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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgtggacctgaagagcgacgaaattttagcagttcatgttttctggtcatgttgatgccattcactttcttccaacaaatagtttatatttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG

Basic information

species Zea mays
transcript GRMZM2G101596_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101596_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g14580.1 (Oryza sativa), 3'ss of exon 2
--gttgtggacctgaagagcgacgaaattttagcagttcatgttttctggt-catgttgatgccattcact--ttcttccaacaaatagtttatatttat--tgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
   |  ||   || ||     |   |||    |||    |||| ||   || |   |  ||  |||| |||  || |    |  |  | |  || |||    ||||||||||| || ||||||||||||||  |||||||||||||  | |||||||
atatcttgtctcttaatcatcaaataat----gcaa---atgtattaaagtaccaatgaatcacatttactagttgtgttgaataccattacatttttgcaatgcagGAATGCGCAGCCCAGATTCCAGTTTGTTGTCATGAATCGTCGTAATACAG

upper sequence: GRMZM2G101596_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ11747 (Selaginella moellendorffii), 3'ss of exon 2
gttgtggacctgaagagcgacgaaattttagcagttcatgttttctggtcatgttgatgccattcactttcttccaacaaatagtttatatttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
                                                      || ||   ||   |||  | |        |||  |  | ||   |||      || ||||| ||||||||||||||||||||||||||||  ||||
-----------------------------------------------------gtggtgtggtttgtttttattctgt-----gttcttggtgatc-tagGCGGATGCAGCCCAGGTTCCAGTTCATTGTCATGAATCGCAGGAGCACAG

upper sequence: GRMZM2G101596_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ22541 (Selaginella moellendorffii), 3'ss of exon 2
gttgtggacctgaagagcgacgaaattttagcagttcatgttttctggtcatgttgatgccattcactttcttccaacaaatagtttatatttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
                                                      || ||   ||   |||  | |        | |  |  | ||   |||      || ||||| |||||||||||||||||||||||||| |  ||||
-----------------------------------------------------gtggtgtggtttgtttttattctgt-----gctcttggtgatc-tagGCGGATGCAGCCCAGGTTCCAGTTCATTGTCATGAATCGCAGAAGCACAG

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|211391322|gb|FK987371.1|FK987371
EST:     AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG                         GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
genomic: AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAGgttcgtctcg ... tttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
EST: gi|93282402|gb|EB674666.1|EB674666
EST:     AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG                         GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
genomic: AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAGgttcgtctcg ... tttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
EST: gi|211393952|gb|FK987388.1|FK987388
EST:     AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG                         GAATGCTCAACCCAGATTCCAGTTCAT-GTCATGAATCGCAGGAATACAG
genomic: AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAGgttcgtctcg ... tttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
EST: gi|37419345|gb|CF647353.1|CF647353
EST:     AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG                         GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
genomic: AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAGgttcgtctcg ... tttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
EST: gi|13125936|gb|BG316611.1|BG316611
EST:     AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG                         GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
genomic: AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAGgttcgtctcg ... tttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
EST: gi|211393945|gb|FK987381.1|FK987381
EST:     AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG                         GAATGCTCAACCCAGATTCCAGTTCATNGTCATGAATCGCACGAATACAGA
genomic: AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAGgttcgtctcg ... tttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGA
EST: gi|91056521|gb|EB166939.1|EB166939
EST:     AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG                         GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
genomic: AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAGgttcgtctcg ... tttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
EST: gi|211391326|gb|FK987375.1|FK987375
EST:     AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG                         GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
genomic: AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAGgttcgtctcg ... tttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
EST: gi|211393953|gb|FK987389.1|FK987389
EST:     AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG                         GAATGCTCAACCCAGATTCCAGTTCAT-GTCATGAATCGCAGGAATACAG
genomic: AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAGgttcgtctcg ... tttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
EST: gi|211393946|gb|FK987382.1|FK987382
EST:     AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG                         GAATGCTCAACCCAGATTCCCAGTTCAT
genomic: AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAGgttcgtctcg ... tttattgcagGAATGCTCAACCCAGATTCC-AGTTCAT
EST: gi|76928738|gb|DV171746.1|DV171746
EST:     AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG                         GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
genomic: AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAGgttcgtctcg ... tttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
EST: gi|93281394|gb|EB673658.1|EB673658
EST:     AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG                         GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
genomic: AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAGgttcgtctcg ... tttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
EST: gi|211393955|gb|FK987391.1|FK987391
EST:     AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG                         GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
genomic: AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAGgttcgtctcg ... tttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
EST: gi|76010496|gb|DT937666.1|DT937666
EST:     AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG                         GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
genomic: AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAGgttcgtctcg ... tttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
EST: gi|7304674|gb|AW600613.1|AW600613
EST:     AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG                         GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
genomic: AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAGgttcgtctcg ... tttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
EST: gi|211393947|gb|FK987383.1|FK987383
EST:     AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG                         GAATGCTCAACCCAGATTCCAGTTCATCGTCATGAATCGCAGGAATACAG
genomic: AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAGgttcgtctcg ... tttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
EST: gi|211391329|gb|FK987378.1|FK987378
EST:     AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG                         GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
genomic: AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAGgttcgtctcg ... tttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
EST: gi|76909432|gb|DV163378.1|DV163378
EST:     AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG                         GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
genomic: AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAGgttcgtctcg ... tttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
EST: gi|91048464|gb|EB158882.1|EB158882
EST:     AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG                         GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
genomic: AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAGgttcgtctcg ... tttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
EST: gi|211391330|gb|FK987379.1|FK987379
EST:     AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG                         GAATGCTCAACCCAGATTCCAGTTCATNGTCATGAATCGCAGGAATACAGA
genomic: AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAGgttcgtctcg ... tttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGA
EST: gi|76011730|gb|DT938900.1|DT938900
EST:     AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG                         GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
genomic: AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAGgttcgtctcg ... tttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
EST: gi|89758076|gb|DY687416.1|DY687416
EST:     AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG                         GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
genomic: AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAGgttcgtctcg ... tttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
EST: gi|211393949|gb|FK987385.1|FK987385
EST:     AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG                         GAATGCTCAACCCAGGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
genomic: AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAGgttcgtctcg ... tttattgcagGAATGCTCAACCCAG-ATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
EST: gi|211391323|gb|FK987372.1|FK987372
EST:     AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG                         GAATGCTCAACCCAGATTCCAGTTCATNGTCATGAATCGCAGGAATACAGA
genomic: AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAGgttcgtctcg ... tttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGA
EST: gi|148930679|gb|EC872906.2|EC872906
EST:     AGCCGGACGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG                         GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCACGAATACAGA
genomic: AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAGgttcgtctcg ... tttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGA
EST: gi|211393951|gb|FK987387.1|FK987387
EST:     AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG                         GAATGCTCAACCCAGATTCCAGTTCATGGTCATGAATCGCAGGAATACAG
genomic: AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAGgttcgtctcg ... tttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
EST: gi|149112671|gb|EE191401.2|EE191401
EST:     AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG                         GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
genomic: AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAGgttcgtctcg ... tttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
EST: gi|148999366|gb|EE036307.2|EE036307
EST:     AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG                         GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
genomic: AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAGgttcgtctcg ... tttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
EST: gi|211393954|gb|FK987390.1|FK987390
EST:     AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG                         GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
genomic: AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAGgttcgtctcg ... tttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
EST: gi|211393950|gb|FK987386.1|FK987386
EST:     AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG                         GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
genomic: AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAGgttcgtctcg ... tttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
EST: gi|78114665|gb|DV533053.1|DV533053
EST:     AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG                         GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
genomic: AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAGgttcgtctcg ... tttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG

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: 48 (upstream exon), 49 (downstream exon)
Score: 44

AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAGgttcgtctcg ... tttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 23

AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAGgttcgtctcg ... tttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 51

AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAGgttcgtctcg ... tttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 41

AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAGgttcgtctcg ... tttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtcatgttgatgccattcactttcttccaacaaatagtttatatttattgcagGAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG
      tgttgat  putative branch site (score: 41)
                              aacaaatagtttatat  TA-rich tract