Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaacattgctacaataggagagtctggaggtagttactgcatctttgcttggtgactccagcttctcatgaccttgctaaactgatatatcttgtttagGTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGGAAAACTGAACAAGCAGAGGATCCCTCTGTCTAACAACCAAGTCATCGAG

Basic information

species Zea mays
transcript GRMZM5G868433_T04
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os08g13690.1 (Oryza sativa), 3'ss of exon 5
aaaacattgctacaataggagag-tctggaggtagttac-tgcatctttgcttggtgactccagcttctcatgaccttgctaaactgatatatcttgtttagGTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGGAAAACTGAACAAGCAGAGGATCCCTCTGTCTAACAACCAAGTCATCGAG
      |       |    | || | | ||| | ||||  | | |  ||  ||      | |  | |  |   | |  |   | ||  | |    || | |||||||| ||| |||||||||||||||| ||||||||||||||||| |||||||| || |||||||||||||| |||||    |||||| ||||||| |||
gggttctcatagtgactttatagcttttgagcttgttagatacttggttatttttaatgttctacctggctgaatcaagt--accttctctggtgtgatcagGTACCCAAACCTGAAGAGTGTCAGGGAATTGATCTACAAGAGGGGTTACGGAAAGCTCAACAAGCAGAGGATTCCTCTTCAGAACAACAAAGTCATTGAG

upper sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 4
aaaacattgctacaatag--gagagtctggaggtagttactgcatctttgcttggtgactccagcttctcatgaccttgctaaactgatatatcttgt---ttagGTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGGAAAACTGAACAAGCAGAGGATCCCTCTGTCTAACAACCAAGTCATCGAG
  |   |   |  ||| |   || ||||| |  |||||   ||  |  |  |   |         |  | ||   ||| ||| | |  |   |||| |   |||||||||| || |||||||||||| | || |||||||||||||||||||| ||||| || |||||||| || ||||||||  | |||||| |||||||||||
--attttaatttgaattgtctagggtctgaaa-tagttcaagc--ccctaatgactagagttgattattgatcttcttactagattagtgattcttatgttttagGTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGGAAAGCTCAACAAGCAAAGAATCCCTCTTACAAACAACAAAGTCATCGAG

upper sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA09G06860.1 (Glycine max), 3'ss of exon 5
aaaacattgctacaataggagagtctggaggtagttactgcatctttgcttggtgactccagcttctcatgaccttgctaaactgatatatcttgtttagGTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGGAAAACTGAACAAGCAGAGGATCCCTCTGTCTAACAACCAAGTCATCGAG
             ||   || |||     |  | | | ||     | | |   |  || ||      || |   |    | | |   | |||   || |||||||| || ||||||||||| |  || |||||||||||||||||||| |||||| | ||||||||||| ||  |  |   | |||||    |  | || 
-----------gtaa-gtgaaagttcaacgacattgattgtcatatggttcattacctgca-----ccacgggttcttaatatttgcaaatccacttcagGTACCCTAATTTGAAGAGTGTAAAAGAATTGATCTACAAGAGGGGCTATGGAAAAGTTAACAAGCAGAGAATTGCCTTAAATGACAACTCTATTGTTGAA

upper sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA15G18170.2 (Glycine max), 3'ss of exon 5
aaaacattgctacaataggagagtctggaggtagttactgcatctttgcttggtgactccagcttctcatgaccttgctaaactgatatatcttgtttagGTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGGAAAACTGAACAAGCAGAGGATCCCTCTGTCTAACAACCAAGTCATCGAG
               || | ||   |  |  ||  |      || | | |   |  || ||      ||||    |   | | |   | |||   || |||||||| || ||||||||||| || || |||||||||||||||||||| |||||| | ||||||||||| ||  || || |  |||||    | || || 
--------------gtaagtgaaagttcaactacattgattctcatggttcattacctgca-----ccatggttct-taatatttgcaaatccacttcagGTACCCTAATTTGAAGAGTGTTAGAGAATTGATCTACAAGAGGGGCTATGGAAAAGTTAACAAGCAGAGAATTGCTTTGACAGACAACTCTATTATTGAA

upper sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT2G01250.1 (Arabidopsis thaliana), 3'ss of exon 5
aaaacattgctacaataggagagtctggaggtagttactgcatctttgcttggtgactccagcttctcatgaccttgctaaactgatatatcttgtttagGTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGGAAAACTGAACAAGCAGAGGATCCCTCTGTCTAACAACCAAGTCATCGAG
   |  |   |||| |   |   ||   |     ||| |       |    | | ||   ||  |   |     |  ||   ||  | | | ||  | || | ||| |||||||||||||||| ||| |||||||||||||| || |||||||| || ||| | ||||||||  || || || |||||    |  | |||
-gtatgtatatacactctca---tcctaaaccctttaatctgatgctatgagataacaagagtcttgaagagtgtgacttttctcttctgtttt--tcagATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAGAGGTTACGGAAAGCTTAACCACCAGAGGATAGCTTTGACTGACAACTCTATTGTAGAG

upper sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv09s0054g00030.t01 (Vitis vinifera), 3'ss of exon 4
-aaaacattgctacaataggagagtctggaggtagt-tactgcatctttgcttg-gtgactccagcttctcatgaccttgctaaactgatatatcttgtttagGTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGGAAAACTGAACAAGCAGAGGATCCCTCTGTCTAACAACCAAGTCATCGAG
  ||  ||    ||  |  |    |||  |  |  | ||     |||   ||||  |         || | |||   ||    |  | | ||||    ||||||||||| || |||||||||||  | || ||||| ||||||||||| ||||||||  ||||||||||||| |   |  || |  |||||    |  | || 
gtaagtatc-tcactctttgtttttcttaaaatcctataaaaagtctaaacttgtatagtattcatttgtaatgtatttat--atttcaaatat----tttagGTACCCCAATTTGAAGAGTGTGCGAGAATTGATTTACAAGAGGGGGTACGGAAAGTTGAACAAGCAGAGAACTGCCTTGACCGACAACTCCATTGTGGAA

upper sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv09s0054g00210.t01 (Vitis vinifera), 3'ss of exon 5
---aaaacattgctacaataggagagtctggaggtagttactgcatctttgcttg-gtgactccagcttctcatgaccttgctaaactgatatatcttgtttagGTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGGAAAACTGAACAAGCAGAGGATCCCTCTGTCTAACAACCAAGTCATCGAG
   |  |  || ||    |       |    |     | |     |||   |||| ||         |||| |||   ||      |  ||||      ||||||||||| || |||||||||||  | ||  |||| |||||||||||||| |||||  ||||||||||||| |   |  || |  |||||    |  | || 
gtaagtatcttactcttttgtttttcttaaaatcctataaaaagttctgaacttgtgtattattcatttctaatgtatttatattgcaaatat------tttagGTACCCCAATTTGAAGAGTGTGCGAGAACTGATTTACAAGAGGGGCTATGGAAAGTTGAACAAGCAGAGAACTGCCTTGACCGACAACTCCATTGTGGAA

upper sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv09s0054g00090.t01 (Vitis vinifera), 3'ss of exon 3
-----aaaacattgctacaataggagagtctggaggtagttactgcatctttgcttggtgact-ccagcttctcatgaccttgctaaactgatatatcttgtttagGTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGGAAAACTGAACAAGCAGAGGATCCCTCTGTCTAACAACCAAGTCATCGAG
     |  |  || ||    |       |   ||     | |     |||   ||||   | |      |||| |||   ||      |  ||||      ||||||||||| || |||||||||||  | ||  |||| |||||||||||||| |||||  ||||||||||||| |   |  || |  |||||    |  | || 
gggtaagtatcttactcttttgtttttcttaagatcctataaaaagttctgaacttgtatattattcatttctaatgtatttatattgcaaatat------tttagGTACCCCAATTTGAAGAGTGTGCGAGAACTGATTTACAAGAGGGGCTATGGAAAGTTGAACAAGCAGAGAACTGCCTTGACCGACAACTCCATTGTGGAA

upper sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv11s0052g00290.t01 (Vitis vinifera), 3'ss of exon 5
aaaacattgctacaataggagagtctggaggtagttactgcatctttgcttggtgactccagcttctcatg-accttgctaaactgatat---atcttgttt-agGTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGGAAAACTGAACAAGCAGAGGATCCCTCTGTCTAACAACCAAGTCATCGAG
                    | ||   ||  |    ||| |||      |  | ||    | || | |||| |   || ||  |  |||    |  |||||| ||||| || || || ||||||||||||||  |||| ||||||||||| || |||||||| ||||||||||| |   ||||| || | |||  | |||| || 
----------------gtatgtgttctgac-tgccaacttcataacc-ttcagggatcatatctccacatgcaatctgttattcatatactgaagattgtttcagGTATCCCAATTTAAAGAGTGTCAGGGAACTGATTTACAAGAGGGGTTATGGAAAACTTAACAAGCAGAGAACTGCTCTGACTGATAACTCAATCATTGAA

upper sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv09s0054g00060.t01 (Vitis vinifera), 3'ss of exon 4
-aaaacattgctacaataggagagtctggaggtagt-tactgcatctttgcttg-gtgactccagcttctcatgaccttgctaaactgatatatcttgtttagGTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGGAAAACTGAACAAGCAGAGGATCCCTCTGTCTAACAACCAAGTCATCGAG
  ||  ||  |  |  |  |    |||  |  |  | ||     |||   ||||  |         |||| |||   ||      |  ||||      ||||||||||| || |||||||||||  | || ||||| ||||||||||| ||| ||||  ||||||||| ||| |   |  || |  |||||    |  | || 
gtaagtatctcacccttttgtttttcttaaaatcctataaaaagtctaaacttgtatagtattcatttctaatgtatttatattgcaaatat------tttagGTACCCCAATTTGAAGAGTGTGTGAGAATTGATTTACAAGAGGGGGTACAGAAAGTTGAACAAGCTGAGAACTGCCTTGACCGACAACTCCATTGTGGAA

upper sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv09s0054g00010.t01 (Vitis vinifera), 3'ss of exon 4
-aaaacattgctacaataggagagtctggaggtagt-tactgcatctttgcttggtgact-ccagcttctcatgaccttgctaaactgatatatcttgtttagGTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGGAAAACTGAACAAGCAGAGGATCCCTCTGTCTAACAACCAAGTCATCGAG
  ||  ||  |     |  |    |||  |  |  | ||     |||   ||||   | |      |||| |||   ||      |  ||||      ||||||||||| || |||||||||||  | || ||||| ||||||||||| || |||||  ||||||||||||| |   |  || |  |||||    |  | || 
gtaagtatctcactcttttgtttttcttaaaatcctataaaaagtctaaacttgtatattattcatttctaatgtatttatattgcaaatat------tttagGTACCCCAATTTGAAGAGTGTGCGAGAATTGATTTACAAGAGGGGGTATGGAAAGTTGAACAAGCAGAGAACTGCCTTGACCGACAACTCCATTGTGGAA

upper sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S11_173V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------aaaacattgctacaa-----taggagagtctggaggtagttactgcatctttgcttggtgactccagcttctcatgaccttgctaaactgatatatcttgtttagGTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGGAAAACTGAACAAGCAGAGGATCCCTCTGTCTAACAACCAAGTCATCGAG
                  ||  | |  || ||     | || |  |  | || |  ||   ||| |  |   || |   |  |  || |||     ||  ||   ||||    ||||   ||  |||||||||||||||||||| ||||||||||||||||| | || ||||||||  | ||||||  | | | | ||||  |  |||||    ||||||| 
gtaattaaactctggagcaattaataatataagcgtttcggtgcctacgaagatgtttttcgcacccctatgtgttagtttaaatttttcacatgttt--taccatgattgtacttgc--agCAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGGAAATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAA

