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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGCCTCATTTACGAGCTGTTGTTCTACATAGCCCAATTTCATCTGGTTTAAGAGTGATGTATCCTGTAAAGCATACATATTGGTTTGACATATATAAGgtggttaatttacttgattacttttaatttgattgcatacttgatctaatatctaataatttatttacag

Basic information

species Zea mays
transcript GRMZM2G003718_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G003718_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os06g42730.1 (Oryza sativa), 5'ss of exon 3
TTTGCCTCATTTACGAGCTGTTGTTCTACATAGCCCAATTTCATCTGGTTTAAGAGTGATGTATCCTGTAAAGCATACATATTGGTTTGACATATATAAGgtggtta-atttacttgattacttttaatttgattgcatacttgatctaatatctaataatttatttacag
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TTTGCCTCATCTGAGGGCTGTTGTTTTACACAGCCCTATTTTATCTGGCTTAAGAGTGATGTATCCTGTAAAGCATACATACTGGTTTGACATATACAAGgtgataacatttctttgtttatgtcaatcttaactt--tgctagatctaatatgcacttttttatttgcag
















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|78083604|gb|DV511997.1|DV511997
EST:     TAAGAGTGATGTATCCTGTAAAGCATACATATTGGTTTGACATATATAAG                         AACATTGACAAAATTCCTC
genomic: TAAGAGTGATGTATCCTGTAAAGCATACATATTGGTTTGACATATATAAGgtggttaatt ... ttatttacagAACATTGACAAAATTCCTC
EST: gi|50333770|gb|CO528896.1|CO528896
EST:     TAAGAGTGATGTATCCTGTAAAGCATACATATTGGTTTGACATATATAAG                         AACATTGACAAAATTCCTCTGGTCAGGTGTCCT
genomic: TAAGAGTGATGTATCCTGTAAAGCATACATATTGGTTTGACATATATAAGgtggttaatt ... ttatttacagAACATTGACAAAATTCCTCTGGTCAGGTGTCCT
EST: gi|71434066|gb|DR815116.1|DR815116
EST:     TAAGAGTGATGTATCCTGTAAAGCATACATATTGGTTTGACATATATAAG                         AACATTGACAAAATTCCTCTGGTCAGGTGTCCTGTATTAGTTATACAT
genomic: TAAGAGTGATGTATCCTGTAAAGCATACATATTGGTTTGACATATATAAGgtggttaatt ... ttatttacagAACATTGACAAAATTCCTCTGGTCAGGTGTCCTGTATTAGTTATACAT
EST: gi|78089451|gb|DV517825.1|DV517825
EST:     TAAGAGTGATGTATCCTGTAAAGCATACATATTGGTTTGACATATATAAG                         AACATTGACAAAATTCCTCTGGTCAGGTGTCCTGTATTAGTTATACAT
genomic: TAAGAGTGATGTATCCTGTAAAGCATACATATTGGTTTGACATATATAAGgtggttaatt ... ttatttacagAACATTGACAAAATTCCTCTGGTCAGGTGTCCTGTATTAGTTATACAT

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: 34 (upstream exon), 48 (downstream exon)
Score: 7

TTTGCCTCATTTACGAGCTGTTGTTCTACATAGCCCAATTTCATCTGGTTTAAGAGTGATGTATCCTGTAAAGCATACATATTGGTTTGACATATATAAGgtggttaatt ... ttatttacagAACATTGACAAAATTCCTCTGGTCAGGTGTCCTGTATTAGTTATACAT


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 11

TTTGCCTCATTTACGAGCTGTTGTTCTACATAGCCCAATTTCATCTGGTTTAAGAGTGATGTATCCTGTAAAGCATACATATTGGTTTGACATATATAAGgtggttaatt ... ttatttacagAACATTGACAAAATTCCTCTGGTCAGGTGTCCTGTATTAGTTATACAT


Block sizes: 48 (upstream exon), 40 (downstream exon)
Score: 16

TTTGCCTCATTTACGAGCTGTTGTTCTACATAGCCCAATTTCATCTGGTTTAAGAGTGATGTATCCTGTAAAGCATACATATTGGTTTGACATATATAAGgtggttaatt ... ttatttacagAACATTGACAAAATTCCTCTGGTCAGGTGTCCTGTATTAGTTATACAT


Block sizes: 24 (upstream exon), 27 (downstream exon)
Score: 5

TTTGCCTCATTTACGAGCTGTTGTTCTACATAGCCCAATTTCATCTGGTTTAAGAGTGATGTATCCTGTAAAGCATACATATTGGTTTGACATATATAAGgtggttaatt ... ttatttacagAACATTGACAAAATTCCTCTGGTCAGGTGTCCTGTATTAGTTATACAT