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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcttgcatctttcttctgatttaacataacagaccttatcttctcagaatccttattttgcagcagccttatgtttcctttctttggtgcagTGAAAACAAACGACATGATGTTGGTGATATACCTGTCTTCTCTGATCCGGAGCGTCATTGCGCTTCACAATTTAATCAACAATAAG

Basic information

species Zea mays
transcript GRMZM2G061745_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G061745_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os04g56646.1 (Oryza sativa), 3'ss of exon 8
gtaatcttgcatctttcttctgatttaacataacagaccttatcttctca----gaatccttattttgcagcagccttatgtttcctttctttggtgcagTGAAAACAAACGACATGATGTTGGTGATATACCTGTCTTCTCTGATCCGGAGCGTCATTGCGCTTCACAATTTAATCAACAATAAG
|||||    ||| ||    |  |||||  ||||  || || | | | ||     |  | ||||| ||  |   |    ||| |    ||||||  |||||| ||||||||||| ||||||||||| |||||| |||||||||| |||||||| ||||| || || || || || ||||| || |||
gtaataacacatgttctcaccaatttactataattgagctgaacctgtcgtctgggtttcttatcttaaaatggttcgatgctaatgttctttcctgcagTTAAAACAAACGATATGATGTTGGTCATATACTTGTCTTCTCTTATCCGGAGTGTCATCGCACTCCATAACTTGATCAATAACAAG

upper sequence: GRMZM2G061745_T02 (Zea mays), 3'ss of exon 7
lower sequence: PP1S197_115V6.1 (Physcomitrella patens), 3'ss of exon 8
gtaatcttgcat--ctttcttctgatttaacataacagaccttatcttc---tcagaatccttattttgcagcagccttatgtttcctttctttggtgcagTGAAAACAAACGACATGATGTTGGTGATATACCTGTCTTCTCTGATCCGGAGCGTCATTGCGCTTCACAATTTAATCAACAATAAG
  ||| ||   |   ||| || || ||| ||     |||  |  | |||   ||  |    | |   |||    |    ||  ||   ||  ||  ||||||||||||||||||||||||||||||||| ||||||||||| || || ||||| || |||||  | |||||  | || || || |||
agaatattagttggttttgttttggtttgactgtgtagatttggttttcatgtctcagaagtcagggtgctcatgttaaatacttgtgttggtta-tgcagTGAAAACAAACGACATGATGTTGGTGATTTACCTGTCTTCCCTTATTCGGAGTGTTATTGCTTTACACAACCTCATAAATAACAAG
















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|32937292|gb|CF042111.1|CF042111
EST:     TAATCTCCTTCCAAATTTGAACGTAAATGAGCTAATTAAAGCCTTTGCAG                         TGAAAACAAACGACATGATGTTGGTGATATACCTGTCTTCTCTGATCCGGA
genomic: TAATCTCCTTCCAAATTTGAACGTAAATGAGCTAATTAAAGCCTTTGCAGgtaatcttgc ... tttggtgcagTGAAAACAAACGACATGATGTTGGTGATATACCTGTCTTCTCTGATCCGGA
EST: gi|60400633|gb|DN233440.1|DN233440
EST:     TAATCTCCTTCCAAATTTGAACGTAAATGAGCTAATTAAAGCCTTTGCAG                         TGAAAACAAACGACATGATGTTGGTGATATACCTGTCTTCTCTGATCCGGA
genomic: TAATCTCCTTCCAAATTTGAACGTAAATGAGCTAATTAAAGCCTTTGCAGgtaatcttgc ... tttggtgcagTGAAAACAAACGACATGATGTTGGTGATATACCTGTCTTCTCTGATCCGGA
EST: gi|32943105|gb|CF047924.1|CF047924
EST:     TAATCTCCTTCCAAATTTGAACGTAAATGAGCTAATTAAAGCCTTTGCAG                         TGAAAACAAACGACATGATGTTGGTGATATACCTGTCTTCTCTGATCCGGA
genomic: TAATCTCCTTCCAAATTTGAACGTAAATGAGCTAATTAAAGCCTTTGCAGgtaatcttgc ... tttggtgcagTGAAAACAAACGACATGATGTTGGTGATATACCTGTCTTCTCTGATCCGGA
EST: gi|32932870|gb|CF037682.1|CF037682
EST:     TAATCTCCTTCCAAATTTGAACGTAAATGAGCTAATTAAAGCCTTTGCAG                         TGAAAACAAACGACATGATGTTGGTGATATACCTGTCTTCTCTGATCCGGA
genomic: TAATCTCCTTCCAAATTTGAACGTAAATGAGCTAATTAAAGCCTTTGCAGgtaatcttgc ... tttggtgcagTGAAAACAAACGACATGATGTTGGTGATATACCTGTCTTCTCTGATCCGGA
EST: gi|37384435|gb|CF629288.1|CF629288
EST:     TGAACGTAAATGAGCTAATTAAAGCCTTTGCAG                         TGAAAACTAACGACATGATGTTGGTGATATACCTGTCTTCTCTGATCCGGA
genomic: TGAACGTAAATGAGCTAATTAAAGCCTTTGCAGgtaatcttgc ... tttggtgcagTGAAAACAAACGACATGATGTTGGTGATATACCTGTCTTCTCTGATCCGGA
EST: gi|5398737|gb|AI812202.1|AI812202
EST:     TAAAGCCTTTGCAG                         TGAAAACAAACGACATGATGTTGGTGATATACCTGTCTTCTCTGATCCGGA
genomic: TAAAGCCTTTGCAGgtaatcttgc ... tttggtgcagTGAAAACAAACGACATGATGTTGGTGATATACCTGTCTTCTCTGATCCGGA

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), 49 (downstream exon)
Score: 187

AGGATTGTAGAGTATATATTCATTATGAGTTCTTTTTTGCAGGATGTCTTTAATCTCCTTCCAAATTTGAACGTAAATGAGCTAATTAAAGCCTTTGCAGgtaatcttgc ... tttggtgcagTGAAAACAAACGACATGATGTTGGTGATATACCTGTCTTCTCTGATCCGGAGCGTCATTGCGCTTCACAATTTAATCAACAATAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 150

AGGATTGTAGAGTATATATTCATTATGAGTTCTTTTTTGCAGGATGTCTTTAATCTCCTTCCAAATTTGAACGTAAATGAGCTAATTAAAGCCTTTGCAGgtaatcttgc ... tttggtgcagTGAAAACAAACGACATGATGTTGGTGATATACCTGTCTTCTCTGATCCGGAGCGTCATTGCGCTTCACAATTTAATCAACAATAAG


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

AGGATTGTAGAGTATATATTCATTATGAGTTCTTTTTTGCAGGATGTCTTTAATCTCCTTCCAAATTTGAACGTAAATGAGCTAATTAAAGCCTTTGCAGgtaatcttgc ... tttggtgcagTGAAAACAAACGACATGATGTTGGTGATATACCTGTCTTCTCTGATCCGGAGCGTCATTGCGCTTCACAATTTAATCAACAATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 112

AGGATTGTAGAGTATATATTCATTATGAGTTCTTTTTTGCAGGATGTCTTTAATCTCCTTCCAAATTTGAACGTAAATGAGCTAATTAAAGCCTTTGCAGgtaatcttgc ... tttggtgcagTGAAAACAAACGACATGATGTTGGTGATATACCTGTCTTCTCTGATCCGGAGCGTCATTGCGCTTCACAATTTAATCAACAATAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcttctcagaatccttattttgcagcagccttatgtttcctttctttggtgcagTGAAAACAAACGACATGATGTTGGTGATATACCTGTCTTCTCTGATCCGGAGCGTCATTGCGCTTCACAATTTAATCAACAATAAG
                             ccttatgtttcctttc  CT-rich tract
               ttatttt  TA-rich tract