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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctcaacattcttaccatgtttctgactcatatctttgcaggcgcacatgcatctttaaaataccagttttccttaatgtgatatggaaagttggcttatgctgagcttgattcatcatgcttgttctatttattttgttgcagGTGCGAGAATTAGTTCTCTCTCAAGATCTCACTCTTATTATTGAACCCGGAAGATCCTTGATTGCTAATACTTGCTGCTTCGTCAATAGAGTAACTGGTG

Basic information

species Zea mays
transcript GRMZM2G020446_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020446_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g24354.1 (Oryza sativa), 3'ss of exon 4
gtaagctcaacattcttaccatgtttctgactcatatctttgcaggcgcacatgcatctttaaa-ataccagtttt--ccttaa-----tgtgatatggaaagttggcttatgctgagcttgattcatcatgcttgttctatttattttgttgcagGTGCGAGAATTAGTTCTCTCTCAAGATCTCACTCTTATTATTGAACCCGGAAGATCCTTGATTGCTAATACTTGCTGCTTCGTCAATAGAGTAACTGGTG
|| ||||||| || | |   || |||| || ||  ||||| | |||| ||  |   | |||||| | | || ||    | ||       ||   | |  ||| ||||| ||||    || |||||| | ||   ||  |   | ||||| ||| ||||||||||||||||||| || | |||||| || || || |||||||| || |||||| | || ||||| |||||||||||||||||||| || |||||||
gtgagctcaatatccatgttatatttccgattctcatcttcgtaggcacat-tatttatttaaatagatcacttcctactttggatttttgcactgttaaaatttggcatatg----gcgtgattc-ttatatgtgcccctgtgatttt-ttgtagGTGCGAGAATTAGTTCTGTCACGAGATCTTACACTCATCATTGAACCTGGGAGATCCCTCATAGCTAACACTTGCTGCTTCGTCAATAGGGTCACTGGTG
















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|76928256|gb|DV171541.1|DV171541
EST:     ACCATCATACCGATGCAGTCTTACCTACACCTATGGATCTCATCACCACT                         GTGCGAGAATTAGTTCTCTCTCAAGATCTCACTCTTATTATTGAACCCGGA
genomic: ACCATCATACCGATGCAGTCTTACCTACACCTATGGATCTCATCAACACTgtaagctcaa ... tttgttgcagGTGCGAGAATTAGTTCTCTCTCAAGATCTCACTCTTATTATTGAACCCGGA
EST: gi|20208183|gb|BQ134272.1|BQ134272
EST:     ACCATCATACCGATGCAGTATTACCTACACCTATGGATCTCATCAACACT                         GTGCGAGAATTAGTTCTCTCTCAAGATCTCACTCTTATTATTGAACCCGGA
genomic: ACCATCATACCGATGCAGTCTTACCTACACCTATGGATCTCATCAACACTgtaagctcaa ... tttgttgcagGTGCGAGAATTAGTTCTCTCTCAAGATCTCACTCTTATTATTGAACCCGGA
EST: gi|211042194|gb|FL157904.1|FL157904
EST:     ACCATCATACCGATGCAGTATTACCTACACCTATGGATCTCATCAACACT                         GTGCGAGAATTAGTTCTCTCTCAAGATCTCACTCTTATTATTGAACCCGGA
genomic: ACCATCATACCGATGCAGTCTTACCTACACCTATGGATCTCATCAACACTgtaagctcaa ... tttgttgcagGTGCGAGAATTAGTTCTCTCTCAAGATCTCACTCTTATTATTGAACCCGGA
EST: gi|6994122|gb|AW453336.1|AW453336
EST:     ACCATCATACCGATGCAGTATTACCTACACCTATGGATCTCATCAACACT                         GTGCGAGAATTAGT-CTCTCTCAAGATCTCACTCTTATTATTGAACCCGGA
genomic: ACCATCATACCGATGCAGTCTTACCTACACCTATGGATCTCATCAACACTgtaagctcaa ... tttgttgcagGTGCGAGAATTAGTTCTCTCTCAAGATCTCACTCTTATTATTGAACCCGGA
EST: gi|211042195|gb|FL157905.1|FL157905
EST:     ACCATCATACCGATGCAGTCTTACCTACACCTATGGATCTCATCAACACT                         GTACGAGAATTAGTTCTCTCTCAAGATCTTACTCTTATTATTGAACCTGGA
genomic: ACCATCATACCGATGCAGTCTTACCTACACCTATGGATCTCATCAACACTgtaagctcaa ... tttgttgcagGTGCGAGAATTAGTTCTCTCTCAAGATCTCACTCTTATTATTGAACCCGGA
EST: gi|211076903|gb|FL402120.1|FL402120
EST:     ACCATCATACCAATGCAGTCTTACCTACACCTATGGATCTCATCAACACT                         GTGCGAGAATTAGTTCTCTCTCAAGATCTCACTCTTATTATTGAACCCGGA
genomic: ACCATCATACCGATGCAGTCTTACCTACACCTATGGATCTCATCAACACTgtaagctcaa ... tttgttgcagGTGCGAGAATTAGTTCTCTCTCAAGATCTCACTCTTATTATTGAACCCGGA
EST: gi|148934358|gb|EC878387.2|EC878387
EST:     ACCATCATACCGATGCAGTCTTACCTACACCTATGGATCTCATCAACACT                         GTGCGAGAATTAGTTCTCTCTCAAGATCTCACTCTTATTATTGAACCCGGA
genomic: ACCATCATACCGATGCAGTCTTACCTACACCTATGGATCTCATCAACACTgtaagctcaa ... tttgttgcagGTGCGAGAATTAGTTCTCTCTCAAGATCTCACTCTTATTATTGAACCCGGA
EST: gi|211452559|gb|FL415488.1|FL415488
EST:     ACCATCATACCAATGCAGTCTTACCTACACCTATGGATCTCATCAACACT                         GTGCGAGAATTAGTTCTCTCTCAAGATCTCACTCTTATTATTGAACCCGGA
genomic: ACCATCATACCGATGCAGTCTTACCTACACCTATGGATCTCATCAACACTgtaagctcaa ... tttgttgcagGTGCGAGAATTAGTTCTCTCTCAAGATCTCACTCTTATTATTGAACCCGGA
EST: gi|211108459|gb|FL406876.1|FL406876
EST:     ACCATCATACCGATGCAGTATTACCTACACCTATGGATCTCATCAACACT                         GTGCGAGAATTAGTTCTCTCTCAAGATCTCACTCTTATTATTGAACCCGGA
genomic: ACCATCATACCGATGCAGTCTTACCTACACCTATGGATCTCATCAACACTgtaagctcaa ... tttgttgcagGTGCGAGAATTAGTTCTCTCTCAAGATCTCACTCTTATTATTGAACCCGGA

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: 223

AGGTTTTAAGTTGGAGTACCTGAATATCGGAGGTGGTTTGGGAATAGATTACCATCATACCGATGCAGTCTTACCTACACCTATGGATCTCATCAACACTgtaagctcaa ... tttgttgcagGTGCGAGAATTAGTTCTCTCTCAAGATCTCACTCTTATTATTGAACCCGGAAGATCCTTGATTGCTAATACTTGCTGCTTCGTCAATAGAGTAACTGGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 130

AGGTTTTAAGTTGGAGTACCTGAATATCGGAGGTGGTTTGGGAATAGATTACCATCATACCGATGCAGTCTTACCTACACCTATGGATCTCATCAACACTgtaagctcaa ... tttgttgcagGTGCGAGAATTAGTTCTCTCTCAAGATCTCACTCTTATTATTGAACCCGGAAGATCCTTGATTGCTAATACTTGCTGCTTCGTCAATAGAGTAACTGGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 153

AGGTTTTAAGTTGGAGTACCTGAATATCGGAGGTGGTTTGGGAATAGATTACCATCATACCGATGCAGTCTTACCTACACCTATGGATCTCATCAACACTgtaagctcaa ... tttgttgcagGTGCGAGAATTAGTTCTCTCTCAAGATCTCACTCTTATTATTGAACCCGGAAGATCCTTGATTGCTAATACTTGCTGCTTCGTCAATAGAGTAACTGGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 136

AGGTTTTAAGTTGGAGTACCTGAATATCGGAGGTGGTTTGGGAATAGATTACCATCATACCGATGCAGTCTTACCTACACCTATGGATCTCATCAACACTgtaagctcaa ... tttgttgcagGTGCGAGAATTAGTTCTCTCTCAAGATCTCACTCTTATTATTGAACCCGGAAGATCCTTGATTGCTAATACTTGCTGCTTCGTCAATAGAGTAACTGGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttggcttatgctgagcttgattcatcatgcttgttctatttattttgttgcagGTGCGAGAATTAGTTCTCTCTCAAGATCTCACTCTTATTATTGAACCCGGAAGATCCTTGATTGCTAATACTTGCTGCTTCGTCAATAGAGTAACTGGTG
                gcttgat  putative branch site (score: 136)
                                        tttatttt  putative PPT
                                ttgttctatttatttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctcaacattcttaccatgtttctgactcatatctttgcaggcgcacatgcatctttaaaataccagttttccttaatgtgatatggaaagttggcttatgctgagcttgattcatcatgcttgttctatttattttgttgcagGTGCGAGAATTAGTTCTCTCTCAAGATCTCACTCTTATTATTGAACCCGGAAGATCCTTGATTGCTAATACTTGCTGCTTCGTCAATAGAGTAACTGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT