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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtctggagtccaagacagcactcagctcaattttattgattcttatattcacgacatgctgtattaaattttgaccagcagttggagatgattataatgtacattgcagGTCGAGTTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGATTATCGCGATTATTTTATCAGAAATCTTCATGATGCTTTGTCGGGGCACACTT

Basic information

species Zea mays
transcript GRMZM2G100872_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G100872_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g40840.1 (Oryza sativa), 3'ss of exon 2
gtttgtctggagtccaagacagcact-cagctcaattttattgattc---ttatattcacgacatgctgtattaaattttgaccagcagttggagatgattataatgtacattgcagGTCGAGTTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGATTATCGCGATTATTTTATCAGAAATCTTCATGATGCTTTGTCGGGGCACACTT
||||| |   |  ||  || ||   |    ||   ||| | | ||||   | |  |||  |  |   |  |||||   |  | ||  ||||  | || |||  |||  |   |||||||||| ||||| ||||||||||| ||||||||||| ||||||||||||||||| |||||||| || ||||||||||||||||| || ||||| |||||||
gtttgccctta-cccttgagagtgttgtgtcttggtttgagtaattcgattcactttctagttacatttgattaatgct--atcataagtttaaaataatttgaatacattatgcagGTCGAATTCATATTGATGGGTGGAACTTTCATGTCATTACCAGCTGATTATCGGGATTATTTCATTAGAAATCTTCATGATGCCTTATCGGGACACACTT

upper sequence: GRMZM2G100872_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA04G36790.1 (Glycine max), 3'ss of exon 2
gtttgtctggagtccaagacagcactcagctcaattttattgattcttatattcacgacatgctgtattaaattttgaccagcagttggagatgattataat-gtacattgcagGTCGAGTTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGATTATCGCGATTATTTTATCAGAAATCTTCATGATGCTTTGTCGGGGCACACTT
    || || ||  ||    |   ||   ||  | | |    || |  |  | || || |||    | || ||||        |  |     | | |||  | ||   || ||||| ||||| ||||| ||||| || || ||||||||  | || |||||||| || ||||| ||||| ||||||||||||||||||||||| || ||||| |
----gtttgaagctcattttatatct---cttgaatattccaatcc--aagtacatgaaatg--agagtagatttactgtgtgaagtccttgtaactatggttgttgttttcagGTTGAGTTTATCTTAATGGGAGGTACCTTCATGTCACTTCCGGCTGATTACCGTGATTACTTTATAAGAAATCTTCATGATGCTTTGTCTGGACACACAT

upper sequence: GRMZM2G100872_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA06G18150.1 (Glycine max), 3'ss of exon 2
gtttgtctggagtccaagacagcactcagctcaattttattgattcttatattcacgacatgctgtattaaattttgaccagcagttggagatgattataat-gtacattgcagGTCGAGTTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGATTATCGCGATTATTTTATCAGAAATCTTCATGATGCTTTGTCGGGGCACACTT
    || |||||  ||    |   ||   ||  | | |    || |  |  | || || ||     | || ||||        |  |    || |||||  | ||   || ||||| || || ||||| ||||| || || ||||||||  | || |||||||| || ||||| ||||| ||||||||||||||||||||||| || ||||| |
----gtttggagctcattttacatct---cttgaatattccaatcc--aagtgcatgaaata--agagtagatttactgtgtaaagtacttataattatggttgttattttcagGTTGAATTTATCTTAATGGGCGGTACCTTCATGTCACTTCCGGCTGATTACCGTGATTACTTTATAAGAAATCTTCATGATGCTTTGTCTGGACACACAT

upper sequence: GRMZM2G100872_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT5G50320.1 (Arabidopsis thaliana), 3'ss of exon 2
gtttgtctggagtccaagacagcactcagctcaattttattgattcttatattcacgacatgctgtattaaattttgaccagcagttggagatgattataatgtacattgcagGTCGAGTTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGATTATCGCGATTATTTTATCAGAAATCTTCATGATGCTTTGTCGGGGCACACTT
       | ||||   | |   |    | |       ||||  ||    | ||     ||  ||    | |   | ||  |  | |      ||||||||   |  ||  ||||| |||||||| |||||||| || |||||||||||  | || ||||| ||||| ||||  || ||  | ||||||||||||||||| || || |||||||
-----gttagagtttgatatttctagtaacctgtgagtattattttcgttctttttaccagtct---cttagcctagaggattactcc----tgattata---tgaatgacagGTTGAGTTCATTTTGATGGGAGGTACTTTCATGTCACTGCCTGCTGAGTATCGGGATTTCTTCATACGGAATCTTCATGATGCTTTATCAGGACACACTT

upper sequence: GRMZM2G100872_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv17s0000g10190.t01 (Vitis vinifera), 3'ss of exon 2
gttt-gtctggagtccaagacagcactcagctcaattttattgattcttatattcacgacatgctgtattaa-----attttgaccagcagttggagatgattataatgtacattgcagGTCGAGTTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGATTATCGCGATTATTTTATCAGAAATCTTCATGATGCTTTGTCGGGGCACACTT
|||| || ||  |||   |     | ||   | | || | |  | |  |  | | ||  | || | ||||       ||  |     |||  | |     ||       |   || ||||| |||||||| || |||||||| || ||||||||  | ||||| || || || ||||| ||||  || ||||| |||||||||||||| || |||||||
gtttagtttgttgtct--ggttataatctaattatttatttacagttgtgcaat-acatcttgatttattggtaagcatacttgtttgcatcttgtttcaatggctgcatgtttt-cagGTAGAGTTCATTTTAATGGGTGGTACCTTCATGTCACTGCCAGCCGAGTACCGTGATTACTTTACAAGGAATCTACATGATGCTTTGTCAGGACACACTT

upper sequence: GRMZM2G100872_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ27078 (Selaginella moellendorffii), 3'ss of exon 2
gtttgtctggagtccaagacagcactcagctcaattttattgattcttatattcacgacatgctgtattaaattttgaccagcagttggagatgattataatgtacattgcagGTCGAGTTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGATTATCGCGATTATTTTATCAGAAATCTTCATGATGCTTTGTCGGGGCACACTT
                                                        ||     | ||| || |||   |       ||    |||  | | |   |    ||||| || |  ||| | ||||| || ||||||||||| || ||||| || || ||||| ||||||||| ||||||| ||||| ||| |||| || ||||| |
------------------------------------------------------gtgatcaagtttatgaattttcttct-----ctgtcactgagcaaagtcatcgccacagGTTGAATATATCCTTATGGGAGGTACTTTCATGTCTTTGCCAGCAGACTACCGCGACTATTTTATCCGAAATCTCCATGACGCTCTGTCTGGTCACACCT

upper sequence: GRMZM2G100872_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ21486 (Selaginella moellendorffii), 3'ss of exon 2
gtttgtctggagtccaagacagcactcagctcaattttattgattcttatattcacgacatgctgtattaaattttgaccagcagttggagatgattataatgtacattgcagGTCGAGTTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGATTATCGCGATTATTTTATCAGAAATCTTCATGATGCTTTGTCGGGGCACACTT
                                                        ||     | ||| || |||   |       ||    |||  | | ||  |    ||||| || |  ||| | ||||| || ||||||||||| || ||||| || || ||||| ||||||||| ||||||| ||||| ||| |||| || ||||| |
------------------------------------------------------gtgatcaagtttatgaattttcttct-----ctgtcactgagcaaagtgatcgccacagGTTGAATATATCCTTATGGGAGGTACTTTCATGTCTTTGCCAGCAGACTACCGCGACTATTTTATCCGAAATCTCCATGACGCTCTGTCTGGTCACACCT

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|76923552|gb|DV169543.1|DV169543
EST:     CCAGGAGCAGGATAGATCAGCTCAAGAGGTTAGGGCATAGTGTGGATAAG                         GTCGAGTTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGATTAT
genomic: CCAGGAGCAGGATAGATCAGCTCAAGAGGTTAGGGCATAGTGTGGATAAGgtttgtctgg ... tacattgcagGTCGAGTTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGATTAT
EST: gi|211469955|gb|FL098251.1|FL098251
EST:     CCAGGAGCAGGATAGATCAGCTCAAGAGGTTAGGGCATAGTGTGGATAAG                         GTCGAGTTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGATTAT
genomic: CCAGGAGCAGGATAGATCAGCTCAAGAGGTTAGGGCATAGTGTGGATAAGgtttgtctgg ... tacattgcagGTCGAGTTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGATTAT
EST: gi|50328156|gb|CO523282.1|CO523282
EST:     CCAGGAGCAGGATAGATCAGCTCAAGAGGTTAGGGCATAGTGTGGATAAG                         GTCGAGTTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGATTAT
genomic: CCAGGAGCAGGATAGATCAGCTCAAGAGGTTAGGGCATAGTGTGGATAAGgtttgtctgg ... tacattgcagGTCGAGTTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGATTAT
EST: gi|78112309|gb|DV530703.1|DV530703
EST:     CCAGGAGCAGGATAGATCAGCTCAAGAGGTTAGGGCATAGTGTGGATAAG                         GTCGAGTTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGATTAT
genomic: CCAGGAGCAGGATAGATCAGCTCAAGAGGTTAGGGCATAGTGTGGATAAGgtttgtctgg ... tacattgcagGTCGAGTTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGATTAT
EST: gi|148941357|gb|EC886266.2|EC886266
EST:     CCAGGAGCAGGATAGATCAGCTCAAGAGGTTAGGGCATAGTGTGGATAAG                         GTCGAGTTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGATTAT
genomic: CCAGGAGCAGGATAGATCAGCTCAAGAGGTTAGGGCATAGTGTGGATAAGgtttgtctgg ... tacattgcagGTCGAGTTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGATTAT
EST: gi|149001061|gb|EE038313.2|EE038313
EST:     CCAGGAGCAGGATAGATCAGCTCAAGAGGTTAGGGCATAGTGTGGATAAG                         GTCGAGTTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGATTAT
genomic: CCAGGAGCAGGATAGATCAGCTCAAGAGGTTAGGGCATAGTGTGGATAAGgtttgtctgg ... tacattgcagGTCGAGTTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGATTAT
EST: gi|91049795|gb|EB160213.1|EB160213
EST:     CCAGGAGCAGGATAGATCAGCTCAAGAGGTTAGGGCATAGTGTGGATAAG                         GTCGAGTTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGATTAT
genomic: CCAGGAGCAGGATAGATCAGCTCAAGAGGTTAGGGCATAGTGTGGATAAGgtttgtctgg ... tacattgcagGTCGAGTTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGATTAT
EST: gi|148940806|gb|EC885631.2|EC885631
EST:     CCAGGAGCAGGATAGATCAGCTCAAGAGGTTAGGGCATAGTGTGGATAAG                         GTCGAGTTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGATTAT
genomic: CCAGGAGCAGGATAGATCAGCTCAAGAGGTTAGGGCATAGTGTGGATAAGgtttgtctgg ... tacattgcagGTCGAGTTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGATTAT
EST: gi|89253138|gb|DY624924.1|DY624924
EST:     CCAGGAGCAGGATAGATCAGCTCAAGAGGTTAGGGCATAGTGTGGATAAG                         GTCGAGTTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGATTAT
genomic: CCAGGAGCAGGATAGATCAGCTCAAGAGGTTAGGGCATAGTGTGGATAAGgtttgtctgg ... tacattgcagGTCGAGTTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGATTAT
EST: gi|78119531|gb|DV537915.1|DV537915
EST:     CCAGGAGCAGGATAGATCAGCTCAAGAGGTTAGGGCATAGTGTGGATAAG                         GTCGAGTTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGATTAT
genomic: CCAGGAGCAGGATAGATCAGCTCAAGAGGTTAGGGCATAGTGTGGATAAGgtttgtctgg ... tacattgcagGTCGAGTTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGATTAT
EST: gi|50330596|gb|CO525722.1|CO525722
EST:     CCAGGAGCAGGATAGATCAGCTCAAGAGGTTAGGGCATAGTGTGGATAAG                         GTCGAGTTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGATTAT
genomic: CCAGGAGCAGGATAGATCAGCTCAAGAGGTTAGGGCATAGTGTGGATAAGgtttgtctgg ... tacattgcagGTCGAGTTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGATTAT

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: 46 (upstream exon), 48 (downstream exon)
Score: 31

GTATAATCCATATGTGCAAGCCAGGAGCAGGATAGATCAGCTCAAGAGGTTAGGGCATAGTGTGGATAAGgtttgtctgg ... tacattgcagGTCGAGTTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGATTATCGCGATTATTTTATCAGAAATCTTCATGATGCTTTGTCGGGGCACACTT


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 18

GTATAATCCATATGTGCAAGCCAGGAGCAGGATAGATCAGCTCAAGAGGTTAGGGCATAGTGTGGATAAGgtttgtctgg ... tacattgcagGTCGAGTTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGATTATCGCGATTATTTTATCAGAAATCTTCATGATGCTTTGTCGGGGCACACTT


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

GTATAATCCATATGTGCAAGCCAGGAGCAGGATAGATCAGCTCAAGAGGTTAGGGCATAGTGTGGATAAGgtttgtctgg ... tacattgcagGTCGAGTTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGATTATCGCGATTATTTTATCAGAAATCTTCATGATGCTTTGTCGGGGCACACTT


Block sizes: 41 (upstream exon), 45 (downstream exon)
Score: 26

GTATAATCCATATGTGCAAGCCAGGAGCAGGATAGATCAGCTCAAGAGGTTAGGGCATAGTGTGGATAAGgtttgtctgg ... tacattgcagGTCGAGTTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGATTATCGCGATTATTTTATCAGAAATCTTCATGATGCTTTGTCGGGGCACACTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgctgtattaaattttgaccagcagttggagatgattataatgtacattgcagGTCGAGTTCATCTTGATGGGTGGGACTTTCATGTCCTTACCAGCTGATTATCGCGATTATTTTATCAGAAATCTTCATGATGCTTTGTCGGGGCACACTT
              ttttgac  putative branch site (score: 26)
     tgtattaaattttga  TA-rich tract