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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaactttcatctctacagtgtagttcatatcatgattaaaatgttgctttcatcatttatttagtcccaatgcttttagctgctacactgatgttgtttgtgtgcagTGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAGGTGCTGTTGACTTTTTAGTCAAGCCTATACGTAAGAATGAACTTAAGAA

Basic information

species Zea mays
transcript GRMZM2G005732_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005732_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g49460.3 (Oryza sativa), 3'ss of exon 5
gtaagtaactttcatctctacagtgtagttcatatcatgattaaaatgttgctttcatcatttatttagtcccaatgcttttagctgctacactgatgttgtttgtgtgcagTGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAGGTGCTGTTGACTTTTTAGTCAAGCCTATACGTAAGAATGAACTTAAGAA
||||||| |||||  ||| ||  |  ||| ||  || ||   ||||||||||  |  ||||||||||| |  | ||||||||||||||||||||| ||| |||| ||||||||||||||||| | |||||||||| ||||||| ||||| ||||||||||| || ||||||||||| ||||||||||| |||||||||||||||||||||||
gtaagtagctttc--ctcaactctacagtacaattcttgtacaaaatgttgcccttgtcatttatttactttctatgcttttagctgctacactgttgtggtttatgtgcagTGATGTCTTCAAATGATGCTATGGGTACAGTTTTTAAGTGTTTGTCAAAGGGCGCTGTTGACTTCTTAGTCAAGCCCATACGTAAGAATGAACTTAAGAA

upper sequence: GRMZM2G005732_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA11G15580.1 (Glycine max), 3'ss of exon 3
gtaagtaactttcatctctacagtgtagttcatatcatgattaaaatgttgctttcatcatttatttagtcccaatgcttttagctgctacactgatgttgtttgtgtgcagTGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAGGTGCTGTTGACTTTTTAGTCAAGCCTATACGTAAGAATGAACTTAAGAA
    |||| |  | |  | |   | || ||  ||  |   ||||     |  |||||     ||||            ||||   |  | |||   | |    ||  |||||||||||| ||   |||| ||||| ||| ||||||||| |||||||||||||| || ||||| |||||||| || || || || | |||||||||||| ||
----gtaagtggcgtaccaaagttatactttttactaaatttaagtatatattttcaatgactattgctcatgtggtgttttgtttattgcacatgt-tcaaatgcatgcagTGATGTCATCTCATGATTCTATGGGTATAGTCTTTAAGTGTTTGTCAAAAGGCGCAGTTGATTTTTTAGTGAAACCAATTCGGAGGAATGAACTTAAAAA

upper sequence: GRMZM2G005732_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA13G19870.1 (Glycine max), 3'ss of exon 2
gtaagtaactttcatctctaca-gtgtagttcatatcatgattaaaatgttgctttcatcatttatttagtcccaatgcttttagctgctacactgatgttgtttgtgtgcagTGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAGGTGCTGTTGACTTTTTAGTCAAGCCTATACGTAAGAATGAACTTAAGAA
||||||        |   || |  |||   |  |       ||    |  |  | |||| || ||   | |  | |  |||||   ||     || |||   || || |||||||||||| ||   |||| ||||| ||  ||||||||| ||||||||||| ||||||||||||||| |||| || || ||||| |||||||| ||||| ||
gtaagttttccaagtgcttatatatgtttgttttgaagcatttctttttctcatctcatgatgta--aaatagctactcttttgtatggc-ttctaatgggattggtctgcagTGATGTCATCTCATGATTCTATGGGTTTAGTCTTTAAGTGTTTGTCAAAGGGTGCTGTTGACTTTCTAGTTAAACCCATACGGAAGAATGAGCTTAAAAA

upper sequence: GRMZM2G005732_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA12G07860.1 (Glycine max), 3'ss of exon 2
gtaagtaactttcatctctacagtgtagttcatatcatgattaaaatgttgctttcatcatttatttagtcccaatgcttttagctgctacactgatgttgtttgtgtgcagTGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAGGTGCTGTTGACTTTTTAGTCAAGCCTATACGTAAGAATGAACTTAAGAA
    ||||    |||  | |   | || |   |  ||   ||||     |  |||||     ||||            ||||   |  | |||   | |    |   |||||||||||| ||   |||| ||||| ||| ||||||||| ||||||||||||||||| ||||| |||||||| || ||||| || | |||||||||||| ||
----gtaagcggcataccaaagttatactctgttccaaatttaagtatatattttcaatgactattgctcatgtggtgttttgtttattgcacatgt-tcaaatacatgcagTGATGTCATCTCATGATTCTATGGGTATAGTCTTTAAGTGTTTGTCAAAAGGTGCAGTTGATTTTTTAGTGAAACCTATTCGGAGGAATGAACTTAAAAA

upper sequence: GRMZM2G005732_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G05520.1 (Glycine max), 3'ss of exon 2
gtaagtaactttcatctctacagtgtagttcatatcatgattaaaatgttgctttca-tcattt-atttagtcccaatgcttttagctgctaca----ctgatgttgtttgtgtgcagTGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAGGTGCTGTTGACTTTTTAGTCAAGCCTATACGTAAGAATGAACTTAAGAA
    |||| |||  |  | || |  || |  || |   | || ||   || ||||   |||| | ||   |    |  |||  |   | |||      || |||   || || |||||||||||| ||   |||| ||||| ||  ||||||||| ||||||||||| ||||||||||||||| |||| || || ||||| |||||||| ||||| ||
----gtaagttt--ttccaactgctta-tatatgtttggtttgaagcatttctttttctcatctcatgctgcaagagagctactcttttctatggcttctaatgggattggtctgcagTGATGTCATCTCATGATTCTATGGGTTTAGTCTTTAAGTGTTTGTCAAAGGGTGCTGTTGACTTTCTAGTTAAACCCATACGGAAGAATGAGCTTAAAAA

upper sequence: GRMZM2G005732_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv13s0067g03390.t01 (Vitis vinifera), 3'ss of exon 2
gtaagtaactttcatctctacagtgtagttcatatcatgattaaaatgttgctttcatcatttatttagtcccaatgcttttagctgctacac-tgatgttgtttgtgtgcagTGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAGGTGCTGTTGACTTTTTAGTCAAGCCTATACGTAAGAATGAACTTAAGAA
|| ||||   |||       |  |  |   |  |  ||   |    |  |||  |  | |||| | |     |||| ||||||  |||| ||| |||||   |||||||||||||||||| ||   |||| || || | | ||||||||||||||||||||| ||||| ||||||||||| || |||||||| || || ||||| ||||| ||
gtgagtattattccaaaacgctttacatgcctaagtatttctctttttctgcaattgttatttttatcaaatcaatacttttaattgcttcacctgatgagttttgtgtgcagTGATGTCATCCCATGATTCTGTGGGCATAGTCTTTAAATGTTTGTCAAAGGGTGCAGTTGACTTTTTTGTGAAGCCTATTCGAAAAAATGAGCTTAAAAA

upper sequence: GRMZM2G005732_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv06s0004g03650.t01 (Vitis vinifera), 3'ss of exon 2
gtaagtaactttcatctctacagtgtagttcatatcatgattaaaatgttgctttc--atcatttatttagtcccaatgcttttagctgctacactgatgttgtttgtgtgcagTGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAGGTGCTGTTGACTTTTTAGTCAAGCCTATACGTAAGAATGAACTTAAGAA
    |||| | |||| |      | |  ||   ||    ||| ||   ||  ||||  |||| |  |   |     |||| || |  | | || |||| | | ||| | |||||||||||| ||   |||| ||||| ||| ||||||||| ||| |||| || ||||| ||||| ||||| || || ||||| || |||||||||||||| ||
----gtaagtatcattttagtgttttcattttcatagaaatttaaggcttattttcctatcactcttgctgatttgatgcattgaatttccaccctgacgatctttttatgcagTGATGTCATCCCATGATTCTATGGGTATAGTCTTTAAGTGTCTGTCCAAGGGTGCAGTTGATTTTTTGGTGAAACCTATTCGAAAGAATGAACTTAAAAA

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|211264499|gb|FL189953.1|FL189953
EST:     GCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGTGATTA                         TGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAG
genomic: GCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGTGATTAgtaagtaact ... ttgtgtgcagTGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAG
EST: gi|211264494|gb|FL189948.1|FL189948
EST:     GCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGTGATTA                         TGATGTCTTCGAGTGATGCTATGAG
genomic: GCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGTGATTAgtaagtaact ... ttgtgtgcagTGATGTCTTCGAGTGATGCTATGAG
EST: gi|211264496|gb|FL189950.1|FL189950
EST:     GCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGNGATTA                         TGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAG
genomic: GCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGTGATTAgtaagtaact ... ttgtgtgcagTGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAG
EST: gi|211262066|gb|FL189945.1|FL189945
EST:     GCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGTGATTA                         TGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGGTTGTCAAAAG
genomic: GCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGTGATTAgtaagtaact ... ttgtgtgcagTGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAG
EST: gi|211264495|gb|FL189949.1|FL189949
EST:     GCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGTGATTA                         TGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAG
genomic: GCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGTGATTAgtaagtaact ... ttgtgtgcagTGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAG
EST: gi|211264502|gb|FL189956.1|FL189956
EST:     GCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGTGATTA                         TGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAG
genomic: GCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGTGATTAgtaagtaact ... ttgtgtgcagTGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAG
EST: gi|211264497|gb|FL189951.1|FL189951
EST:     GCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGTGATTA                         TGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAG
genomic: GCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGTGATTAgtaagtaact ... ttgtgtgcagTGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAG
EST: gi|211264493|gb|FL189947.1|FL189947
EST:     GCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGTGATTA                         TGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAG
genomic: GCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGTGATTAgtaagtaact ... ttgtgtgcagTGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAG
EST: gi|211264506|gb|FL189960.1|FL189960
EST:     GCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGTGATTA                         TGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAG
genomic: GCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGTGATTAgtaagtaact ... ttgtgtgcagTGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAG
EST: gi|211264501|gb|FL189955.1|FL189955
EST:     GCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGTGATTA                         TGATGGTCTTCGAGTGATGCTATGAGTACAGTCTTTTAAATGTTTTGTCAA
genomic: GCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGTGATTAgtaagtaact ... ttgtgtgcagTGATG-TCTTCGAGTGATGCTATGAGTACAGTCTTT-AAATGTTT-GTCAA
EST: gi|211264507|gb|FL189961.1|FL189961
EST:     GCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGTGATTA                         TGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAA
genomic: GCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGTGATTAgtaagtaact ... ttgtgtgcagTGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAA-
EST: gi|211266931|gb|FL189964.1|FL189964
EST:     GCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGTGATTA                         TGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAG
genomic: GCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGTGATTAgtaagtaact ... ttgtgtgcagTGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAG
EST: gi|211264498|gb|FL189952.1|FL189952
EST:     GCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGTGATTA                         TGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAA
genomic: GCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGTGATTAgtaagtaact ... ttgtgtgcagTGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAA
EST: gi|211264500|gb|FL189954.1|FL189954
EST:     GCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGTGATTA                         TGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAG
genomic: GCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGTGATTAgtaagtaact ... ttgtgtgcagTGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAG
EST: gi|211266930|gb|FL189963.1|FL189963
EST:     GCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGTGATTA                         TGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAG
genomic: GCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGTGATTAgtaagtaact ... ttgtgtgcagTGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAG
EST: gi|211264503|gb|FL189957.1|FL189957
EST:     GCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGTGATTA                         TGATGTCTTCGAGTGATGCTATGAGTACAG
genomic: GCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGTGATTAgtaagtaact ... ttgtgtgcagTGATGTCTTCGAGTGATGCTATGAGTACAG
EST: gi|211262065|gb|FL189944.1|FL189944
EST:     GCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGTGATTA                         TGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAG
genomic: GCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGTGATTAgtaagtaact ... ttgtgtgcagTGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAG

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 3 RNA-Seq libraries.


Block sizes: 37 (upstream exon), 49 (downstream exon)
Score: 19

GATCTTGTTTTGACTGAGGTTTTTATGCCCGGTGTATCTGGTATTTCTCTGCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGTGATTAgtaagtaact ... ttgtgtgcagTGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAGGTGCTGTTGACTTTTTAGTCAAGCCTATACGTAAGAATGAACTTAAGAA


Block sizes: 35 (upstream exon), 30 (downstream exon)
Score: 2

GATCTTGTTTTGACTGAGGTTTTTATGCCCGGTGTATCTGGTATTTCTCTGCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGTGATTAgtaagtaact ... ttgtgtgcagTGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAGGTGCTGTTGACTTTTTAGTCAAGCCTATACGTAAGAATGAACTTAAGAA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 11

GATCTTGTTTTGACTGAGGTTTTTATGCCCGGTGTATCTGGTATTTCTCTGCTGAGTAGAATCATGAGCCACAATATTTGCAAGAACATTCCAGTGATTAgtaagtaact ... ttgtgtgcagTGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAGGTGCTGTTGACTTTTTAGTCAAGCCTATACGTAAGAATGAACTTAAGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatttatttagtcccaatgcttttagctgctacactgatgttgtttgtgtgcagTGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAGGTGCTGTTGACTTTTTAGTCAAGCCTATACGTAAGAATGAACTTAAGAA
                                 cactgat  putative branch site (score: 11)
     tatttagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtaactttcatctctacagtgtagttcatatcatgattaaaatgttgctttcatcatttatttagtcccaatgcttttagctgctacactgatgttgtttgtgtgcagTGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAGGTGCTGTTGACTTTTTAGTCAAGCCTATACGTAAGAATGAACTTAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT