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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccttgataaggctttcatgcatttgaaattgtcaacttcctggtgacattgatctttgacatttagtaccttataaatacaaggctccagaagagctcattaggcttaagcctgtataatatgctgcataaattctttttgtaacagatgcaggttttgttttatcttccttgactatattttggaagTTCAAATTCCACGATTGTTCCATTGTTTGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCTGAG

Basic information

species Zea mays
transcript GRMZM2G172621_T01
intron # 4
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G172621_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g48200.1 (Oryza sativa), 3'ss of exon 4
gtatccttgataaggctttcatgcatttgaaattgtcaacttcctggtgacattgatctttgacatttagtaccttataaatacaaggc----tccagaagagctcattaggcttaagcctgtataatatgctgcataaattctttttgtaacagatgcaggttttgttttatcttccttgactatattt---tggaagTTCAAATTCCACGATTGTTCCATTGTTTGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCTGAG
              |  | | |    ||  | || |||||||| |||||| |||   | |    |  ||  |   | |   || ||  |    ||   ||  | ||| |  |    |   | | | ||||  ||||||   | ||| ||     |||||   ||| |||||     |||| |||||||||   |  ||||||||||||||| ||||| ||  ||||||||||||| || || || |||||||||||||||||||||||||||||||| |||||||| ||||| |||
--------------gtatcctta---ttatatttatcaacttcttggtgatattatgcataagtagctaacatactttgcgtataatacaatctctgtaactgatcaatcagggcgaat-tatttcatattgtgcatac-ctatttctgatctggatgctattttggtttt-----ccttaactatatttctcttcaagTTCAAATTCCACCATTGTCCCCCTGTTTGAGAAGGTTCTAAGCGCCAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTACCAAAAGCCTGTGCGGAG

upper sequence: GRMZM2G172621_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA14G38490.1 (Glycine max), 3'ss of exon 1
gtatccttgataaggctttcatgcatttgaaattgtcaacttcctggtgacattgatctttgacatttagtaccttataaatacaaggctccagaagagctcattaggcttaagcct-gtataatatgctgcataaattctttttgtaacagatgcaggttttgttttatcttccttgactatattttggaagTTCAAATTCCACGATTGTTCCATTGTTTGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCTGAG
                                                                                                           || || |  | |  |  ||  |  | |  ||  | | | |||   ||     |  |      | | ||||||   |||  |   ||||  || || || || || |||||||||||||||||  ||||||| ||||||||||| || || || || |||||||| |||||| |||||||||||
-----------------------------------------------------------------------------------------------------------gcataggttttgcctgttacacatcgtctatgttatatataa---atttgattcatcaccagtttcccttgatgttatcattacagtttgaagtctactatagTGCCATTGTTTGAGAAGGTATTGAGTGCCAGTGATGCAGGTCGAATTGGTCGACTTGTTCTCCCAAAATCTTGTGCTGAG

upper sequence: GRMZM2G172621_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA18G05840.1 (Glycine max), 3'ss of exon 6
gtatccttgataaggctttcatgcatttgaaattgtcaacttcctggtgacattgatctttgacatttagtaccttataaatacaaggctccagaagagctcattaggcttaagcctgtataatatgctgcataaattctttttgtaacagatgcaggttttgttttatcttccttgactatattttggaagTTCAAATTCCACGATTGTTCCATTGTTTGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCTGAG
                                                                                      |  |||   | |  |  |     ||     | |  || ||     ||| | |||  | |||  |  |   | || |    ||  |||| | | | |||   |  ||||  || |||||  | || ||||| |||||||||||  ||||||| ||||||||||| || || || || |||||||| |||||||| |||||||||
--------------------------------------------------------------------------------------gtatcctttatatttttt---atttggttgtcttgaacatatataatagactctgatagtataaagt-tggtttattcagtagtttcccttaatgtat---gatagTTTGAAATCCACTGTAGTGCCATTATTTGAGAAGGTGTTGAGTGCCAGTGATGCAGGTCGAATTGGCCGTCTTGTTCTCCCAAAAGCCTGTGCTGAG

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|5566953|gb|AI881864.1|AI881864
EST:     CGTTATTGGCCAAGAATAACAGACCAAGAGCTGCAACAGATATCTGGAGA                         TTCAAATTCCACGATTGTTCCATTGTTTGAGAAGGTCCTGAGTGCGAGTGA
genomic: CGTTATTGGCCAAGAATAACAGACCAAGAGCTGCAACAGATATCTGGAGAgtatccttga ... attttggaagTTCAAATTCCACGATTGTTCCATTGTTTGAGAAGGTCCTGAGTGCGAGTGA




















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: 46 (upstream exon), 46 (downstream exon)
Score: 34

GTGTTGCTAGACCACCTGCTGATGGAAGGGGACGCAATCAATTACTTCCTCGTTATTGGCCAAGAATAACAGACCAAGAGCTGCAACAGATATCTGGAGAgtatccttga ... attttggaagTTCAAATTCCACGATTGTTCCATTGTTTGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCTGAG


Block sizes: 47 (upstream exon), 43 (downstream exon)
Score: 18

GTGTTGCTAGACCACCTGCTGATGGAAGGGGACGCAATCAATTACTTCCTCGTTATTGGCCAAGAATAACAGACCAAGAGCTGCAACAGATATCTGGAGAgtatccttga ... attttggaagTTCAAATTCCACGATTGTTCCATTGTTTGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCTGAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 41

GTGTTGCTAGACCACCTGCTGATGGAAGGGGACGCAATCAATTACTTCCTCGTTATTGGCCAAGAATAACAGACCAAGAGCTGCAACAGATATCTGGAGAgtatccttga ... attttggaagTTCAAATTCCACGATTGTTCCATTGTTTGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCTGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 58

GTGTTGCTAGACCACCTGCTGATGGAAGGGGACGCAATCAATTACTTCCTCGTTATTGGCCAAGAATAACAGACCAAGAGCTGCAACAGATATCTGGAGAgtatccttga ... attttggaagTTCAAATTCCACGATTGTTCCATTGTTTGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttttgtaacagatgcaggttttgttttatcttccttgactatattttggaagTTCAAATTCCACGATTGTTCCATTGTTTGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCTGAG
 ttccttgac  putative branch site 
                     ttttgttttatctt  TA-rich tract