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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgcgatttggaaatctcaatcaaatccctgtgaattcgatgctgttggtgtgggttgttgctgatggttttattggatttggttcggtagGTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG

Basic information

species Zea mays
transcript GRMZM2G162284_T02
intron # 1
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 1
lower sequence: LOC_Os09g37910.1 (Oryza sativa), 3'ss of exon 1
-----------------------gtactgcgatttggaaatct---caatcaaatccctgtg--aattcga---tgc-tgttgg--tgtgggttgttgctgatggttttattggatttggttc------ggtagGTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG
                       | | |||   | | |  ||       |    |   ||||    ||||    ||  ||||||  | |||||||||| || ||||| |  | | ||| ||||      |||||| |||||||||||| ||||| |||||||| ||  ||||||||||||
gtaaatccatggctggctgcctcgaaatgctgctcgaatctccgcgtgttgggttgtttgtgttggttcgggagtgtgtgttgggttttgggttgttg-tgttggttctgatcggttttgttcttactcggtagGGCTCGAGATGAAGGCGAGGTCGAGGTCCAGCAATGGCGACTCCAG
















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|211010350|gb|FL233636.1|FL233636
EST:     CTCCCGTTTACGTGCACACCTCCAAACCCTCATCACGATCCGGCTCCAAG                         GTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG
genomic: CTCCCGTTTACGTGCACACCTCCAAACCCTCATCACGATCCGGCTCCAAGgtactgcgat ... ggttcggtagGTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG
EST: gi|14203924|gb|BG837601.1|BG837601
EST:     CTCCCGTTTACGTGCACACCTCCAAACCCTCATCACGATCCGGCTCCAAG                         GTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG
genomic: CTCCCGTTTACGTGCACACCTCCAAACCCTCATCACGATCCGGCTCCAAGgtactgcgat ... ggttcggtagGTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG
EST: gi|211010348|gb|FL233634.1|FL233634
EST:     TCCCGTTTACGTGCACACCTCCAAACCCTCATCACGATCCCGGCTCCAAG                         GTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG
genomic: TCCCGTTTACGTGCACACCTCCAAACCCTCATCACGAT-CCGGCTCCAAGgtactgcgat ... ggttcggtagGTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG
EST: gi|211010355|gb|FL233641.1|FL233641
EST:     CTCCCGTTTACGTGCACACCTCCAAACCCTCATCACGATCCGGCTCCAAG                         GTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG
genomic: CTCCCGTTTACGTGCACACCTCCAAACCCTCATCACGATCCGGCTCCAAGgtactgcgat ... ggttcggtagGTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG
EST: gi|71436984|gb|DR818034.1|DR818034
EST:     CCGTTTACGTGCACACCTCCAAACCCTCATCACGATCCGGCTCCAAG                         GTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG
genomic: CCGTTTACGTGCACACCTCCAAACCCTCATCACGATCCGGCTCCAAGgtactgcgat ... ggttcggtagGTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG
EST: gi|211010351|gb|FL233637.1|FL233637
EST:     CTCCCGTTTACGTGCACACCTCCAAACCCTCATCACGATCCGGCTCCAAG                         GTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG
genomic: CTCCCGTTTACGTGCACACCTCCAAACCCTCATCACGATCCGGCTCCAAGgtactgcgat ... ggttcggtagGTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG
EST: gi|211010356|gb|FL233642.1|FL233642
EST:     CTCCCGTTTACGGGCACACCTCCAAACCCTCATCACGATCCGGCTCCAAG                         GTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG
genomic: CTCCCGTTTACGTGCACACCTCCAAACCCTCATCACGATCCGGCTCCAAGgtactgcgat ... ggttcggtagGTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG
EST: gi|78112438|gb|DV530832.1|DV530832
EST:     CTCCCGTTTACGTGCACACCTCCAAACCCTCATCACGATCCGGCTCCAAG                         GTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG
genomic: CTCCCGTTTACGTGCACACCTCCAAACCCTCATCACGATCCGGCTCCAAGgtactgcgat ... ggttcggtagGTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG
EST: gi|33100122|gb|CF060082.1|CF060082
EST:     CACCTCCAAACCCTCATCACGATCCGGCTCCAAG                         GTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG
genomic: CACCTCCAAACCCTCATCACGATCCGGCTCCAAGgtactgcgat ... ggttcggtagGTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG
EST: gi|87155374|gb|DY400163.1|DY400163
EST:     CTCC-AACCCTCATCACGATCCGGCTCC-AG                         GTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG
genomic: CTCCAAACCCTCATCACGATCCGGCTCCAAGgtactgcgat ... ggttcggtagGTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG
EST: gi|211010354|gb|FL233640.1|FL233640
EST:     CTCCCGTTTACGGGCACACCTCCAAACCCTCATCACGATCCGGCTCCAAG                         GTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG
genomic: CTCCCGTTTACGTGCACACCTCCAAACCCTCATCACGATCCGGCTCCAAGgtactgcgat ... ggttcggtagGTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgatgctgttggtgtgggttgttgctgatggttttattggatttggttcggtagGTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG
                       tgctgat  putative branch site (score: 3)
                                ttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgcgatttggaaatctcaatcaaatccctgtgaattcgatgctgttggtgtgggttgttgctgatggttttattggatttggttcggtagGTCTCGAGATGAAGTCGAGGGCGAGGTCCGGCGGTGGCGACTCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG