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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccatactgccatctcaaggaatattccgtctgaaaagaactcatggaacccaatgttccgccagctaactgtttgctctgatgattgttcttggtgtcagGTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAG

Basic information

species Zea mays
transcript GRMZM2G068277_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068277_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g02690.1 (Oryza sativa), 3'ss of exon 11
ccatac-tgccatctcaaggaatattccgt---ctgaaaagaactcatggaacccaatgttccgccagctaactgtttgctctgatgattgttcttggtgtcagGTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAG
| ||   ||||||||    | ||  ||  |   |||||||| | ||      |||| |  |  |     | ||  | |    ||  | ||  |||||    |||||||| |||||||| |||||||| |||||||||||||  || ||||| ||||| ||||| ||||| ||||||||||||
caatgtatgccatctttcagtatcctcttttacctgaaaaggagtcgactttccca-taatttgtt--tttacattctagagtgtcgttttatcttg-caccagGTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAG
















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|76281959|gb|DV021527.1|DV021527
EST:     AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCG                         GTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
genomic: AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCGgtaagataca ... ttggtgtcagGTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
EST: gi|60345943|gb|DN212916.1|DN212916
EST:     AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCG                         GTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
genomic: AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCGgtaagataca ... ttggtgtcagGTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
EST: gi|78122195|gb|DV540579.1|DV540579
EST:     AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCG                         GTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
genomic: AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCGgtaagataca ... ttggtgtcagGTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
EST: gi|211478808|gb|FL379717.1|FL379717
EST:     AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCG                         GTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
genomic: AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCGgtaagataca ... ttggtgtcagGTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
EST: gi|71443220|gb|DR824270.1|DR824270
EST:     AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCG                         GTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
genomic: AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCGgtaagataca ... ttggtgtcagGTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
EST: gi|211359065|gb|FL430712.1|FL430712
EST:     AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAADTCTTATAATGAAGCG                         GTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
genomic: AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCGgtaagataca ... ttggtgtcagGTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
EST: gi|50331676|gb|CO526802.1|CO526802
EST:     AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCG                         GTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
genomic: AGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCGgtaagataca ... ttggtgtcagGTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
EST: gi|5915607|gb|AW053248.1|AW053248
EST:     TTATAATGAAGCG                         GTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT
genomic: TTATAATGAAGCGgtaagataca ... ttggtgtcagGTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATT

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: 46 (upstream exon), 49 (downstream exon)
Score: 159

GAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCGgtaagataca ... ttggtgtcagGTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAG


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

GAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCGgtaagataca ... ttggtgtcagGTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAG


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 75

GAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCGgtaagataca ... ttggtgtcagGTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAG


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 102

GAAGTATCTTGTAGAGGCCACAAAAGAAGCATCCAATTCTTATAATGAAGCGgtaagataca ... ttggtgtcagGTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaacccaatgttccgccagctaactgtttgctctgatgattgttcttggtgtcagGTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAG
                                       ttgttctt  CT-rich tract