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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtagatcatgttaagtttttcccttagattattttgactgtttaatgtttatgttcaatgtttctaatatatttacctgtaactttaccagATTACCCACAAAATAAACAAACTGTCCTTTGGGACAGAATTCCCTGGTGTTGTCAATCCACTTGATGG

Basic information

species Zea mays
transcript GRMZM2G044457_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044457_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g41120.1 (Oryza sativa), 3'ss of exon 7
gtaagtagatcatgttaagtttttcccttagattattttgactgtttaatgtttatgttcaatgtttctaatatatttacctgtaactttaccagATTACCCACAAAATAAACAAACTGTCCTTTGGGACAGAATTCCCTGGTGTTGTCAATCCACTTGATGG
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gtaagtaggtc-caataaatgttcctttt------ccttaaa-----agtgtttttattcagtgtttctgatatgtttgtgtataattttaccagATCACACACAAAATAAATAAACTGTCTTTTGGGACAGAATTCCCTGGTGTTGTTAATCCACTTGATGG
















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|211162555|gb|FL361310.1|FL361310
EST:     AATCGAACATAGATGTGCCTGAGCTGTCATTACTTGAAGGTGGTTTCAAT                         ATTACCCACAAAATAAACAAACTGTCCTTTGGGACAGAATTTCCTGGTGTT
genomic: AATCGAACATAGATGTGCCTGAGCTGTCATTACTTGAAGGTGGTTTCAATgtaagtagat ... actttaccagATTACCCACAAAATAAACAAACTGTCCTTTGGGACAGAATTCCCTGGTGTT
EST: gi|211541072|gb|FL347103.1|FL347103
EST:     AATCGAACATAGATGTGCCTGAGCTGTCATTACTTGAAGGTGGTTTCAAT                         ATTACCCACAAAATAAACAAACTGTCCTTTGGGACAGAATTTCCTGGTGTT
genomic: AATCGAACATAGATGTGCCTGAGCTGTCATTACTTGAAGGTGGTTTCAATgtaagtagat ... actttaccagATTACCCACAAAATAAACAAACTGTCCTTTGGGACAGAATTCCCTGGTGTT

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), 45 (downstream exon)
Score: 64

CAGTAAAGTTGCTGGAAATTTTCACTTTGCCCCAGGCAAAGGTTTTTATGAATCGAACATAGATGTGCCTGAGCTGTCATTACTTGAAGGTGGTTTCAATgtaagtagat ... actttaccagATTACCCACAAAATAAACAAACTGTCCTTTGGGACAGAATTCCCTGGTGTTGTCAATCCACTTGATGG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 146

CAGTAAAGTTGCTGGAAATTTTCACTTTGCCCCAGGCAAAGGTTTTTATGAATCGAACATAGATGTGCCTGAGCTGTCATTACTTGAAGGTGGTTTCAATgtaagtagat ... actttaccagATTACCCACAAAATAAACAAACTGTCCTTTGGGACAGAATTCCCTGGTGTTGTCAATCCACTTGATGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 161

CAGTAAAGTTGCTGGAAATTTTCACTTTGCCCCAGGCAAAGGTTTTTATGAATCGAACATAGATGTGCCTGAGCTGTCATTACTTGAAGGTGGTTTCAATgtaagtagat ... actttaccagATTACCCACAAAATAAACAAACTGTCCTTTGGGACAGAATTCCCTGGTGTTGTCAATCCACTTGATGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 109

CAGTAAAGTTGCTGGAAATTTTCACTTTGCCCCAGGCAAAGGTTTTTATGAATCGAACATAGATGTGCCTGAGCTGTCATTACTTGAAGGTGGTTTCAATgtaagtagat ... actttaccagATTACCCACAAAATAAACAAACTGTCCTTTGGGACAGAATTCCCTGGTGTTGTCAATCCACTTGATGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgtttaatgtttatgttcaatgtttctaatatatttacctgtaactttaccagATTACCCACAAAATAAACAAACTGTCCTTTGGGACAGAATTCCCTGGTGTTGTCAATCCACTTGATGG
                                              ctttacc  CT-rich tract
     ttaatgtttatgttca  TA-rich tract