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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttcttcgcaaccatttaatctacttgtagtgttgcttaaatatctttgtttcatgtagtgaaatttattttcctaaaattccacagGCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATTGAAAGAACTACAAGGGAACATTGGCAACCGTGGTCTTTTTGGCTGAGCT

Basic information

species Oryza sativa
transcript LOC_Os04g41100.6
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g41100.6 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G179097_T03 (Zea mays), 3'ss of exon 6
gtacttcttcgcaaccatttaatctacttgtagtgttgcttaaatatctttgtttcatgtagtgaaatttattttccta---------aaattccacagGCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATTGAAAGAACTACAAGGGAACATTGGCAACCGTGGTCTTTTTGGCTGAGCT
|||  | ||   |||  | |   | ||||   |    | |||  |   | | ||||||  |   ||||| |||| | ||         ||| | ||||||||| ||| | ||||| ||||||||||||||||||| ||||||||||| ||||||||||| ||||||||||| ||||||| ||| |||||||| ||| ||
gtaaatttt--taactttctctcccactta-ggctcagtttacgtggttctatttcatacatccaaattgatttccatatataatttgaaaatacacagGCGTTCCAGAAGGTATCTGAAGAGTCCTGATCCTCTGGAAGAGCAACGTTTGAAAGAACTGCAAGGGAACATAGGCAACCATGGGCTTTTTGGGTGAACT

upper sequence: LOC_Os04g41100.6 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G139038_T01 (Zea mays), 3'ss of exon 6
gtacttcttcgcaaccatttaatctacttgtagtgttgc-ttaaatatctttgtttcatgta-gtgaaatttattttccta---------aaattccacagGCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATTGAAAGAACTACAAGGGAACATTGGCAACCGTGGTCTTTTTGGCTGAGCT
||| || ||   |||||| |  | |   | | ||       ||  |   | | ||||||  | |  ||||| |||| | ||         ||||| ||||||||||||||||| ||| ||||||||||||||||||| |||||||||||  |||||||||| ||||||||||| ||||||||||| |||||||||||| ||
gtatttttt--taaccatctcctttcactctggtccaatgctacgttgttctatttcataaatgcaaaattgatttccatatataatttgaaattacacagGCGTACCAAACGTTATCTGAAGAGTCCTGATCCTCTGGAAGAGCAACGTCTGAAAGAACTGCAAGGGAACATAGGCAACCGTGGGCTTTTTGGCTGAACT
















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|29677523|gb|CB673798.1|CB673798
EST:     AAATCAAAGGATTTCATGCCAACATTCCCTGCTTTAAATGAATTAGACAG                         GCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
genomic: AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttc ... aattccacagGCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
EST: gi|29679249|gb|CB675524.1|CB675524
EST:     AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAG                         GCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
genomic: AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttc ... aattccacagGCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
EST: gi|29632914|gb|CB637923.1|CB637923
EST:     AAATCAAAGGATTTCATGCCAACATTCCCTGCTTTAAATGAATTAGACAG                         GCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
genomic: AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttc ... aattccacagGCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
EST: gi|218494622|gb|FG958132.1|FG958132
EST:     AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAG                         GCGTTACCAA-CGGTATTTGAAGA
genomic: AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttc ... aattccacagGCGT-ACCAAACGGTATTTGAAGA
EST: gi|66913038|gb|CX099886.1|CX099886
EST:     AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAG                         GCGTACCAAACGGTATTTGAAGAATCCTGATCCTCTAGAAGAGCAACGATT
genomic: AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttc ... aattccacagGCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
EST: gi|29638284|gb|CB643293.1|CB643293
EST:     AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAG                         GCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
genomic: AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttc ... aattccacagGCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
EST: gi|29670899|gb|CB667174.1|CB667174
EST:     AAATCAAAGGATTTCATGCCAACATTCCCTGCTTTAAATGAATTAGACAG                         GCGTACCAAACGGTATTTGAAGAGTCCTGATCCTTTAGAAGAGCAACGATT
genomic: AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttc ... aattccacagGCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
EST: gi|18385570|gb|BM418769.1|BM418769
EST:     AAATCAAAGGATTTCATGCC-ACATTCCCTGCTCTAAATGAATTAGACAG                         GCGTACC-AACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
genomic: AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttc ... aattccacagGCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
EST: gi|29630958|gb|CB635967.1|CB635967
EST:     AAATCAAAGGATTTCATGCCAACATTCCCTGCTTTAAATGAATTAGACAG                         GCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
genomic: AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttc ... aattccacagGCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
EST: gi|86910572|gb|CI294713.1|CI294713
EST:     AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAG                         GCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
genomic: AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttc ... aattccacagGCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
EST: gi|29672610|gb|CB668885.1|CB668885
EST:     AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAG                         GCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
genomic: AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttc ... aattccacagGCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
EST: gi|29674831|gb|CB671106.1|CB671106
EST:     AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAG                         GCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
genomic: AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttc ... aattccacagGCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
EST: gi|58611941|gb|CK039653.1|CK039653
EST:     AAATCAAAGGATTTCATGCCAACATTCCCGGCTCTAAATGAATTAGACAG                         GCGTACCAAACGGTATTTGAAGAGTCCTG
genomic: AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttc ... aattccacagGCGTACCAAACGGTATTTGAAGAGTCCTG
EST: gi|29638205|gb|CB643214.1|CB643214
EST:     AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAG                         GCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
genomic: AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttc ... aattccacagGCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
EST: gi|89180245|gb|CI044524.1|CI044524
EST:     CAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAG                         GCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
genomic: CAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttc ... aattccacagGCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
EST: gi|29629173|gb|CB634184.1|CB634184
EST:     AAATCAAAGGATTTCATGCCAACATTCCCTGCTTTAAATGAATTAGACAG                         GCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
genomic: AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttc ... aattccacagGCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
EST: gi|86479976|gb|CI122609.1|CI122609
EST:     AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAG                         GCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
genomic: AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttc ... aattccacagGCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
EST: gi|58607487|gb|CK035520.1|CK035520
EST:     AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAG                         GCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
genomic: AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttc ... aattccacagGCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
EST: gi|29640025|gb|CB645034.1|CB645034
EST:     AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAG                         GCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
genomic: AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttc ... aattccacagGCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcttaaatatctttgtttcatgtagtgaaatttattttcctaaaattccacagGCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATTGAAAGAACTACAAGGGAACATTGGCAACCGTGGTCTTTTTGGCTGAGCT
                                       tcctaaa  putative branch site (score: 2)
                           tgaaatttattttcct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttcttcgcaaccatttaatctacttgtagtgttgcttaaatatctttgtttcatgtagtgaaatttattttcctaaaattccacagGCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATTGAAAGAACTACAAGGGAACATTGGCAACCGTGGTCTTTTTGGCTGAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC