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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACTgtatgattctgactccctttcttttgtgtgtggttttgttgatccagcgacgcagatcttgaaacgttactacaccctatattttctgtgctattttaga...

Basic information

species Zea mays
transcript GRMZM2G044348_T04
intron # 5
splice site 5'
intron type U2

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|149012865|gb|EE042709.2|EE042709
EST:     AAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACT                         CACTCTCGGTGGAGTTCACAAAGTCCCAGATTATTGCCTCAATACCTGGAT
genomic: AAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACTgtatgattct ... gtttattcagCACTCTCGGTGGAGTTCACAAAGTCCCAGATTATTGCCTCAATACCTGGAT
EST: gi|211345313|gb|FL467149.1|FL467149
EST:     AAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACT                         CACTCTCGGTGGAGTTCACAAAGTCCCAGATTGTTGCCTCAATACCTGGAT
genomic: AAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACTgtatgattct ... gtttattcagCACTCTCGGTGGAGTTCACAAAGTCCCAGATTATTGCCTCAATACCTGGAT
EST: gi|71435689|gb|DR816739.1|DR816739
EST:     AAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACT                         CACTCTCGGTGGAGTTCACAAAGTCCCAGATTATTGCCTCAATACCTGGAT
genomic: AAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACTgtatgattct ... gtttattcagCACTCTCGGTGGAGTTCACAAAGTCCCAGATTATTGCCTCAATACCTGGAT
EST: gi|148948442|gb|EC893960.2|EC893960
EST:     AAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACT                         CACTCTCGGTGGAGTTCACAAAGTCCCAGATTATTGCCTCAATACCTGGAT
genomic: AAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACTgtatgattct ... gtttattcagCACTCTCGGTGGAGTTCACAAAGTCCCAGATTATTGCCTCAATACCTGGAT
EST: gi|149027788|gb|EE286084.2|EE286084
EST:     AAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACT                         CACTCTCGGTGGAGTTCACAAAGTCCCAGATTATTGCCT
genomic: AAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACTgtatgattct ... gtttattcagCACTCTCGGTGGAGTTCACAAAGTCCCAGATTATTGCCT
EST: gi|148991460|gb|EE032969.2|EE032969
EST:     CAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCCTTCTTCCACT                         CACTCTCGGTGGAGTTCACAAAGTCCCAGATTATTGCCTCAATACCTGGAT
genomic: AAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACTgtatgattct ... gtttattcagCACTCTCGGTGGAGTTCACAAAGTCCCAGATTATTGCCTCAATACCTGGAT
EST: gi|148948218|gb|EC893734.2|EC893734
EST:     AAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACT                         CACTCTCGGTGGAGTTCACAAAGTCCCAGATTATTGCCTCAATACCTGGAT
genomic: AAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACTgtatgattct ... gtttattcagCACTCTCGGTGGAGTTCACAAAGTCCCAGATTATTGCCTCAATACCTGGAT
EST: gi|91875915|gb|EB405872.1|EB405872
EST:     AAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACT                         CACTCTCGGTGGAGTTCACAAAGTCCCAGATTATTGCCTCAATACCTGGAT
genomic: AAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACTgtatgattct ... gtttattcagCACTCTCGGTGGAGTTCACAAAGTCCCAGATTATTGCCTCAATACCTGGAT
EST: gi|149097124|gb|EE182936.2|EE182936
EST:     AAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACT                         CACTCTCGGTGGAGTTCACAAAGTCCCAGATTATTGCCTNCA-TACCTGGA
genomic: AAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACTgtatgattct ... gtttattcagCACTCTCGGTGGAGTTCACAAAGTCCCAGATTATTGCCT-CAATACCTGGA
EST: gi|166541555|gb|EG203293.1|EG203293
EST:     CGTCTGGCGGGCTCCATTCTTCCACT                         CACTCTCGGTGGAGTTCACAAAGTCCCAGATTGTTGCCTCAATACCTGGAT
genomic: CGTCTGGCGGGCTCCATTCTTCCACTgtatgattct ... gtttattcagCACTCTCGGTGGAGTTCACAAAGTCCCAGATTATTGCCTCAATACCTGGAT
EST: gi|149001048|gb|EE038297.2|EE038297
EST:     AAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACT                         CACTCTCGGTGGAGTTCACAAAGTCCCAGATTATTGCCTCAATACCTGGAT
genomic: AAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACTgtatgattct ... gtttattcagCACTCTCGGTGGAGTTCACAAAGTCCCAGATTATTGCCTCAATACCTGGAT
EST: gi|149100817|gb|EE186911.2|EE186911
EST:     AAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACT                         CACTCTCGGTGGAGTTCACAAAGTCCCAGATTATTGCCTCAATACCTGGAT
genomic: AAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACTgtatgattct ... gtttattcagCACTCTCGGTGGAGTTCACAAAGTCCCAGATTATTGCCTCAATACCTGGAT
EST: gi|78088713|gb|DV517106.1|DV517106
EST:     AAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACT                         CACTCTCGGTGGAGTTCACAAAGTCCCAGATTATTGCCTCAATACCTGGAT
genomic: AAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACTgtatgattct ... gtttattcagCACTCTCGGTGGAGTTCACAAAGTCCCAGATTATTGCCTCAATACCTGGAT
EST: gi|149067509|gb|EE157716.2|EE157716
EST:     AAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACT                         CACTCTCGGTGGAGTTCACAAAGTCCCAGATTATTGCCTCAATACCTGGAT
genomic: AAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACTgtatgattct ... gtttattcagCACTCTCGGTGGAGTTCACAAAGTCCCAGATTATTGCCTCAATACCTGGAT
EST: gi|148976595|gb|EE025942.2|EE025942
EST:     AAAAGAGTGGAATGATAATCTCATCGTCTGGGGGGCTCCATTCTTCCACT                         CACTCTCGGTGGAGTTCACAAAGTCCCAGATTATT
genomic: AAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACTgtatgattct ... gtttattcagCACTCTCGGTGGAGTTCACAAAGTCCCAGATTATT
EST: gi|31360319|gb|CD444676.1|CD444676
EST:     AAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACT                         CACTCTCGGGGGAGTTCACAAAGTCCCAGATTGTTGCCTCAATACCTGGAT
genomic: AAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACTgtatgattct ... gtttattcagCACTCTCGGTGGAGTTCACAAAGTCCCAGATTATTGCCTCAATACCTGGAT
EST: gi|148943973|gb|EC889054.2|EC889054
EST:     AAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACT                         CACTCTCGGTGGAGTTCACAAAGTCCCAGATTATTGCCTCAATACCTGGAT
genomic: AAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACTgtatgattct ... gtttattcagCACTCTCGGTGGAGTTCACAAAGTCCCAGATTATTGCCTCAATACCTGGAT
EST: gi|148930101|gb|EC872413.2|EC872413
EST:     AAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACT                         CACTCTCGGTGGAGTTCACAAAGTCCCAGATTATTGCCTCAATACCTGGAT
genomic: AAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACTgtatgattct ... gtttattcagCACTCTCGGTGGAGTTCACAAAGTCCCAGATTATTGCCTCAATACCTGGAT

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: 42 (upstream exon), 49 (downstream exon)
Score: 215

CGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACTgtatgattct ... gtttattcagCACTCTCGGTGGAGTTCACAAAGTCCCAGATTATTGCCTCAATACCTGGATTTTTCTTTTGCTTGTGGTATGCGTCAAAGAAGCATTGGCTTGCAAACAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 227

CGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACTgtatgattct ... gtttattcagCACTCTCGGTGGAGTTCACAAAGTCCCAGATTATTGCCTCAATACCTGGATTTTTCTTTTGCTTGTGGTATGCGTCAAAGAAGCATTGGCTTGCAAACAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 285

CGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACTgtatgattct ... gtttattcagCACTCTCGGTGGAGTTCACAAAGTCCCAGATTATTGCCTCAATACCTGGATTTTTCTTTTGCTTGTGGTATGCGTCAAAGAAGCATTGGCTTGCAAACAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 324

CGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACTgtatgattct ... gtttattcagCACTCTCGGTGGAGTTCACAAAGTCCCAGATTATTGCCTCAATACCTGGATTTTTCTTTTGCTTGTGGTATGCGTCAAAGAAGCATTGGCTTGCAAACAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACTgtatgattctgactccctttcttttgtgtgtggttttgttgatccagcgacgcagatcttgaaacgttactacaccctatattttctgtgctattttaga

- - - - - - - - - - - - - - - - - - - -  AGTGGA