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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatatatctgtgatcaatcaactgtggattcatattagtcgaaagtatgttctgtcaagcagatcctgatacaagttgctttatgctctgtagTGTTCAAGTGAAAGAGTTACAAAATCCAGATGACGTTTTTGACACAATTCTTGGTCTTATTGTTCGTTTGGCAGAGCATGGACTGATACATTGTGACTTT

Basic information

species Zea mays
transcript GRMZM2G472991_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G472991_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g66520.1 (Oryza sativa), 3'ss of exon 6
gtaagcatatatctgtgatcaatcaactgtggattcatattagtcgaaagtatgttctgtcaagcagatcctgat-acaagttgctttatgctctgtagTGTTCAAGTGAAAGAGTTACAAAATCCAGATGACGTTTTTGACACAATTCTTGGTCTTATTGTTCGTTTGGCAGAGCATGGACTGATACATTGTGACTTT
         ||  ||  |||| | | |  |   ||  |||   |      |  |||   | | ||||    |||| |   |    |||    | | ||| |||||||| |||||||||||||||||||| || |||||||||||||||||||| ||| ||||||||||||| |||||||| |||||||||||||| |||
--------gtaagtgacatca-ttatcattaagttactatc--taaggtttgagtttctttaggcaggaattgatcaagtgccatttttccttatatagCGTTCAAGTAAAAGAGTTACAAAATCCAGACGATGTTTTTGACACAATTCTTGGCCTTGTTGTTCGTTTGGCGGAGCATGGGCTGATACATTGTGATTTT

upper sequence: GRMZM2G472991_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT3G51270.2 (Arabidopsis thaliana), 3'ss of exon 7
-------gtaagcatatatctgtgatcaatcaactgtggattcatattagtcgaaagtatgtt-ctgtcaagcagatcctgatacaagttgctttatgctctgtagTGTTCAAGTGAAAGAGTTACAAAATCCAGATGACGTTTTTGACACAATTCTTGGTCTTATTGTTCGTTTGGCAGAGCATGGACTGATACATTGTGACTTT
       | ||||  |    | || |  |   |||     |    |  |||   |    |  | |||| || || ||| |   |||  || | ||    | || || ||||| |||||  | ||||| || || ||     |||| || |  ||  ||||| || ||||||||||||| |||||||| || || ||||||||||| 
tttctaagaaagctaaaccatttgcttcactcact--cactaagaaacagttacaccctttctgctgtgaatcacatcttttcacatttttcatt----tatgcagGGTTCAGGTGAAGCAATTACAGAACCCTGAGACAATTTTCGAGAAGATCATTGGTATTGTTGTTCGTTTGGCTGAGCATGGTCTAATTCATTGTGACTTC

upper sequence: GRMZM2G472991_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv05s0094g01560.t01 (Vitis vinifera), 3'ss of exon 6
gtaagcatatatctgtgatcaatcaactgtggattcatattagtcgaaagtatgttctgtcaagc-agatcctgatacaagtt--------gctttatgctctgtagTGTTCAAGTGAAAGAGTTACAAAATCCAGATGACGTTTTTGACACAATTCTTGGTCTTATTGTTCGTTTGGCAGAGCATGGACTGATACATTGTGACTTT
       | | ||  |    |||   || ||   | | || |||   ||||   | |||  |    |     | |||||  ||        | | ||| |  || ||||| || |||||  | || |||||||| ||    |||||||| |||||| |||||||| |||||| | ||||||| ||||| || || ||||||||||| 
-----tttctgtccttttggaattggctttgatataaaatgagt--gaagttgatcctgatagattatggttttatacacattaacaatcagttctatccaatgcagTGTGCAGGTGAAGCAATTGCAAAATCCTGACATAGTTTTTGAAACAATTATTGGTCTTGTTGTTCATCTGGCAGAACATGGCCTTATTCATTGTGACTTC

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|33094905|gb|CF054899.1|CF054899
EST:     GATTGCAATCGCCATTGTGTGATCATGTCACTTGTGCAGGGATATCCTCT                         TGTTCAAGTGAAAGAGTTACAAAATCCAGATGACGTTTTTGACACAATTCT
genomic: GATTGCAATCGCCATTGTGTGATCATGTCACTTGTGCAGGGATATCCTCTgtaagcatat ... tgctctgtagTGTTCAAGTGAAAGAGTTACAAAATCCAGATGACGTTTTTGACACAATTCT
EST: gi|71429251|gb|DR810301.1|DR810301
EST:     GATTGCAATCGCCATTGTGTGATCATGTCACTTGTGCAGGGATATCCTCT                         TGTTCAAGTGAAAGAGTTACAAAATCCAGATGACG
genomic: GATTGCAATCGCCATTGTGTGATCATGTCACTTGTGCAGGGATATCCTCTgtaagcatat ... tgctctgtagTGTTCAAGTGAAAGAGTTACAAAATCCAGATGACG
EST: gi|93016530|gb|EB642050.1|EB642050
EST:     GATTGCAATCGCCATTGTGTGATCATGTCACTTGTGCAGGGATATCCTCT                         TGTTCAAGTGAAAGAGTTACAAAATCCAGATGACGTTTTTGACACAATTCT
genomic: GATTGCAATCGCCATTGTGTGATCATGTCACTTGTGCAGGGATATCCTCTgtaagcatat ... tgctctgtagTGTTCAAGTGAAAGAGTTACAAAATCCAGATGACGTTTTTGACACAATTCT
EST: gi|33095027|gb|CF055021.1|CF055021
EST:     GATTGCAATCGCCATTGTGTGATCATGTCACTTGTGCAGGGATATCCTCT                         TGTTCAAGTGAAAGAGTTACAAAATCCAGATGACGTTTTTGACACAATTCT
genomic: GATTGCAATCGCCATTGTGTGATCATGTCACTTGTGCAGGGATATCCTCTgtaagcatat ... tgctctgtagTGTTCAAGTGAAAGAGTTACAAAATCCAGATGACGTTTTTGACACAATTCT
EST: gi|26456479|gb|CA828062.1|CA828062
EST:     GATTGCAATCGCCATTGTGTGATCATGTCACTTGTGCAGGGATATCCTCT                         TGTTCAAGTGAAAGAGTTACAAAATCCAGATGACGTTTTTGACACAATTCT
genomic: GATTGCAATCGCCATTGTGTGATCATGTCACTTGTGCAGGGATATCCTCTgtaagcatat ... tgctctgtagTGTTCAAGTGAAAGAGTTACAAAATCCAGATGACGTTTTTGACACAATTCT
EST: gi|20301471|gb|BQ164414.1|BQ164414
EST:     GATTGCAATCGCCATTGTGTGATCATGTCACTTGTGCAGGGATATCCTCT                         TGTTCAAGTGAAAGAGTTACAAAATCCAGATGACGTTTTTGACACAATTCT
genomic: GATTGCAATCGCCATTGTGTGATCATGTCACTTGTGCAGGGATATCCTCTgtaagcatat ... tgctctgtagTGTTCAAGTGAAAGAGTTACAAAATCCAGATGACGTTTTTGACACAATTCT
EST: gi|78112924|gb|DV531318.1|DV531318
EST:     GATTGCAATCGCCATTGTGTGATCATGTCACTTGTGCAGGGATATCCTCT                         TGTTCAAGTGAAAGAGTTACAAAATCCAGATGACGTTTTTGACACAATTCT
genomic: GATTGCAATCGCCATTGTGTGATCATGTCACTTGTGCAGGGATATCCTCTgtaagcatat ... tgctctgtagTGTTCAAGTGAAAGAGTTACAAAATCCAGATGACGTTTTTGACACAATTCT
EST: gi|76014835|gb|DT942005.1|DT942005
EST:     GATTGCAATCGCCATTGTGTGATCATGTCACTTGTGCAGGGATATCCTCT                         TTTGTTCA-GTGAA-GAGTTACAAAATCCAGATGACGTTTTTGACACAATT
genomic: GATTGCAATCGCCATTGTGTGATCATGTCACTTGTGCAGGGATATCCTCTgtaagcatat ... tgctctgtagT--GTTCAAGTGAAAGAGTTACAAAATCCAGATGACGTTTTTGACACAATT
EST: gi|78120952|gb|DV539336.1|DV539336
EST:     GATTGCAATCGCCATTGTGTGATCATGTCACTTGTGCAGGGATATCCTCT                         TGTTCAAGTGAGAGAGTTACAAAATCC
genomic: GATTGCAATCGCCATTGTGTGATCATGTCACTTGTGCAGGGATATCCTCTgtaagcatat ... tgctctgtagTGTTCAAGTGAAAGAGTTACAAAATCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgaaagtatgttctgtcaagcagatcctgatacaagttgctttatgctctgtagTGTTCAAGTGAAAGAGTTACAAAATCCAGATGACGTTTTTGACACAATTCTTGGTCTTATTGTTCGTTTGGCAGAGCATGGACTGATACATTGTGACTTT
                         tcctgat  putative branch site (score: 3)
                                         tttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcatatatctgtgatcaatcaactgtggattcatattagtcgaaagtatgttctgtcaagcagatcctgatacaagttgctttatgctctgtagTGTTCAAGTGAAAGAGTTACAAAATCCAGATGACGTTTTTGACACAATTCTTGGTCTTATTGTTCGTTTGGCAGAGCATGGACTGATACATTGTGACTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA