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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatttgcatgtctgtggtttgtgtcttgctagttgctacctactccactcaattttatgattgctggttttgtgacaattttatctcctttcttgacagGATTTTGAAGAACAACCAACTCACCGGACCCATCCCCTCCACACTGTCACAGATTCCAAATCTCAAGACCTT

Basic information

species Zea mays
transcript GRMZM2G082855_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G082855_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g03970.1 (Oryza sativa), 3'ss of exon 4
aaatttgcatgtctgtggtttgtgtcttgctagttgctacctactccactcaattttatgattgctggttttgtgacaattttatctcctttcttga--cagGATTTTGAAGAACAACCAACTCACCGGACCCATCCCCTCCACACTGTCACAGATTCCAAATCTCAAGACCTT
 |   || |  |||   ||| | ||  |  |||||  |  |         | ||  |  | |||  |   |        || | |||| ||| ||||  ||||||||||||||||||||| ||||| ||||||||||| |||||| |||| || ||||||||||||||||| ||
gatactgaacatctt--gttggagtagtagtagtttttttcatggttttgcgatgcttgggttgtagtggtaacattttttctctctcatttattgatgcagGATTTTGAAGAACAACCAGCTCACGGGACCCATCCCTTCCACATTGTCCCAAATTCCAAATCTCAAGACATT
















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|86472326|gb|DY238696.1|DY238696
EST:     TATGGAGACATCCCCTTCTCCATCTCTAAGCTCAAGCAACTTGAGGACCT                         GATTTTGAAGAACAACCAACTCACCGGACCCATCCCCTCCACACTGTCACA
genomic: TATGGAGACATCCCCTTCTCCATCTCTAAGCTCAAGCAACTTGAGGACCTgtaagctcta ... ttcttgacagGATTTTGAAGAACAACCAACTCACCGGACCCATCCCCTCCACACTGTCACA
EST: gi|148934014|gb|EC878019.2|EC878019
EST:     TATGGAGACATCCCCTTCTCCATCTCTAAGCTCAAGCAACTTGAGGACCT                         GATTCTGAAGAACAACCAACTCACCGGACCCATCCCCTCCACACTGTCACA
genomic: TATGGAGACATCCCCTTCTCCATCTCTAAGCTCAAGCAACTTGAGGACCTgtaagctcta ... ttcttgacagGATTTTGAAGAACAACCAACTCACCGGACCCATCCCCTCCACACTGTCACA
EST: gi|148940443|gb|EC885241.2|EC885241
EST:     TATGGAGACATCCCCTTCTCCATCTCTAAGCTCAAGCAACTTGAGGACCT                         GATTTTGAAGAACAACCAACTCACCGGACCCATCCCCTCCACACTGTCACA
genomic: TATGGAGACATCCCCTTCTCCATCTCTAAGCTCAAGCAACTTGAGGACCTgtaagctcta ... ttcttgacagGATTTTGAAGAACAACCAACTCACCGGACCCATCCCCTCCACACTGTCACA
EST: gi|149079906|gb|EE168912.2|EE168912
EST:     TATGGAGACATCCCCTTCTCCATCTCTAAGCTCAAGCAACTTGAGGACCT                         GATTTTGAAGAACAACCAACTCACCGGACCCATCCCCTCCACACTGTCACA
genomic: TATGGAGACATCCCCTTCTCCATCTCTAAGCTCAAGCAACTTGAGGACCTgtaagctcta ... ttcttgacagGATTTTGAAGAACAACCAACTCACCGGACCCATCCCCTCCACACTGTCACA
EST: gi|148941048|gb|EC885905.2|EC885905
EST:     TATGGAGACATCCCCTTCTCCATCTCTAAGCTCAAGCAACTTGAGGACCT                         GATTTTGAAGAACAACCAACTCACCGGACCCATCCCCTCCACACTGTCACA
genomic: TATGGAGACATCCCCTTCTCCATCTCTAAGCTCAAGCAACTTGAGGACCTgtaagctcta ... ttcttgacagGATTTTGAAGAACAACCAACTCACCGGACCCATCCCCTCCACACTGTCACA
EST: gi|149096378|gb|EE182110.2|EE182110
EST:     TATGGAGACATCCCCTTCTCCATCTCTAAGCTCAAGCAACTTGAGGACCT                         GATTTTGAAGAACAACCAACTCACCGGACCCATCCCCTCCACACTGTCACA
genomic: TATGGAGACATCCCCTTCTCCATCTCTAAGCTCAAGCAACTTGAGGACCTgtaagctcta ... ttcttgacagGATTTTGAAGAACAACCAACTCACCGGACCCATCCCCTCCACACTGTCACA
EST: gi|101383199|gb|EB813654.1|EB813654
EST:     GACATCCCCTTCTCCATCTCTAAGCTCAAGCAACTTGAGGACCT                         GATTTTGAAGAACAACCAACTCACCGGACCCATCCCCTCCACACTGTCACA
genomic: GACATCCCCTTCTCCATCTCTAAGCTCAAGCAACTTGAGGACCTgtaagctcta ... ttcttgacagGATTTTGAAGAACAACCAACTCACCGGACCCATCCCCTCCACACTGTCACA
EST: gi|148957491|gb|EC903572.2|EC903572
EST:     TATGGAGACATCCCCTTCTCCATCTCTAAGCTCAAGCAACTTGAGGACCT                         GATTTTGAAGAACAACCAACTCACCGGACCCATCCCCTCCACACTGTCACA
genomic: TATGGAGACATCCCCTTCTCCATCTCTAAGCTCAAGCAACTTGAGGACCTgtaagctcta ... ttcttgacagGATTTTGAAGAACAACCAACTCACCGGACCCATCCCCTCCACACTGTCACA

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: 403

GGATTTGTCGGGCAACTTGCTGTATGGAGACATCCCCTTCTCCATCTCTAAGCTCAAGCAACTTGAGGACCTgtaagctcta ... ttcttgacagGATTTTGAAGAACAACCAACTCACCGGACCCATCCCCTCCACACTGTCACAGATTCCAAATCTCAAGACCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 68

GGATTTGTCGGGCAACTTGCTGTATGGAGACATCCCCTTCTCCATCTCTAAGCTCAAGCAACTTGAGGACCTgtaagctcta ... ttcttgacagGATTTTGAAGAACAACCAACTCACCGGACCCATCCCCTCCACACTGTCACAGATTCCAAATCTCAAGACCTT


Block sizes: 20 (upstream exon), 30 (downstream exon)
Score: 1

GGATTTGTCGGGCAACTTGCTGTATGGAGACATCCCCTTCTCCATCTCTAAGCTCAAGCAACTTGAGGACCTgtaagctcta ... ttcttgacagGATTTTGAAGAACAACCAACTCACCGGACCCATCCCCTCCACACTGTCACAGATTCCAAATCTCAAGACCTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 282

GGATTTGTCGGGCAACTTGCTGTATGGAGACATCCCCTTCTCCATCTCTAAGCTCAAGCAACTTGAGGACCTgtaagctcta ... ttcttgacagGATTTTGAAGAACAACCAACTCACCGGACCCATCCCCTCCACACTGTCACAGATTCCAAATCTCAAGACCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccactcaattttatgattgctggttttgtgacaattttatctcctttcttgacagGATTTTGAAGAACAACCAACTCACCGGACCCATCCCCTCCACACTGTCACAGATTCCAAATCTCAAGACCTT
                                  ttttatctcctttctt  CT-rich tract
      aattttatgatt  TA-rich tract