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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgctctgctgttgaacaaaatctaccacgtgcattccttttctactgcagctggtcatatctgttcgtataacctatgcctaaacaactaagctttaatcttacaccttttattctatagaatgcactatcctgagacaaaagaaatggcattcaatgttgcttgttctcattactgtagGATACTTACGATGACAGTGATAATGAAGATATAGATCGTGCCATTGCATTATCGCTAGCTGAGGAAGATCATAATAAGGGAAAGTCGGTGGCTATTG

Basic information

species Zea mays
transcript GRMZM2G099328_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G099328_T04 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g40490.1 (Oryza sativa), 3'ss of exon 4
gtatgtgctctgctgttgaacaaaatctaccacgtgcattccttttctactgc-agctggtcatatctgttcgtataacctatgcctaaacaactaa--gctttaatcttacaccttttattctatagaatgcactatcctgagacaaaagaaatggcattcaatgttgcttgttctcattactgtagGATACTTACGATGACAGTGATAATGAAGATATAGATCGTGCCATTGCATTATCGCTAGCTGAGGAAGATCATAATAAGGGAAAGTCGGTGGCTATTG
                               |  | | | |||||| |  ||  | |||  ||||| |||||   |||  |   |  | | || | |  | | |||      |    |   ||| ||||||||    |||||||| |||||||  | || ||| ||||||   |  | ||| |||||||   | || ||||| |||||||||||||||||||||||||| |||||| | ||  || | || |||   || |||||||||||  | || |      
----------------------------gttagtttcttgccttttatgttgttatctgcacatat-tgttc---taagtttctctcagagaaatcattgttctaagtgattaaacctcgatctgtagaatgcctattcctgagataaaagaatggtcactcagtgttgc--atcttgattgctgtagGGAGCGTATGATGAAAGTGATAATGAAGATATAGATCGTGCTATTGCACTGTCTTTATCAGAAGAA---CAAAATAAGGGAAAAGCTGTTG------
















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|211513637|gb|FL388499.1|FL388499
EST:     GTCACTATGATGGAGACTGGCATGAAGGTCATTCATCTGATCACACCAGA                         GATACTTACGATGACAGTGATAATGAAGATATAGATCGTGCCATTGCATTA
genomic: GTCACTATGATGGAGACTGGCATGAAGGTCATTCATCTGATCACACCAGAgtatgtgctc ... attactgtagGATACTTACGATGACAGTGATAATGAAGATATAGATCGTGCCATTGCATTA
EST: gi|76910059|gb|DV163681.1|DV163681
EST:     GTCACTATGATGGAGACTGGCATGAAGGTCATTCATCTGATCACACCAGA                         GATACTTACGATGACAGTGATAATGAAGATATAGATCGTGCCATTGCATTA
genomic: GTCACTATGATGGAGACTGGCATGAAGGTCATTCATCTGATCACACCAGAgtatgtgctc ... attactgtagGATACTTACGATGACAGTGATAATGAAGATATAGATCGTGCCATTGCATTA
EST: gi|149080806|gb|EE169875.2|EE169875
EST:     GTCACTATGATGGAGACTGGCATGAAGGTCATTCATCTGATCACACCAGA                         GATACTTACGATGACAGTGATAATGAAGATATAGATCGTGCCATTGCATTA
genomic: GTCACTATGATGGAGACTGGCATGAAGGTCATTCATCTGATCACACCAGAgtatgtgctc ... attactgtagGATACTTACGATGACAGTGATAATGAAGATATAGATCGTGCCATTGCATTA
EST: gi|71773669|gb|DR971566.1|DR971566
EST:     GTCACTATGATGGAGACTGGCATGAAGGTCATTCATCTGATCACACCAGA                         GATACTTACGATGACAGTGATAATGAAGATATAGATCGTGCCATTGCATTA
genomic: GTCACTATGATGGAGACTGGCATGAAGGTCATTCATCTGATCACACCAGAgtatgtgctc ... attactgtagGATACTTACGATGACAGTGATAATGAAGATATAGATCGTGCCATTGCATTA
EST: gi|149012210|gb|EE042508.2|EE042508
EST:     GTCACTATGATGGAGACTGGCATGAAGGTCATTCATCTGATCACACCAGA                         GATACTTACGATGACAGTGATAATGAAGATATAGATCGTGCCATTGCATTA
genomic: GTCACTATGATGGAGACTGGCATGAAGGTCATTCATCTGATCACACCAGAgtatgtgctc ... attactgtagGATACTTACGATGACAGTGATAATGAAGATATAGATCGTGCCATTGCATTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actatcctgagacaaaagaaatggcattcaatgttgcttgttctcattactgtagGATACTTACGATGACAGTGATAATGAAGATATAGATCGTGCCATTGCATTATCGCTAGCTGAGGAAGATCATAATAAGGGAAAGTCGGTGGCTATTG
                                        ttctcatt  CT-rich tract
             aaaagaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgctctgctgttgaacaaaatctaccacgtgcattccttttctactgcagctggtcatatctgttcgtataacctatgcctaaacaactaagctttaatcttacaccttttattctatagaatgcactatcctgagacaaaagaaatggcattcaatgttgcttgttctcattactgtagGATACTTACGATGACAGTGATAATGAAGATATAGATCGTGCCATTGCATTATCGCTAGCTGAGGAAGATCATAATAAGGGAAAGTCGGTGGCTATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA