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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTATTCCTGATGTTGCAGCGTTTCCCTGTTGAGTCAAAAGGCCGCCGGAAAAAATTGAATGAGgtactttgctacctgttgtcatccactatagaaatatatctgatgacgtgtttgtttaacattaaatacattatccccttttacgcag

Basic information

species Zea mays
transcript GRMZM2G171469_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171469_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g02850.2 (Oryza sativa), 5'ss of exon 8
GTTATTCCTGATGTTGCAGCGTTTCCCTGTTGAGTCAAAAGGCCGCCGGAAAAAATTGAATGAGgtactttgctacctgttgtcatccactatagaaatatatctgatgacgtgtttgtttaacattaaatacattatccccttttacgcag
| |||| |||||||| |||||||| || ||||| ||||||||  | || ||||| ||||||||||||||     | || || ||||   ||        | |  | ||    |   |  ||  ||||    |||  |||  ||||| |  ||
GCTATTTCTGATGTTACAGCGTTTTCCAGTTGAATCAAAAGGAAGGCGTAAAAAGTTGAATGAGgtact-----atcttttatcattggcttctattccagaattaatactttagataatttgcatttctaacac-atctactttttcatag
















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|78108686|gb|DV527104.1|DV527104
EST:     GCAGCGGTTTCC-TGTTGAGTCAAAAGGCCGCCGGAAAAAATTGAATGAG                         GTTGGCTATGTGACCACCCTTTGCTTT
genomic: GCAGCG-TTTCCCTGTTGAGTCAAAAGGCCGCCGGAAAAAATTGAATGAGgtactttgct ... ttttacgcagGTTGGCTATGTGACCACCATTTGCTTT
EST: gi|91873273|gb|EB403230.1|EB403230
EST:     GCAGCGTTTCCCTGTTGAGTCAAAAGGCCGCCGGAAAAAATTTGA-TGAA                         GTTGGCTATGTGACCACCATTTGCTTTGGTTGCTTCTTGATCAGATGCAT
genomic: GCAGCGTTTCCCTGTTGAGTCAAAAGGCCGCCGGAAAAAATT-GAATGAGgtactttgct ... ttttacgcagGTTGGCTATGTGACCACCATTTGCTTTGGTTGCTTCTTGATCAGATGCAT
EST: gi|5895618|gb|AW036864.1|AW036864
EST:     TGCAGCGTTTCCCTGTTGAGTCAAAAGGCCGCCGGAAAAAATTGAATGAG                         GTTGGCTATGTGACCACCATTTGCTTTGGTTGCTTCTTGATCAGATGCATA
genomic: TGCAGCGTTTCCCTGTTGAGTCAAAAGGCCGCCGGAAAAAATTGAATGAGgtactttgct ... ttttacgcagGTTGGCTATGTGACCACCATTTGCTTTGGTTGCTTCTTGATCAGATGCATA

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: 49 (upstream exon), 46 (downstream exon)
Score: 56

GTTATTCCTGATGTTGCAGCGTTTCCCTGTTGAGTCAAAAGGCCGCCGGAAAAAATTGAATGAGgtactttgct ... ttttacgcagGTTGGCTATGTGACCACCATTTGCTTTGGTTGCTTCTTGATCAGATGCATAATG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 100

GTTATTCCTGATGTTGCAGCGTTTCCCTGTTGAGTCAAAAGGCCGCCGGAAAAAATTGAATGAGgtactttgct ... ttttacgcagGTTGGCTATGTGACCACCATTTGCTTTGGTTGCTTCTTGATCAGATGCATAATG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 117

GTTATTCCTGATGTTGCAGCGTTTCCCTGTTGAGTCAAAAGGCCGCCGGAAAAAATTGAATGAGgtactttgct ... ttttacgcagGTTGGCTATGTGACCACCATTTGCTTTGGTTGCTTCTTGATCAGATGCATAATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 125

GTTATTCCTGATGTTGCAGCGTTTCCCTGTTGAGTCAAAAGGCCGCCGGAAAAAATTGAATGAGgtactttgct ... ttttacgcagGTTGGCTATGTGACCACCATTTGCTTTGGTTGCTTCTTGATCAGATGCATAATG