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|15632349|gb|BI679442.1|BI679442
EST:     AAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGG                         GTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGG
genomic: AAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGGgtaatttctc ... tcttgtttagGTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGG
EST: gi|94477419|gb|EB706377.1|EB706377
EST:     AAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGG                         GTACCCGAACTTGAAGAGGGTCAGGGAGTTGATCTTCAAGAAGGGCTACGG
genomic: AAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGGgtaatttctc ... tcttgtttagGTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGG
EST: gi|211173107|gb|FK956292.1|FK956292
EST:     AAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGG                         GTACCCGAACTTGAAGAGTGTCAAGGAGTTGATCTACAAGAGGGGCTACGG
genomic: AAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGGgtaatttctc ... tcttgtttagGTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGG
EST: gi|33104385|gb|CF064345.1|CF064345
EST:     TAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGG                         GTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGG
genomic: TAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGGgtaatttctc ... tcttgtttagGTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGG
EST: gi|211171435|gb|FK956283.1|FK956283
EST:     AAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGG                         GTACCCGAACTGGANGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGG
genomic: AAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGGgtaatttctc ... tcttgtttagGTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGG
EST: gi|15590144|gb|BI674760.1|BI674760
EST:     AAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGG                         GTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGG
genomic: AAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGGgtaatttctc ... tcttgtttagGTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGG
EST: gi|166483736|gb|EG189505.1|EG189505
EST:     AACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGG                         GTACCCGAAACTTAGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTAC
genomic: AACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGGgtaatttctc ... tcttgtttagGTACCCG-AACTT-GAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTAC
EST: gi|20299953|gb|BQ162896.1|BQ162896
EST:     AAAGCAACCATTAACATGCTTCGCAGGGTTGAACCTTATGTTGCATATGG                         GTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGG
genomic: AAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGGgtaatttctc ... tcttgtttagGTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGG
EST: gi|9733002|gb|BE511754.1|BE511754
EST:     AAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGG                         GTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGG
genomic: AAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGGgtaatttctc ... tcttgtttagGTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGG
EST: gi|15313739|gb|BI478933.1|BI478933
EST:     AAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGG                         GTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGG
genomic: AAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGGgtaatttctc ... tcttgtttagGTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGG

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: 1075

ATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGGgtaatttctc ... tcttgtttagGTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGGAAAACTGAACAAGCAGAGGATCCCTCTGTCTAACAACCAAGTCATCGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1000

ATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGGgtaatttctc ... tcttgtttagGTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGGAAAACTGAACAAGCAGAGGATCCCTCTGTCTAACAACCAAGTCATCGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 648

ATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGGgtaatttctc ... tcttgtttagGTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGGAAAACTGAACAAGCAGAGGATCCCTCTGTCTAACAACCAAGTCATCGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 519

ATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGGgtaatttctc ... tcttgtttagGTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGGAAAACTGAACAAGCAGAGGATCCCTCTGTCTAACAACCAAGTCATCGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcttggtgactccagcttctcatgaccttgctaaactgatatatcttgtttagGTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGGAAAACTGAACAAGCAGAGGATCCCTCTGTCTAACAACCAAGTCATCGAG
                                             tcttgttt  CT-rich tract
                                        atatatcttgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaacattgctacaataggagagtctggaggtagttactgcatctttgcttggtgactccagcttctcatgaccttgctaaactgatatatcttgtttagGTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGGAAAACTGAACAAGCAGAGGATCCCTCTGTCTAACAACCAAGTCATCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT