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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAGgtacttttcctttgttctgacttccgatatatcttgtaaaaatgactaacttcgtatcttgcatgaatgagaaacgggaaccttagctgacctgaattag...

Basic information

species Oryza sativa
transcript LOC_Os07g14270.3
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g14270.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G074687_T01 (Zea mays), 5'ss of exon 5
CCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAGgtacttttcctttgttctgacttccgatatatcttgtaaaaatgactaacttcgtatcttgcatgaatgagaaacgggaaccttagct--gacctgaattag--
|| |||||||||||||||||||| ||||||||||||||||||||||||||||| |||||| | ||   || |  || |  |  ||||   |  ||  | |||  |   |     | || || |||| |   |  ||    |  ||  ||    |  ||   
CCTGAGGACTGGGATGACAAGGAATACATTCCTGACCCTGAGGACAAGAAGCCAGAGgtagtgttttatt-tcttggcacc--atatgcttattattagtgaaaagtcttagggcatgtat-aatgcgtgtcttgagttgtgtcttcgaatgtatctatgg

upper sequence: LOC_Os07g14270.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G358059_T01 (Zea mays), 5'ss of exon 5
CCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAGgtact-tttcctttgttctgacttccgatatatcttgtaaaaatgacta--acttcgtatcttgcat-gaatgaga---aacgggaaccttagc-tgacctgaattag-----------------------------------------------------------
|| |||||||||||||||||||||||||||||||||||||||||||||||||| |||||| | |||  ||| ||    |        ||| |     |  ||||||  | ||   | |||  || | ||   |   || | |||  ||    | ||   | | |                                                            
CCTGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCAGAGgtagtgttttatttcttggcgccctaagcttatgtctcttacctgactacaatttaagagcttctattgtatagtatttaatgagaaatttgctattacgcaagtcactagtttccttaattttggtgaacagtacagctcattgcctttttcccattattttccag

upper sequence: LOC_Os07g14270.3 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv07s0005g01390.t01 (Vitis vinifera), 5'ss of exon 5
CCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAGgtacttttcctttgttctgacttccgatatatcttgtaaaaatgacta--acttcgtatcttgcatgaatgagaaacgggaaccttagctgacctgaattag
|| || |  |||||||| || ||||| |||||||||||||| || |||||||| |||||| ||||||||  |   ||      |  || ||  ||||    | ||  | |  |   | |   ||  |||    |    |||  | ||    ||||    
CCTGAAGCTTGGGATGATAAAGAGTATATTCCTGACCCTGAAGATAAGAAGCCAGAGgtagttttccttcatctgga-----aacttaactcataaattccaatagaaatatgagacctttttgtttgac---catataccacatcttgtatgaag---

upper sequence: LOC_Os07g14270.3 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv14s0060g01290.t01 (Vitis vinifera), 5'ss of exon 5
CCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAGgtacttttcctttgttctgacttccgatatatcttgtaaaaatgactaacttcgtatcttgca--tgaatgagaaacgggaacct-tagctgacctgaattag
|| || || |||||||| ||||||||||||||||| ||||| ||  ||||||| |||||     | | |  || |     |   |    |||| |  ||   ||||  | || |  | ||  | | |||  |||    |  |  ||              
CCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAGCCAGAGgtgacaattcctcattttagtgccttgtg---cttgaagcaacatctaaaattgttttgtacaattaactgactaacatatatttacag--------------

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|88729754|gb|CI753264.1|CI753264
EST:     ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAG                         GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
genomic: ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAGgtacttttcc ... ctgtttccagGGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
EST: gi|33796309|gb|CF324022.1|CF324022
EST:     ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAG                         GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAGCCT
genomic: ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAGgtacttttcc ... ctgtttccagGGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAGCCT
EST: gi|163920423|gb|EG710621.1|EG710621
EST:     ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAG                         GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
genomic: ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAGgtacttttcc ... ctgtttccagGGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
EST: gi|33793505|gb|CF322636.1|CF322636
EST:     ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAG                         GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
genomic: ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAGgtacttttcc ... ctgtttccagGGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
EST: gi|88718533|gb|CI742043.1|CI742043
EST:     ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAG                         GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
genomic: ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAGgtacttttcc ... ctgtttccagGGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
EST: gi|88722171|gb|CI745681.1|CI745681
EST:     ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAG                         GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
genomic: ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAGgtacttttcc ... ctgtttccagGGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
EST: gi|58660986|gb|CK049666.1|CK049666
EST:     ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAG                         GGATACGATGATATTCC
genomic: ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAGgtacttttcc ... ctgtttccagGGATACGATGATATTCC
EST: gi|29675378|gb|CB671653.1|CB671653
EST:     ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAG                         GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
genomic: ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAGgtacttttcc ... ctgtttccagGGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
EST: gi|88691187|gb|CI735266.1|CI735266
EST:     ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAG                         GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
genomic: ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAGgtacttttcc ... ctgtttccagGGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
EST: gi|58656433|gb|CK045113.1|CK045113
EST:     ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAG                         GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
genomic: ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAGgtacttttcc ... ctgtttccagGGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
EST: gi|29675242|gb|CB671517.1|CB671517
EST:     ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAG                         GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
genomic: ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAGgtacttttcc ... ctgtttccagGGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
EST: gi|14192066|gb|AU184277.1|AU184277
EST:     GGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAG                         GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
genomic: GGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAGgtacttttcc ... ctgtttccagGGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
EST: gi|29644253|gb|CB649260.1|CB649260
EST:     GGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAG                         GGATACGATGATATTCCCAAGGAAATCCTTGACCCTGATGCTAAGAAG
genomic: GGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAGgtacttttcc ... ctgtttccagGGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
EST: gi|33793940|gb|CF322858.1|CF322858
EST:     ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAG                         GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
genomic: ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAGgtacttttcc ... ctgtttccagGGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
EST: gi|58596614|gb|CK007142.1|CK007142
EST:     ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAG                         GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
genomic: ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAGgtacttttcc ... ctgtttccagGGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
EST: gi|88690114|gb|CI734193.1|CI734193
EST:     ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAG                         GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
genomic: ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAGgtacttttcc ... ctgtttccagGGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
EST: gi|88730078|gb|CI753693.1|CI753693
EST:     ACTGGGATGACAAGGAGTACATTCCTGACGCTGAGGACAAGAAGCCTGAG                         GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
genomic: ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAGgtacttttcc ... ctgtttccagGGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
EST: gi|66915891|gb|CX102739.1|CX102739
EST:     ACTGGGATGACAAGGAGTACATTCCTGACCCCGAGGACAAGAAGCCTGAG                         GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
genomic: ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAGgtacttttcc ... ctgtttccagGGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
EST: gi|8856749|gb|AU094067.1|AU094067
EST:     ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAG                         GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
genomic: ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAGgtacttttcc ... ctgtttccagGGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
EST: gi|29662655|gb|CB658930.1|CB658930
EST:     GGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAG                         GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
genomic: GGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAGgtacttttcc ... ctgtttccagGGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
EST: gi|29663170|gb|CB659445.1|CB659445
EST:     GGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAG                         GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
genomic: GGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAGgtacttttcc ... ctgtttccagGGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
EST: gi|29660493|gb|CB656768.1|CB656768
EST:     ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAG                         GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
genomic: ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAGgtacttttcc ... ctgtttccagGGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
EST: gi|29629338|gb|CB634349.1|CB634349
EST:     ACTGGGATGACAAGGAGTACATTCCTGACCCCGAGGACAAGAAGCCTGAG                         GGATATGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
genomic: ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAGgtacttttcc ... ctgtttccagGGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
EST: gi|58679227|gb|CK067914.1|CK067914
EST:     ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAG                         GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG
genomic: ACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAGgtacttttcc ... ctgtttccagGGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAGgtacttttcctttgttctgacttccgatatatcttgtaaaaatgactaacttcgtatcttgcatgaatgagaaacgggaaccttagctgacctgaattag

- - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - AGAAGC