCCTTTACAAAGACCTGAATTGTTCTGCAAAGGGCAGCTAACAAAGgtagcatcat ... ttctttgcagCCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATG
EST: gi|87152067|gb|DY396856.1|DY396856
EST:     TGCTCCCTTTACAAAGACCTGAATTGTTCTGCAAAGGGCAGCTAACAAAG                         CCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATG
genomic: TGCTCCCTTTACAAAGACCTGAATTGTTCTGCAAAGGGCAGCTAACAAAGgtagcatcat ... ttctttgcagCCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATG
EST: gi|19058833|gb|BM737500.1|BM737500
EST:     TGCTCCCTTTACAAAGACCTGAATTGTTCTGCAAAGGGCAGCTAACAAAG                         CCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATG
genomic: TGCTCCCTTTACAAAGACCTGAATTGTTCTGCAAAGGGCAGCTAACAAAGgtagcatcat ... ttctttgcagCCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATG
EST: gi|19058784|gb|BM737451.1|BM737451
EST:     TGCTCCCTTTACAAAGACCTGAATTGTTCTGCAAAGGGCAGCTAACAAAG                         CCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATG
genomic: TGCTCCCTTTACAAAGACCTGAATTGTTCTGCAAAGGGCAGCTAACAAAGgtagcatcat ... ttctttgcagCCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATG
EST: gi|211048836|gb|FL187596.1|FL187596
EST:     TGCTCCCTTTACAAAGACCTGAATTGTTCTGCAAAGGGCAGCTAACAAAG                         CCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATG
genomic: TGCTCCCTTTACAAAGACCTGAATTGTTCTGCAAAGGGCAGCTAACAAAGgtagcatcat ... ttctttgcagCCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATG

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: 125

TGATATTGGAGCCTTGGAGAATGTAAAGGACACATTAAAGGAGCTGGTGATGCTCCCTTTACAAAGACCTGAATTGTTCTGCAAAGGGCAGCTAACAAAGgtagcatcat ... ttctttgcagCCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 124

TGATATTGGAGCCTTGGAGAATGTAAAGGACACATTAAAGGAGCTGGTGATGCTCCCTTTACAAAGACCTGAATTGTTCTGCAAAGGGCAGCTAACAAAGgtagcatcat ... ttctttgcagCCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 126

TGATATTGGAGCCTTGGAGAATGTAAAGGACACATTAAAGGAGCTGGTGATGCTCCCTTTACAAAGACCTGAATTGTTCTGCAAAGGGCAGCTAACAAAGgtagcatcat ... ttctttgcagCCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 168

TGATATTGGAGCCTTGGAGAATGTAAAGGACACATTAAAGGAGCTGGTGATGCTCCCTTTACAAAGACCTGAATTGTTCTGCAAAGGGCAGCTAACAAAGgtagcatcat ... ttctttgcagCCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattgtagattattttgatgtactatggtcatgatccccaatttattctttgcagCCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATAT
            ttttgat  putative branch site (score: 168)
                                         tttattcttt  putative PPT
     tagattattttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgtatattagtagtgttagatatgttgggcgtttgaaaacttcaattgtagattattttgatgtactatggtcatgatccccaatttattctttgcagCCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - tatgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgatc