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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaatttgctcgatggactctaaatgattagtaaacgttaggatgtttccataatcgttgatgtcttttcgtcttctaataatgcttcttttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGG

Basic information

species Zea mays
transcript GRMZM2G094978_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094978_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g36750.1 (Oryza sativa), 3'ss of exon 6
taaatttgctcgatggactctaaatgattagtaaacgttaggatgtttccataatcgttgatgtcttttc-gtcttctaataatgcttctttt--acatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGG
 ||  ||  ||||   |   |  ||  || ||||    ||  || |||    |    || ||   ||||| || | |||| |    || | ||  | ||  || ||||||||| |||||||||||||||||||||| ||||| || |||||||| || ||||||||||||||||||||||||||
-aagctttgtcgacatatgatgtat--tttgtaataaataccatttttatcaacagtttaatagtttttcagtttactaacaccttttttcttggatatttagTTGTGTTGTTGTTGAAGACAGTACTATAGGGCTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGG
















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|91056651|gb|EB167069.1|EB167069
EST:     GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG                         CTGTGTTGTTATTGAAGACAGAACTATAGG
genomic: GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGG
EST: gi|71448345|gb|DR829395.1|DR829395
EST:     GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG                         CTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
genomic: GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
EST: gi|71764323|gb|DR962260.1|DR962260
EST:     GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG                         CTGTGTTTGT-ATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTG
genomic: GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTT-GTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTG
EST: gi|211136606|gb|FL156037.1|FL156037
EST:     GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG                         CTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAAGCGGCAAAAGCTG
genomic: GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCA-GCGGCAAAAGCTG
EST: gi|149095606|gb|EE165515.2|EE165515
EST:     GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG                         CTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
genomic: GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
EST: gi|71300514|gb|DR786312.1|DR786312
EST:     GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG                         CTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGG
genomic: GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
EST: gi|71300530|gb|DR786320.1|DR786320
EST:     GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG                         CTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
genomic: GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
EST: gi|101382873|gb|EB813490.1|EB813490
EST:     GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG                         CTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
genomic: GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
EST: gi|50327117|gb|CO522243.1|CO522243
EST:     GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG                         CTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
genomic: GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
EST: gi|101388003|gb|EB816016.1|EB816016
EST:     GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG                         CTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
genomic: GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
EST: gi|71766392|gb|DR964329.1|DR964329
EST:     GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG                         CTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
genomic: GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttccataatcgttgatgtcttttcgtcttctaataatgcttcttttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGG
                            ttctaat  putative branch site (score: 2)
                                     tgcttctttt  putative PPT
                            ttctaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaatttgctcgatggactctaaatgattagtaaacgttaggatgtttccataatcgttgatgtcttttcgtcttctaataatgcttcttttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - -gatggac
- - - - - - - - - - - - - - - - - - - - - atgtttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttct