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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgctgtgcctcttgtttctctttgtaattatgctagtgtctcaacaaaactaaatttatttattctgggttttgcatttgttagGTGGATATGCGGCTGGATACTATAGTTACAAG

Basic information

species Glycine max
transcript GLYMA01G02480.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G02480.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv00s0211g00060.t01 (Vitis vinifera), 3'ss of exon 16
gtttgctgtgcctcttgtttctctttgtaattatgctagtgtctcaacaaaactaaatttatttattctgggtt-ttgcatttgttagGTGGATATGCGGCTGGATACTATAGTTACAAG
||||||      |  ||||  | ||  ||| ||    ||| | ||        | ||||||| | || | | || |||    | | ||||||||| || |||||||||||||||||||||
gtttgcc---ttttctgttaattttgctaaatacagcagtttttccttg----tgaatttatctcttattgcttcttgtgaatatcagGTGGATACGCAGCTGGATACTATAGTTACAAG
















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|31308726|gb|CD393929.1|CD393929
EST:     GGTTCCTTTGCAGCTTTAGCCATATATTTGCAG                         GTGGATATGCGGCTGGATACTATAGTTACAAG
genomic: GGTTCCTTTGCAGCTTTAGCCATATATTTGCAGgtttgctgtg ... catttgttagGTGGATATGCGGCTGGATACTATAGTTACAAG
EST: gi|16277230|gb|BI942273.1|BI942273
EST:     TCCATTACCAGAGGATAGGTTCCTTTGCAGCTTTAGCCATATATTTGCAG                         GTGGATATGCGGCTGGATACTATAGTTACAAG
genomic: TCCATTACCAGAGGATAGGTTCCTTTGCAGCTTTAGCCATATATTTGCAGgtttgctgtg ... catttgttagGTGGATATGCGGCTGGATACTATAGTTACAAG
EST: gi|58024369|gb|CX711110.1|CX711110
EST:     TCCATTACCAGAGGATAGGTTCCTTTGCAGCTTTAGCCATATATTTGCAG                         GTGGATATGCGGCTGGATACTATAGTTACAAG
genomic: TCCATTACCAGAGGATAGGTTCCTTTGCAGCTTTAGCCATATATTTGCAGgtttgctgtg ... catttgttagGTGGATATGCGGCTGGATACTATAGTTACAAG
EST: gi|31310299|gb|CD395502.1|CD395502
EST:     TCCATTACCAGAGGATAGGTTCCTTTGCAGCTTTAGCTATATATTTGCAG                         GTGGATATGCGGCTGGATACTATAGTTACAAG
genomic: TCCATTACCAGAGGATAGGTTCCTTTGCAGCTTTAGCCATATATTTGCAGgtttgctgtg ... catttgttagGTGGATATGCGGCTGGATACTATAGTTACAAG
EST: gi|209720203|gb|BW674541.1|BW674541
EST:     AGGATAGGTTCCTTTGCAGCTTTAGCCATATATTTGCAG                         GTGGATATGCGGCTGGATACTATAGTTACAAG
genomic: AGGATAGGTTCCTTTGCAGCTTTAGCCATATATTTGCAGgtttgctgtg ... catttgttagGTGGATATGCGGCTGGATACTATAGTTACAAG
EST: gi|254336792|gb|GR842971.1|GR842971
EST:     TCCATTACCAGAGGATAGGTTCCTTTGCAGCTTTAGCCATATATTTGCAG                         GTGGATATGCGGCTGGATACTATAGTTACAAG
genomic: TCCATTACCAGAGGATAGGTTCCTTTGCAGCTTTAGCCATATATTTGCAGgtttgctgtg ... catttgttagGTGGATATGCGGCTGGATACTATAGTTACAAG
EST: gi|58021287|gb|CX708029.1|CX708029
EST:     TCCATTACCAGAGGATAGGTTCCTTTGCAGCTTTAGCCATATATTTGCAG                         GTGGATATGCGGCTGGATACTATAGTTACAAG
genomic: TCCATTACCAGAGGATAGGTTCCTTTGCAGCTTTAGCCATATATTTGCAGgtttgctgtg ... catttgttagGTGGATATGCGGCTGGATACTATAGTTACAAG
EST: gi|58018001|gb|CX704743.1|CX704743
EST:     TCCATTACCAGAGGATAGGTTCCTTTGCAGCTTTAGCCATATATTTGCAG                         GTGGATATGCGGCTGGATACTATAGTTACAAG
genomic: TCCATTACCAGAGGATAGGTTCCTTTGCAGCTTTAGCCATATATTTGCAGgtttgctgtg ... catttgttagGTGGATATGCGGCTGGATACTATAGTTACAAG
EST: gi|16284148|gb|BI945931.1|BI945931
EST:     TCCATTACCAGAGGATAGGTTCCTTTGCAGCTTTAGCCATATATTTGCAG                         GTGGATATGCGGCTGGATACTATAGTTACAAG
genomic: TCCATTACCAGAGGATAGGTTCCTTTGCAGCTTTAGCCATATATTTGCAGgtttgctgtg ... catttgttagGTGGATATGCGGCTGGATACTATAGTTACAAG
EST: gi|31462999|gb|CD405027.1|CD405027
EST:     TCCATTACCAGAGGATAGGTTCCTTTGCAGCTTTAGCCATATATTTGCAG                         GTGGATATGCGGCTGGATACTATAGTTACAAG
genomic: TCCATTACCAGAGGATAGGTTCCTTTGCAGCTTTAGCCATATATTTGCAGgtttgctgtg ... catttgttagGTGGATATGCGGCTGGATACTATAGTTACAAG
EST: gi|58022383|gb|CX709124.1|CX709124
EST:     TCCATTACCAGAGGATAGGTTCCTTTGCAGCTTTAGCCATATATTTGCAG                         GTGGATATGCGGCTGGATACTATAGTTACAAG
genomic: TCCATTACCAGAGGATAGGTTCCTTTGCAGCTTTAGCCATATATTTGCAGgtttgctgtg ... catttgttagGTGGATATGCGGCTGGATACTATAGTTACAAG
EST: gi|17022026|gb|BM093060.1|BM093060
EST:     TCCATTACCAGAGGATAGGTTCCTTTGCAGCTTTAGCCATATATTTGCAG                         GTGGATATGCGGCTGGATACTATAGTTACAAG
genomic: TCCATTACCAGAGGATAGGTTCCTTTGCAGCTTTAGCCATATATTTGCAGgtttgctgtg ... catttgttagGTGGATATGCGGCTGGATACTATAGTTACAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgctagtgtctcaacaaaactaaatttatttattctgggttttgcatttgttagGTGGATATGCGGCTGGATACTATAGTTACAAG
                  aactaaa  putative branch site (score: 2)
           tcaacaaaactaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgctgtgcctcttgtttctctttgtaattatgctagtgtctcaacaaaactaaatttatttattctgggttttgcatttgttagGTGGATATGCGGCTGGATACTATAGTTACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA