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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgatacggtttgaccacctatttcatccattctcgttgtttttccggttttgattttgatgggatttgtttgtttttgccgaagGCTCTCGGTGAGGAAGACCAAGGTTGAGAAGGACCCAAACAAGCCCAAGAGGCCTCCGACCGCGTTCTTCGTCTTCAT

Basic information

species Zea mays
transcript GRMZM2G162284_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G162284_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os09g37910.3 (Oryza sativa), 3'ss of exon 1
-------------------gtacgatacggtttgaccacctatttcatccattctcgttgtttttccggttttgattttgatgggatttgtttgtttttgccgaagGCTCTCGGTGAGGAAGACCAAGGTTGAGAAGGACCCAAACAAGCCCAAGAGGCCTCCGACCGCGTTCTTCGTCTTCAT
                    |  | |   | | |        ||   | | || | ||||  ||   ||||||||||| |  ||  |||  | || |||   |||||||||||||||||||||||||||  ||||||||||| |||||||| |||||||| |||| |||||||||||| |||||
gtgagttttgttggtggttttgtgcttgtgctcgcgggtggtttcggttcgttttggttgggttg--ggttttgatttgg--ggttttttgtggtgtttcgtgaagGCTCTCGGTGAGGAAGACCAAGGCGGAGAAGGACCCGAACAAGCCGAAGAGGCCACCGAGCGCGTTCTTCGTGTTCAT
















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|22472639|gb|BU037119.1|BU037119
EST:     GGCGACTCCAG                         GCTCTCGGTGAGGAAGACCAAGGTTGAGAAGGACCCAAACAAGCCCAAGAG
genomic: GGCGACTCCAGgtacgatacg ... tttgccgaagGCTCTCGGTGAGGAAGACCAAGGTTGAGAAGGACCCAAACAAGCCCAAGAG
EST: gi|31359518|gb|CD443875.1|CD443875
EST:     GATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG                         GCTCTCGGTGAGGAAGACCAAGGTTGAGAAGGACCCAAACAAGCCCAAGAG
genomic: GATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAGgtacgatacg ... tttgccgaagGCTCTCGGTGAGGAAGACCAAGGTTGAGAAGGACCCAAACAAGCCCAAGAG
EST: gi|211010350|gb|FL233636.1|FL233636
EST:     GTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG                         GCTCTCGGTGAGGAAGACCAAGGTTGAGAAGGACCCAAACAAGCCCAAGAG
genomic: GTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAGgtacgatacg ... tttgccgaagGCTCTCGGTGAGGAAGACCAAGGTTGAGAAGGACCCAAACAAGCCCAAGAG
EST: gi|14203924|gb|BG837601.1|BG837601
EST:     GTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG                         GCTCTCGGTGAGGAAGACCAAGGTTGAGAAGGACCCAAACAAGCCCAAGAG
genomic: GTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAGgtacgatacg ... tttgccgaagGCTCTCGGTGAGGAAGACCAAGGTTGAGAAGGACCCAAACAAGCCCAAGAG
EST: gi|26558436|gb|CA830671.1|CA830671
EST:     TCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG                         GCTCTCGGTGAGGAAGACCAAGGTTGAGAAGGACCCAAACAAGCCCAAGAG
genomic: TCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAGgtacgatacg ... tttgccgaagGCTCTCGGTGAGGAAGACCAAGGTTGAGAAGGACCCAAACAAGCCCAAGAG
EST: gi|21891488|gb|BQ744701.1|BQ744701
EST:     TCCGGCGGTGGCGACTCCAG                         GCTCTCGGTGAGGAAGACCAAGGTTGAGAAGGACCCAAACAAGCCCAAGAG
genomic: TCCGGCGGTGGCGACTCCAGgtacgatacg ... tttgccgaagGCTCTCGGTGAGGAAGACCAAGGTTGAGAAGGACCCAAACAAGCCCAAGAG
EST: gi|211010348|gb|FL233634.1|FL233634
EST:     GTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG                         GCTCTCGGTGAGGAAGACCAAGGTTGAGAAGGACCCAAACAAGCCCAAGAG
genomic: GTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAGgtacgatacg ... tttgccgaagGCTCTCGGTGAGGAAGACCAAGGTTGAGAAGGACCCAAACAAGCCCAAGAG
EST: gi|211010355|gb|FL233641.1|FL233641
EST:     GTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG                         GCTCTCGGTGAGGAAGACCAAGGTTGAGAAGGACCCAAACAAGCCCAAGAG
genomic: GTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAGgtacgatacg ... tttgccgaagGCTCTCGGTGAGGAAGACCAAGGTTGAGAAGGACCCAAACAAGCCCAAGAG
EST: gi|71436984|gb|DR818034.1|DR818034
EST:     GTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG                         GCTCTCGGTGAGGAAGACCAAGGTTGAGAAGGACCCAAACAAGCCCAAGAG
genomic: GTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAGgtacgatacg ... tttgccgaagGCTCTCGGTGAGGAAGACCAAGGTTGAGAAGGACCCAAACAAGCCCAAGAG
EST: gi|211010351|gb|FL233637.1|FL233637
EST:     GTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG                         GCTCTCGGTGAGGAAGACCAAGGTTGAGAAGGACCCAAACAAGCCCAAGAG
genomic: GTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAGgtacgatacg ... tttgccgaagGCTCTCGGTGAGGAAGACCAAGGTTGAGAAGGACCCAAACAAGCCCAAGAG
EST: gi|211010356|gb|FL233642.1|FL233642
EST:     GTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG                         GCTCTCGGTGAGGAAGACCAAGGTTGAGAAGGACCCAAACAAGCCCAAGAG
genomic: GTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAGgtacgatacg ... tttgccgaagGCTCTCGGTGAGGAAGACCAAGGTTGAGAAGGACCCAAACAAGCCCAAGAG
EST: gi|78112438|gb|DV530832.1|DV530832
EST:     GTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG                         GCTCTCGGTGAGGAAGACCAAGGTTGAGAAGGACCCAAACAAGCCCAAGAG
genomic: GTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAGgtacgatacg ... tttgccgaagGCTCTCGGTGAGGAAGACCAAGGTTGAGAAGGACCCAAACAAGCCCAAGAG
EST: gi|33100122|gb|CF060082.1|CF060082
EST:     GTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG                         GCCTCTCGGTGAGGAAGACCAAGGTTGAGAAGGACCCAAACAAGCCCAAGA
genomic: GTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAGgtacgatacg ... tttgccgaagG-CTCTCGGTGAGGAAGACCAAGGTTGAGAAGGACCCAAACAAGCCCAAGA
EST: gi|87155374|gb|DY400163.1|DY400163
EST:     GTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG                         GCTCTCGGTGAGGAAGACCAAGGTTGAGAAGGACCCAAACAAGCCCAAGAG
genomic: GTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAGgtacgatacg ... tttgccgaagGCTCTCGGTGAGGAAGACCAAGGTTGAGAAGGACCCAAACAAGCCCAAGAG
EST: gi|211010354|gb|FL233640.1|FL233640
EST:     GTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG                         GCTCTCGGTGAGGAAGACCAAGGTTGAGAAGGACCCAAACAAGCCCAAGAG
genomic: GTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAGgtacgatacg ... tttgccgaagGCTCTCGGTGAGGAAGACCAAGGTTGAGAAGGACCCAAACAAGCCCAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctcgttgtttttccggttttgattttgatgggatttgtttgtttttgccgaagGCTCTCGGTGAGGAAGACCAAGGTTGAGAAGGACCCAAACAAGCCCAAGAGGCCTCCGACCGCGTTCTTCGTCTTCAT
                        ttttgat  putative branch site (score: 4)
                                       tttgttttt  putative PPT
                                  atttgtttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgatacggtttgaccacctatttcatccattctcgttgtttttccggttttgattttgatgggatttgtttgtttttgccgaagGCTCTCGGTGAGGAAGACCAAGGTTGAGAAGGACCCAAACAAGCCCAAGAGGCCTCCGACCGCGTTCTTCGTCTTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG