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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taacatgtttgctacggttatgtttttgcaacttgtgaatttgattaaaatgctattgagctatgctttttggcaactgactgctacaaattgcttgcagGTTGGTGATTGACAAAGAGACTGGCAAGCCAAAAGGTTATGGCTTTTGCGAGTACAAGGACGAGGAAACTGCTCTAAGTGCACGGCGGAACCTTCAGGGT

Basic information

species Zea mays
transcript GRMZM2G174919_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174919_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g07490.1 (Oryza sativa), 3'ss of exon 2
taacatgtttgcta-cggtta----tgtttttgcaacttgtgaatttgattaaaatgctattgagctatgctttttggcaactgactgctacaaattgcttgcagGTTGGTGATTGACAAAGAGACTGGCAAGCCAAAAGGTTATGGCTTTTGCGAGTACAAGGACGAGGAAACTGCTCTAAGTGCACGGCGGAACCTTCAGGGT
|  || |||| ||| | | |     |||||||  | || || |       ||| ||  | | ||    | ||  |  ||   | |    |      |  |||||| ||||| ||||| ||||| || || |||||||| |||||||| ||||| ||||||||||| ||||| ||||||||||||||||| ||||||||||| |||
tgccaagtttcctagcagctgcaagtgttttttaatctggtaacacgtggtaagatagtttcgac---tactcataagctcttaaacatttggtgct--ttgcagATTGGTTATTGATAAAGAAACAGGGAAGCCAAAGGGTTATGGGTTTTGTGAGTACAAGGATGAGGAGACTGCTCTAAGTGCACGCCGGAACCTTCAAGGT

upper sequence: GRMZM2G174919_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA10G36350.1 (Glycine max), 3'ss of exon 2
taacatgtttgctacggttatgtttttgcaacttgtgaat-ttgattaaaatgctattgagctatgctttttggcaactgactgctacaaattgcttgcagGTTGGTGATTGACAAAGAGACTGGCAAGCCAAAAGGTTATGGCTTTTGCGAGTACAAGGACGAGGAAACTGCTCTAAGTGCACGGCGGAACCTTCAGGGT
| | || ||| ||    ||   |        ||| ||  | ||||  |||    ||||  | |      ||   | | |  |  || |   ||     |||  | || ||||||| ||| ||||| || |||||||||||||| || || ||||| ||||| || || || ||| ||||||| || || || |||||||||
tgagattttttctgtaatttcttggaactgccttttgcttcttgaccaaaggtttatttggttgaagacttgaactattcccatcttctt-ttatccacagACTAGTTATTGACAGAGAAACTGGGAAACCAAAAGGTTATGGATTCTGTGAGTATAAGGATGAAGAGACGGCTTTAAGTGCTCGACGAAATCTTCAGGGT

upper sequence: GRMZM2G174919_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA20G31220.2 (Glycine max), 3'ss of exon 2
taacatgtttgctacggttatgtttttgcaacttgtgaat-ttgattaaaatgctattgagctatgctttttggcaactgactgctacaaattgcttgcagGTTGGTGATTGACAAAGAGACTGGCAAGCCAAAAGGTTATGGCTTTTGCGAGTACAAGGACGAGGAAACTGCTCTAAGTGCACGGCGGAACCTTCAGGGT
| | || ||| ||    ||   |        ||| ||  | ||||  ||     ||||  | |      ||     | |  |  || |   ||   |||||  | || ||||||| ||| ||||| || |||||||||||||| || || ||||||||||| || || || ||| | ||||| || || || |||||||||
tgagattttttctgtaatttcatggaactcccttttgcttcttgaccaatggtttatttggttgaagacttgaattattcccatcttctt-ttatctgcagACTAGTTATTGACAGAGAAACTGGGAAACCAAAAGGTTATGGATTCTGTGAGTACAAGGATGAAGAGACGGCTTTGAGTGCTCGACGAAATCTTCAGGGT

upper sequence: GRMZM2G174919_T03 (Zea mays), 3'ss of exon 1
lower sequence: PP1S36_103V6.1 (Physcomitrella patens), 3'ss of exon 2
taacatgtttgctacggttatgtttttgcaacttgtgaatttgattaaaatgctattgagctatgctttttggcaactgactgctacaaat-tgcttg-----cagGTTGGTGATTGACAAAGAGACTGGCAAGCCAAAAGGTTATGGCTTTTGCGAGTACAAGGACGAGGAAACTGCTCTAAGTGCACGGCGGAACCTTCAGGGT
   | | | |  |||    ||| ||||  | | |   |   ||  ||  ||    || | | ||  |||| |    || |||| |  |||| |  |||     |||||||||  | || | |||||||||||| || ||||| ||||| || ||||||| ||  ||||||||||||||||| ||||| || ||||| ||||| |||
cgtcttatgtattac----atgctttttaatcatcacacaatggatagtatcagctttaccaatttttttcgtt--ctcactgatttaaatgtatttgaatcccagGTTGGTACTGGATAGAGAGACTGGCAAACCCAAAGGGTATGGATTCTGCGAGTTCAGAGACGAGGAAACTGCTCTGAGTGCTCGTCGGAATCTTCAAGGT

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|211229884|gb|FL170973.1|FL170973
EST:     GAGCAGCTCGTGCAGATTTGCGAAGAGGTTGGCCCAGTCGTATCCTTCAG                         GTTGGTGATTGACAAAGAGACTGGCAAGCCAAAAGGTTATGGCTTTTGCGA
genomic: GAGCAGCTCGTGCAGATTTGCGAAGAGGTTGGCCCAGTCGTATCCTTCAGgtgcgcttct ... ttgcttgcagGTTGGTGATTGACAAAGAGACTGGCAAGCCAAAAGGTTATGGCTTTTGCGA
EST: gi|211231934|gb|FL170974.1|FL170974
EST:     GAGCAGCTCGTGCAGATTTGCGAAGAGGTTGGCCCAGTCGTATCCTTCAG                         GTTGGTGATTGACAAAGAGACTGGCAAGCCAAAAGGTTATGGCTTTTGCGA
genomic: GAGCAGCTCGTGCAGATTTGCGAAGAGGTTGGCCCAGTCGTATCCTTCAGgtgcgcttct ... ttgcttgcagGTTGGTGATTGACAAAGAGACTGGCAAGCCAAAAGGTTATGGCTTTTGCGA
EST: gi|211229883|gb|FL170972.1|FL170972
EST:     GAGCAGCTCGTGCAGATTTGCGAAGAGGTTGGCCCAGTCGTATCCTTMAG                         GTTGGTGATTGACAAAGAGACTGGCAAGCCAAAAGGTTATGGCTTTTGCGA
genomic: GAGCAGCTCGTGCAGATTTGCGAAGAGGTTGGCCCAGTCGTATCCTTCAGgtgcgcttct ... ttgcttgcagGTTGGTGATTGACAAAGAGACTGGCAAGCCAAAAGGTTATGGCTTTTGCGA
EST: gi|31360834|gb|CD445191.1|CD445191
EST:     GAGCAGCTCGTGCAGATTTGCGAAGAGGTTGGCCCAGTCGTATCCTTCAG                         GTTGGTGATTGACAAAGAGACTGGCAAGCCAAAAGGTTATGGCTTTTGCGA
genomic: GAGCAGCTCGTGCAGATTTGCGAAGAGGTTGGCCCAGTCGTATCCTTCAGgtgcgcttct ... ttgcttgcagGTTGGTGATTGACAAAGAGACTGGCAAGCCAAAAGGTTATGGCTTTTGCGA
EST: gi|16916231|gb|BM072752.1|BM072752
EST:     GAGCAGCTCGTGCAGATTTGCGAAGAGGTTGGCCCAGTCGTATCCTTCAG                         GTTGGTGATTGACAAAGAGACTGGCAAGCCAAAAGGTTATGGCTTTTGCGA
genomic: GAGCAGCTCGTGCAGATTTGCGAAGAGGTTGGCCCAGTCGTATCCTTCAGgtgcgcttct ... ttgcttgcagGTTGGTGATTGACAAAGAGACTGGCAAGCCAAAAGGTTATGGCTTTTGCGA
EST: gi|71596191|gb|DR906942.1|DR906942
EST:     GAGCAGCTCGTGCAGATTTGCGAAGAGGTTGGCCCAGTCGTATCCTTCAG                         GTTGGTGATTGACAAAGAGACTGGCAAGCCAAAAGGTTATGGCTTTTGCGA
genomic: GAGCAGCTCGTGCAGATTTGCGAAGAGGTTGGCCCAGTCGTATCCTTCAGgtgcgcttct ... ttgcttgcagGTTGGTGATTGACAAAGAGACTGGCAAGCCAAAAGGTTATGGCTTTTGCGA

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: 48 (upstream exon), 46 (downstream exon)
Score: 85

TTGGCAACATACCATACGATGCGACAGAGGAGCAGCTCGTGCAGATTTGCGAAGAGGTTGGCCCAGTCGTATCCTTCAGgtgcgcttct ... ttgcttgcagGTTGGTGATTGACAAAGAGACTGGCAAGCCAAAAGGTTATGGCTTTTGCGAGTACAAGGACGAGGAAACTGCTCTAAGTGCACGGCGGAACCTTCAGGGT


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 85

TTGGCAACATACCATACGATGCGACAGAGGAGCAGCTCGTGCAGATTTGCGAAGAGGTTGGCCCAGTCGTATCCTTCAGgtgcgcttct ... ttgcttgcagGTTGGTGATTGACAAAGAGACTGGCAAGCCAAAAGGTTATGGCTTTTGCGAGTACAAGGACGAGGAAACTGCTCTAAGTGCACGGCGGAACCTTCAGGGT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 69

TTGGCAACATACCATACGATGCGACAGAGGAGCAGCTCGTGCAGATTTGCGAAGAGGTTGGCCCAGTCGTATCCTTCAGgtgcgcttct ... ttgcttgcagGTTGGTGATTGACAAAGAGACTGGCAAGCCAAAAGGTTATGGCTTTTGCGAGTACAAGGACGAGGAAACTGCTCTAAGTGCACGGCGGAACCTTCAGGGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 115

TTGGCAACATACCATACGATGCGACAGAGGAGCAGCTCGTGCAGATTTGCGAAGAGGTTGGCCCAGTCGTATCCTTCAGgtgcgcttct ... ttgcttgcagGTTGGTGATTGACAAAGAGACTGGCAAGCCAAAAGGTTATGGCTTTTGCGAGTACAAGGACGAGGAAACTGCTCTAAGTGCACGGCGGAACCTTCAGGGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaatgctattgagctatgctttttggcaactgactgctacaaattgcttgcagGTTGGTGATTGACAAAGAGACTGGCAAGCCAAAAGGTTATGGCTTTTGCGAGTACAAGGACGAGGAAACTGCTCTAAGTGCACGGCGGAACCTTCAGGGT
                             aactgac  putative branch site (score: 115)
                                       tacaaatt  TA-rich tract