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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgtttttcttatcctcttgtgtgcttccttttgttgaatagttgattgcatataatgaagtatggaatttccctgttatattaacatggaccataatcatcagGCAAGTCCACGGATACGCTTCAACAAGGAGGGAACTCTATTGGCTGTCTCCACTGCTGACAATGGTATCAAGATCTTAGCAAATGCTGATGGACTTCGGT

Basic information

species Zea mays
transcript GRMZM2G030422_T01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030422_T02 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os03g14980.2 (Oryza sativa), 3'ss of exon 15
gtgagttgtttttcttatcctcttgtgtgcttccttttgttgaatagttgattgcatataatgaagtatggaatttccctgttatattaacatggaccataatcatcagGCAAGTCCACGGATACGCTTCAACAAGGAGGGAACTCTATTGGCTGTCTCCACTGCTGACAATGGTATCAAGATCTTAGCAAATGCTGATGGACTTCGGT
||||||  |||   |||||      |    |      || ||| | ||| |    ||  |||||   | | ||||||| | |||   |||| | |     ||| || |||||||||||||| | || ||||||||||| || |||||  ||||||| || ||   ||| ||||||||||||||||||||||||||||||||| | ||||
gtgagtgttttcctttatctgtagatactttggtaaatggtgattggttcaa---atgaaatgagtaaggaaatttccatcttaatctaacctagcatgcaattattagGCAAGTCCACGGGTCCGATTCAACAAGGAAGGTACTCTGCTGGCTGTTTCTACCCATGAAAATGGTATCAAGATCTTAGCAAATGCTGATGGAGTACGGT
















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|211268556|gb|FL032964.1|FL032964
EST:     TGGACAGCACGGGTCTTCTGACTACCATTGATGCTGATGGTGGCTTAACT                         GCAAGTCCACGGATACGCTTCAACAAGGAGGGAACTCTATTGGCTGTCTCC
genomic: TGGACAGCACGGGTCTTCTGACTACCATTGATGCTGATGGTGGCTTAACTgtgagttgtt ... taatcatcagGCAAGTCCACGGATACGCTTCAACAAGGAGGGAACTCTATTGGCTGTCTCC
EST: gi|22490238|gb|BU050161.1|BU050161
EST:     TGGACAGCACGGGTCTTCTGACTACCATTGATGCTGATGGTGGCTTAACT                         GCAAGTCCACGGATACGCTTCAACAAGGAGGGAACTCTATTGGCTGTCTCC
genomic: TGGACAGCACGGGTCTTCTGACTACCATTGATGCTGATGGTGGCTTAACTgtgagttgtt ... taatcatcagGCAAGTCCACGGATACGCTTCAACAAGGAGGGAACTCTATTGGCTGTCTCC
EST: gi|211270985|gb|FL032966.1|FL032966
EST:     TGGACAGCACGGGTCTTCTGACTACCATTGATGCTGATGGTGGCTTAACT                         GCAAGTCCACGGATACGCTTCAACAAGGAGGGAACTCTATTGGCTGTCTCC
genomic: TGGACAGCACGGGTCTTCTGACTACCATTGATGCTGATGGTGGCTTAACTgtgagttgtt ... taatcatcagGCAAGTCCACGGATACGCTTCAACAAGGAGGGAACTCTATTGGCTGTCTCC
EST: gi|31360139|gb|CD444496.1|CD444496
EST:     TGGACGGGGCGGGTCTTCTGACTACCATTGATGCTGATGGTGGCTTAACT                         GCAAGTCCACGGATACGCTTCAACAAGGAGGGAACTCTATTGGCTGTCTCC
genomic: TGGACAGCACGGGTCTTCTGACTACCATTGATGCTGATGGTGGCTTAACTgtgagttgtt ... taatcatcagGCAAGTCCACGGATACGCTTCAACAAGGAGGGAACTCTATTGGCTGTCTCC
EST: gi|87152395|gb|DY397184.1|DY397184
EST:     TGGACAGCACGGGTCTTCTGACTACCATTGATGCTGATGGTGGCTTAACT                         GCAAGTCCACGGATACGCTTCAACAAGGAGGGAACTCTATTGGCTGTCTCC
genomic: TGGACAGCACGGGTCTTCTGACTACCATTGATGCTGATGGTGGCTTAACTgtgagttgtt ... taatcatcagGCAAGTCCACGGATACGCTTCAACAAGGAGGGAACTCTATTGGCTGTCTCC
EST: gi|211270984|gb|FL032965.1|FL032965
EST:     TGGACAGCACGGGTCTTCTGACTACCATTGATGCTGATGGTGGCTTAACT                         GCAAGTCCACGGATACGCTTCAACAAGGAGGGAACTCTATTGGCTGTCTCC
genomic: TGGACAGCACGGGTCTTCTGACTACCATTGATGCTGATGGTGGCTTAACTgtgagttgtt ... taatcatcagGCAAGTCCACGGATACGCTTCAACAAGGAGGGAACTCTATTGGCTGTCTCC
EST: gi|31356149|gb|CD440506.1|CD440506
EST:     TGGACAGCACGGGTCTTCTGACTACCATTGATGCTGATGGTGGCTTAACT                         GCAAGTCCACGGATACGCTTCAACAAGGAGGGAACTCTATTGGCTGTCTCC
genomic: TGGACAGCACGGGTCTTCTGACTACCATTGATGCTGATGGTGGCTTAACTgtgagttgtt ... taatcatcagGCAAGTCCACGGATACGCTTCAACAAGGAGGGAACTCTATTGGCTGTCTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catataatgaagtatggaatttccctgttatattaacatggaccataatcatcagGCAAGTCCACGGATACGCTTCAACAAGGAGGGAACTCTATTGGCTGTCTCCACTGCTGACAATGGTATCAAGATCTTAGCAAATGCTGATGGACTTCGGT
                              tattaac  putative branch site (score: 1)
                         tgttatattaacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttgtttttcttatcctcttgtgtgcttccttttgttgaatagttgattgcatataatgaagtatggaatttccctgttatattaacatggaccataatcatcagGCAAGTCCACGGATACGCTTCAACAAGGAGGGAACTCTATTGGCTGTCTCCACTGCTGACAATGGTATCAAGATCTTAGCAAATGCTGATGGACTTCGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA