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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagcttttgtttagaaatgtttcatttttaatgcacttactggtggtgacatcagtcaattttttcctgaactagttgtgtacagatgtttttttgaaacagctgcattcaaattttagaattaatgaattatattgtttcatttgttttttgaagAATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGCGGCAAATTTCTCACACATGCTTGGTTTTGACGACCCAAAAATGCTGGAG

Basic information

species Zea mays
transcript GRMZM2G063851_T04
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063851_T04 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 11
gtagcttttgtttagaaatgtttcatttttaatgcacttactggtggtgacatcagtcaattttttcctgaactagttgtgtacagatgtttttttgaaacagctgcattcaaattttagaattaatgaattatattgtttcatttgttttttgaagAATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGCGGCAAATTTCTCACACATGCTTGGTTTTGACGACCCAAAAATGCTGGAG
                                                       ||   ||||||    ||    |     |||  | |  |||  |  ||      |  |||||||  || |     | ||      ||   | |||   ||||| || ||||||  ||||||| | |||| ||| |||||| |  |||||||||| ||||| || |||||||||||||| ||||| || || |||||||| |||
-------------------------------------------------------gtagctttttttaccaatgcatcca--acatctttactttccaggcaatcctgt--aaattttgtaactgcaatagtaaccctattttctggttcactgaagGATCTTCAAGGATGGGAAAACTATAGCAGCTGATAATGCACTGGACTATGCAGCAAACTTTTCACACATGCTTGGGTTTGATGATCCCAAAATGCTCGAG

upper sequence: GRMZM2G063851_T04 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 11
gtagcttttgtttagaaatgtttcatttttaatgcacttactggtggtgacatcagtcaattttttcctgaactagttgtgtacagatgtttttttgaaacagctgcattcaaattttagaat-taatg--aattatattgtttcatttgttttttgaagAATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGCGGCAAATTTCTCACACATGCTTGGTTTTGACGACCCAAAAATGCTGGAG
                                                          |  |||||    |   | |      ||  | |  ||   |  ||      |  |||||||  | |  |||   ||| ||   ||||   | ||| | ||||| || |||||| | |||||| | |||| ||| |||||| |  |||| ||||| |||||||| |||||||||||||| ||||| || || |||||||| |||
--------------------------------------------------------gtagctttttatcaattcattcac---catctttacttaccaggcaatc-tgtaaaaattttcaactgcaatagcaataatgccgtttt-ctggttctctgaagGATATTCAAGGGAGGGAAAACTATAGCAGCTGATAATGCACTGGATTATGCAGCAAATTTTTCACACATGCTTGGGTTTGATGATCCCAAAATGCTTGAG
















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|211131287|gb|FL186946.1|FL186946
EST:     TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAG                         AATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAAGTTCTTTGGACTATG
genomic: TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttg ... ttttttgaagAATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAA-TTCTTTGGACTATG
EST: gi|21480820|gb|BQ577503.1|BQ577503
EST:     TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAG                         AATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGC
genomic: TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttg ... ttttttgaagAATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGC
EST: gi|78179069|gb|DV549442.1|DV549442
EST:     TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAG                         AATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGC
genomic: TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttg ... ttttttgaagAATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGC
EST: gi|211131286|gb|FL186945.1|FL186945
EST:     TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAG                         AATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGC
genomic: TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttg ... ttttttgaagAATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGC
EST: gi|78109451|gb|DV527867.1|DV527867
EST:     TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACTGGAG                         AATTTTCAAGAGTGGGAAATCAATAGAAGCCGATTATTCTTTGGACTAT
genomic: TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttg ... ttttttgaagAATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTAT
EST: gi|6964715|gb|AW433408.1|AW433408
EST:     TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAG                         AATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGAC-ATGC
genomic: TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttg ... ttttttgaagAATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGC
EST: gi|76010585|gb|DT937755.1|DT937755
EST:     GTTTACCGGAG                         AATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGC
genomic: GTTTACCGGAGgtagcttttg ... ttttttgaagAATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGC
EST: gi|7238183|gb|AW573405.1|AW573405
EST:     TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAG                         AATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGC
genomic: TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttg ... ttttttgaagAATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGC
EST: gi|7145414|gb|AW506895.1|AW506895
EST:     TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAG                         AATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGC
genomic: TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttg ... ttttttgaagAATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGC
EST: gi|67040702|gb|CO466957.1|CO466957
EST:     TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAG                         AATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGC
genomic: TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttg ... ttttttgaagAATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgcattcaaattttagaattaatgaattatattgtttcatttgttttttgaagAATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGCGGCAAATTTCTCACACATGCTTGGTTTTGACGACCCAAAAATGCTGGAG
                  aattaat  putative branch site (score: 3)
                                    tttcatttgtttttt  putative PPT
     attcaaattttagaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagcttttgtttagaaatgtttcatttttaatgcacttactggtggtgacatcagtcaattttttcctgaactagttgtgtacagatgtttttttgaaacagctgcattcaaattttagaattaatgaattatattgtttcatttgttttttgaagAATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGCGGCAAATTTCTCACACATGCTTGGTTTTGACGACCCAAAAATGCTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA