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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCAAATATGGTCCTTCAGTGGCAAGCATCTTTACAAGGTGTCAAAGGATCATTTCTATCAGgtaaatgttcaatcattctccttttggatgcagttcaatgatatatacaattgtcttctgtggtaagtatcttttacatggactgaacggtggtacag

Basic information

species Zea mays
transcript GRMZM2G174757_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174757_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os10g41960.1 (Oryza sativa), 5'ss of exon 10
GACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCAAATATGGTCCTTCAGTGGCAAGCATCTTTACAAGGTGTCAAAGGATCATTTCTATCAGgta--aatgttcaatcattctccttt-tggatgc----agttcaatgatatatacaattgtcttctgtggtaagtatcttttacatggactgaacggtggtacag
  |||||||||||||||| ||||||||||||||||| || ||||||||||| |||||||||||||| |||||||||||||||||||| || |||| |||||||   | |||| ||| | | | ||| ||||  |       ||| || | || || |||||  ||  |      | || ||||| |  | | |    ||||||||
ATCTGCAGTTACCTCAGTCCATGAAATGGAGAATGGTTTCCAAATATGGTCTTTCAGTGGCAAGCAACTTTACAAGGTGTCAAAGGACCACTTCTTTCAGgtatggaggttccatcctacccttttctggactctcatgtctcattgctttacaccattgtaatcctt------tgtcatttactttaatttac---tggtacag

upper sequence: GRMZM2G174757_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA07G14870.1 (Glycine max), 5'ss of exon 10
GACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCAAATATGGTCCTTCAGTGGCAAGCATCTTTACAAGGTGTCAAAGGATCATTTCTATCAGgtaaatgttcaatcattctccttttggatgcagtt--caatgatatatacaattgtctt-ctgtggta-agtatcttttacatggac---tgaacggtggtacag
 ||||| || || ||||||||||||||||||||||| ||  | |||||||| |||| |||||||||||| ||   | |    |||||||| |||| |||||||    ||| | ||||  |  ||      | |||  |||| |||  ||  ||  | || |  ||||| | |   |  |   || |       |||||| ||   
AACTGCGGTGACTTCAGTTCATGAAATGGAGAATGGTTTCAATATATGGTCTTTCAATGGCAAGCATCTATATCGGATTCTGAAGGATCACTTCTTTCAGgtac---ttcga-catttgcacttgatgcactgttggcaattatacttattatattattaccatggtacaatgaatcatgtgtgaatgttcatacggtgatagg-

upper sequence: GRMZM2G174757_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA03G00470.1 (Glycine max), 5'ss of exon 10
GACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCAAATATGGTCCTTCAGTGGCAAGCATCTTTACAAGGTGTCAAAGGATCATTTCTATCAGgtaaatgttcaatcattctccttttggatgcagttcaatgatatatacaattgtcttctgtggtaagtatcttttacatggactgaacggt-ggtacag---
 |||||||| || ||||||||||||||||||||||| ||  | |||||||| |||| |||||||||||| ||   | |    ||||||||||||| |||||||   ||| |    | ||| |  || ||      |||| ||| ||  | |    |       | | |    | ||  |  |      | | |||   |   
AACTGCAGTGACTTCAGTTCATGAAATGGAGAATGGTTTCAATATATGGTCTTTCAATGGCAAGCATCTATATCGGATTCTGAAGGATCATTTCTTTCAGgta--cgttgacatttgctcttgatgcattgttggcaattatacatgtattaccatggcacaatgaatgatgtgtatgttcatatggtgataggtttggaca

upper sequence: GRMZM2G174757_T01 (Zea mays), 5'ss of exon 10
lower sequence: Vv04s0008g07070.t01 (Vitis vinifera), 5'ss of exon 10
GACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCAAATATGGTCCTTCAGTGGCAAGCATCTTTACAAGGTGTCAAAGGATCATTTCTATCAGgtaaatgttcaatcattctccttttggatgcagttcaatgatatatacaattgtcttctgtggtaagtatcttttacatggactgaacggtg----gtacag--
 ||| ||||||| ||||||||||| ||||| ||||||||| | |||||||||||||  |||||||  || ||   | |   ||||||||| ||||  |||||||  | | ||| ||  |  |      ||   || |||| | | | |  |||  | ||||  |||   |  || |||   | | | |  |     |||||   
AACTTCAGTTACTTCAGTTCATGAGATGGAAAATGGCTTTAACATATGGTCCTTCAACGGCAAGCTCCTGTATCGGATACTAAAGGATCACTTCTTCCAGgtaa--gatgaattataatattaactcctgggtttaaatggtcttt-ctcttga-tgctgtcataatggttattgacaacaagttaccattacattgtacaagt

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|32929764|gb|CF034576.1|CF034576
EST:     CCTTCAGTGGCAAGCATCTTTACAAGGTGTCAAAGGATCATTTCTATCAG                         TTTATATGGCGCCCGAGACCGCCCTCACTACTGACGACCGAGAAGGAAGAA
genomic: CCTTCAGTGGCAAGCATCTTTACAAGGTGTCAAAGGATCATTTCTATCAGgtaaatgttc ... ggtggtacagTTTATATGGCGCCCGAGACCGCCCTCACTACTGACGGCCGAGAAGGAAGAA
EST: gi|6994119|gb|AW453333.1|AW453333
EST:     CCTTCAGTGGCAAGCATCTTTACAAGGTGTCAAAGGATCATTTCTATCAG                         TTTATATGGCGCCCGAGACCGCCCTCACTACTGACGGCCGAGAAGGAAGAC
genomic: CCTTCAGTGGCAAGCATCTTTACAAGGTGTCAAAGGATCATTTCTATCAGgtaaatgttc ... ggtggtacagTTTATATGGCGCCCGAGACCGCCCTCACTACTGACGGCCGAGAAGGAAGAA
EST: gi|6564113|gb|AW231735.1|AW231735
EST:     CCTTCAGTGGCAAGCATCTTTACAAGGTGTCAAAGGATCATTTCTATCAG                         TTTATATGGCGCCCGAGACCGCCCTCACTACTGACGGCCGAGAAGGAAGAA
genomic: CCTTCAGTGGCAAGCATCTTTACAAGGTGTCAAAGGATCATTTCTATCAGgtaaatgttc ... ggtggtacagTTTATATGGCGCCCGAGACCGCCCTCACTACTGACGGCCGAGAAGGAAGAA
EST: gi|32929752|gb|CF034564.1|CF034564
EST:     CCTTCAGTGGCAAGCATCTTTACAAGGTGTCAAAGGGTCATTTCTATCAG                         TTTATATGGCGCCCGAGACCGCCCTCACTACTGACGGCCGAGAAGGAAGAA
genomic: CCTTCAGTGGCAAGCATCTTTACAAGGTGTCAAAGGATCATTTCTATCAGgtaaatgttc ... ggtggtacagTTTATATGGCGCCCGAGACCGCCCTCACTACTGACGGCCGAGAAGGAAGAA
EST: gi|149098248|gb|EE184214.2|EE184214
EST:     CCTTCAGTGGCAAGCATCTTTACAAGGTGTCAAAGGATCATTTCTATCAG                         TTTATATGGCGCCCGAGACCGCCCTCACTACTGACGGCCGAGAAGGAAGAA
genomic: CCTTCAGTGGCAAGCATCTTTACAAGGTGTCAAAGGATCATTTCTATCAGgtaaatgttc ... ggtggtacagTTTATATGGCGCCCGAGACCGCCCTCACTACTGACGGCCGAGAAGGAAGAA
EST: gi|32928528|gb|CF033340.1|CF033340
EST:     CCTTCAGTGGCAAGCATCTTTACAAGGTGTCAAAGGATCATTTCTATCAG                         TTTATATGGCGCCCGAGACCGCCCTCACTACTGACGGCCGAGAAGGAAGAA
genomic: CCTTCAGTGGCAAGCATCTTTACAAGGTGTCAAAGGATCATTTCTATCAGgtaaatgttc ... ggtggtacagTTTATATGGCGCCCGAGACCGCCCTCACTACTGACGGCCGAGAAGGAAGAA

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: 522

GACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCAAATATGGTCCTTCAGTGGCAAGCATCTTTACAAGGTGTCAAAGGATCATTTCTATCAGgtaaatgttc ... ggtggtacagTTTATATGGCGCCCGAGACCGCCCTCACTACTGACGGCCGAGAAGGAAGAAGAGATCTCAAGGAACCTGAAGAAGTATAGCAAGAAGTACGAACAAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 459

GACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCAAATATGGTCCTTCAGTGGCAAGCATCTTTACAAGGTGTCAAAGGATCATTTCTATCAGgtaaatgttc ... ggtggtacagTTTATATGGCGCCCGAGACCGCCCTCACTACTGACGGCCGAGAAGGAAGAAGAGATCTCAAGGAACCTGAAGAAGTATAGCAAGAAGTACGAACAAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 283

GACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCAAATATGGTCCTTCAGTGGCAAGCATCTTTACAAGGTGTCAAAGGATCATTTCTATCAGgtaaatgttc ... ggtggtacagTTTATATGGCGCCCGAGACCGCCCTCACTACTGACGGCCGAGAAGGAAGAAGAGATCTCAAGGAACCTGAAGAAGTATAGCAAGAAGTACGAACAAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 371

GACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCAAATATGGTCCTTCAGTGGCAAGCATCTTTACAAGGTGTCAAAGGATCATTTCTATCAGgtaaatgttc ... ggtggtacagTTTATATGGCGCCCGAGACCGCCCTCACTACTGACGGCCGAGAAGGAAGAAGAGATCTCAAGGAACCTGAAGAAGTATAGCAAGAAGTACGAACAAGAAG