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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGGGGGAGCAGCTGAACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAGgtattattacttttgctttactcttcagtatttctacaagtcctttttctgtcaacttgactttccaccttgtacag

Basic information

species Zea mays
transcript GRMZM2G132712_T03
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G132712_T03 (Zea mays), 5'ss of exon 20
lower sequence: LOC_Os08g40530.2 (Oryza sativa), 5'ss of exon 4
GATGGGGGAGCAGCTGAACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAGgtattattacttt-------tgctttactc----------ttcagtatttctacaagtccttttt--ctgtcaa---cttgactt--tccaccttgtacag-------------------------------------------------
||||||||||  ||||||||| | || ||||| ||||||||||| |||||||||||||||||||||||||||   ||||       | |  |||||          |||| |  || |  |  ||| ||||   |||  |   | ||  ||  || |  || || |                                                  
GATGGGGGAGATGCTGAACTTTCAGGATCGCCAACTGAAAAGGCTATTCTTTCTTGGGGCCTTAAGgtattaaccctttatctggcttccatactcaagtggttccttcaatggttgtgtacatccgttttggatgtagaggccatgttttaatctattttctaaaaaagttactccagtggttccttcaatgactagttcttccactttgaacag
















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|211422272|gb|FK992813.1|FK992813
EST:     AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAG                         ATAGGGATGGATTTCGACGACGTGAGGACAAAATCTTCAGTTATTCATGTT
genomic: AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAGgtattattac ... ccttgtacagATAGGGATGGATTTCGACGATGTGAGGACAAAATCTTCAGTTATTCATGTT
EST: gi|211422266|gb|FK992807.1|FK992807
EST:     AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAG                         ATAGGGATGGATTTCGACGACGTGAGGACAAAATCTTCAGTTATTCATGTT
genomic: AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAGgtattattac ... ccttgtacagATAGGGATGGATTTCGACGATGTGAGGACAAAATCTTCAGTTATTCATGTT
EST: gi|211422265|gb|FK992806.1|FK992806
EST:     AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAG                         ATAGGGATGGATTTCGACGACGTGAGGACAAAATCTTCAGTTATTCATGTT
genomic: AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAGgtattattac ... ccttgtacagATAGGGATGGATTTCGACGATGTGAGGACAAAATCTTCAGTTATTCATGTT
EST: gi|211422271|gb|FK992812.1|FK992812
EST:     AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAG                         ATAGGGATGGATTTCGACGACGTGAGGACAAAATCTTCAGTTATTCATGTT
genomic: AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAGgtattattac ... ccttgtacagATAGGGATGGATTTCGACGATGTGAGGACAAAATCTTCAGTTATTCATGTT
EST: gi|211422274|gb|FK992815.1|FK992815
EST:     AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAG                         ATAGGGATGGATTTCGACGACGTGAGGACAAAATCTTCAGTTATTCATGTT
genomic: AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAGgtattattac ... ccttgtacagATAGGGATGGATTTCGACGATGTGAGGACAAAATCTTCAGTTATTCATGTT
EST: gi|211422270|gb|FK992811.1|FK992811
EST:     AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAG                         ATAGGGATGGATTTCGACGACGTGAGGACAAAATCTTCAGTTATTCATGTT
genomic: AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAGgtattattac ... ccttgtacagATAGGGATGGATTTCGACGATGTGAGGACAAAATCTTCAGTTATTCATGTT
EST: gi|211422268|gb|FK992809.1|FK992809
EST:     AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAG                         ATAGGGATGGATTTCGACGACGTGAGGACAAAATCTTCAGTTATTCATGTT
genomic: AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAGgtattattac ... ccttgtacagATAGGGATGGATTTCGACGATGTGAGGACAAAATCTTCAGTTATTCATGTT
EST: gi|211422273|gb|FK992814.1|FK992814
EST:     AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAG                         ATAGGGATGGATTTCGACGACGTGAGGACAAAATCTTCAGTTATTCATGTT
genomic: AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAGgtattattac ... ccttgtacagATAGGGATGGATTTCGACGATGTGAGGACAAAATCTTCAGTTATTCATGTT
EST: gi|211422275|gb|FK992816.1|FK992816
EST:     AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAG                         ATAGGGATGGATTTCGACGACGTGAGGACAAAATCTTCAGTTATTCATGTT
genomic: AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAGgtattattac ... ccttgtacagATAGGGATGGATTTCGACGATGTGAGGACAAAATCTTCAGTTATTCATGTT
EST: gi|31350151|gb|CD434508.1|CD434508
EST:     AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAG                         ATAGGGATGGATTTCGACGACGTGAGGACAAAATCTTCAGTTATTCATGTT
genomic: AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAGgtattattac ... ccttgtacagATAGGGATGGATTTCGACGATGTGAGGACAAAATCTTCAGTTATTCATGTT
EST: gi|71443249|gb|DR824299.1|DR824299
EST:     AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAG                         ATAGGGATGGATTTCGACGATGTGAGGACAAAATCTTCAGTTATTCATGTT
genomic: AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAGgtattattac ... ccttgtacagATAGGGATGGATTTCGACGATGTGAGGACAAAATCTTCAGTTATTCATGTT

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: 57

GATGGGGGAGCAGCTGAACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAGgtattattac ... ccttgtacagATAGGGATGGATTTCGACGATGTGAGGACAAAATCTTCAGTTATTCATGTTTTTCCATTTAACTCGGAGAAGAAACGTGGCGCTGTTGCAGTACAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 91

GATGGGGGAGCAGCTGAACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAGgtattattac ... ccttgtacagATAGGGATGGATTTCGACGATGTGAGGACAAAATCTTCAGTTATTCATGTTTTTCCATTTAACTCGGAGAAGAAACGTGGCGCTGTTGCAGTACAG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 93

GATGGGGGAGCAGCTGAACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAGgtattattac ... ccttgtacagATAGGGATGGATTTCGACGATGTGAGGACAAAATCTTCAGTTATTCATGTTTTTCCATTTAACTCGGAGAAGAAACGTGGCGCTGTTGCAGTACAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 59

GATGGGGGAGCAGCTGAACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAGgtattattac ... ccttgtacagATAGGGATGGATTTCGACGATGTGAGGACAAAATCTTCAGTTATTCATGTTTTTCCATTTAACTCGGAGAAGAAACGTGGCGCTGTTGCAGTACAG