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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttgcatattcctagctttcttggaatgccttgcttttgtgtctcttgaatgttaagatattaccttatgattacagCCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAG

Basic information

species Oryza sativa
transcript LOC_Os07g14270.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g14270.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G074687_T01 (Zea mays), 3'ss of exon 4
gtattttgcatattcctagctttcttggaatgccttgcttttgtgtctcttgaatg-ttaagat--attaccttatgattacagCCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAG
||   |  |||| |  |   | |  || | | | || |||     | | |  |||  || || |  ||    | ||||||  |||| |||||||||||||||||||| ||||||||||||||||||||||||||||| |||
gtgaat-acataatatttattgttgtgaatttcttttcttgaacctgtttgtaataattgaggtttatgtgttgatgattgtagCCTGAGGACTGGGATGACAAGGAATACATTCCTGACCCTGAGGACAAGAAGCCAGAG

upper sequence: LOC_Os07g14270.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G358059_T01 (Zea mays), 3'ss of exon 4
----gtattttgcatattcctagctttcttggaatgccttgcttt---tgtgtctcttgaatgttaagatattaccttatgattacagCCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAG
    | |   |  |||||  |   | | ||  |||  |||  |||     ||| |   ||   || || | |||  |  ||||| ||||| |||||||||||||||||||||||||||||||||||||||||||||||||| |||
gtgtgaagagttaatatttattattgtgtttcaatttctttgtttgcacctgtttggagataattgaggt-ttatgtgttgattgcagCCTGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCAGAG

upper sequence: LOC_Os07g14270.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA10G28890.1 (Glycine max), 3'ss of exon 4
-----gtattttgcatattcctagctttcttggaatgccttgcttttgtgtc--tcttgaatgttaagatattaccttatgattacagCCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAG
      |  ||  || | |  ||| ||  |||  |    | | ||| || ||  | ||||   ||   |   |    |||  | ||||||||| || ||||||||||| || || |||||||| |||||||| ||||| || |||
gtacttttcttcccagagttgtagtttaattgtcagatttggttttggtttcggttttgatcatttctaatctttaatatactcacagCCAGAAGATTGGGATGACAAAGAATATATTCCTGATCCTGAGGATAAGAAACCAGAG

upper sequence: LOC_Os07g14270.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT1G09210.1 (Arabidopsis thaliana), 3'ss of exon 4
--------------------------------------------------------------------------------------gtattttgcatattcctagctttcttgga-----atgcctt-gcttttgtgtctcttgaatgttaagatattaccttatgattacagCCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAG-------------------------------------------
                                                                                        ||     |  |  ||      |||||      || |||  | |    |   || |  |  || |    ||   ||||   ||||||| ||||||||||| ||  | || |||||| |||||||||| |||||||| |||||                                            
gtattctatttcttatgaacaaccaggctaaactgagaaccaaccacttatactcaattttggagcaaactagaactaaccacaaaccataccaaagctctctgatgaacttggttgattatacctgagataccatccatcatacaaattgatccttttatttatttgtacagCCTGAGGACTGGGACGAACAAGAATACATTTCTGACCCTGAAGACAAGAAACCTGACGGTTACGATGATATCCCTAAGGAGATCCCAGACACCGACTCAA

upper sequence: LOC_Os07g14270.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv14s0060g01290.t01 (Vitis vinifera), 3'ss of exon 4
gtattttgcatattcctagctttcttggaatgccttgcttttgtgtct---cttgaatg-----ttaagatattaccttatgattacagCCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAG
||| ||  | ||| | |   ||   |  | |  |||  |    |  ||    ||| |||     | | |  |||   | ||||| |||||| || || |||||||| ||||||||||||||||| ||||| ||  ||||||| |||
gtaatt-acttatgcatcaattcagtccagtttctttttaacttaactaattttggatgaacaataatgcgattttataatgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAGCCAGAG

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:     ACTGGGATATTCTGCCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAG                         CCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG
genomic: ACTGGGATATTCTGCCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAGgtattttgca ... atgattacagCCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG
EST: gi|33796309|gb|CF324022.1|CF324022
EST:     ACTGGGATATTCTGCCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAG                         CCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG
genomic: ACTGGGATATTCTGCCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAGgtattttgca ... atgattacagCCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG
EST: gi|163920423|gb|EG710621.1|EG710621
EST:     ACTGGGATATTCTGCCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAG                         CCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG
genomic: ACTGGGATATTCTGCCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAGgtattttgca ... atgattacagCCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG
EST: gi|33793505|gb|CF322636.1|CF322636
EST:     ACTGGGATATTCTGCCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAG                         CCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG
genomic: ACTGGGATATTCTGCCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAGgtattttgca ... atgattacagCCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG
EST: gi|88718533|gb|CI742043.1|CI742043
EST:     ACTGGGATATTCTGCCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAG                         CCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG
genomic: ACTGGGATATTCTGCCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAGgtattttgca ... atgattacagCCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG
EST: gi|88722171|gb|CI745681.1|CI745681
EST:     ACTGGGATATTCTGCCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAG                         CCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG
genomic: ACTGGGATATTCTGCCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAGgtattttgca ... atgattacagCCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG
EST: gi|58660986|gb|CK049666.1|CK049666
EST:     ACTGGGATATTCTGGCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAG                         CCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG
genomic: ACTGGGATATTCTGCCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAGgtattttgca ... atgattacagCCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG
EST: gi|29675378|gb|CB671653.1|CB671653
EST:     ACTGGGATATTCTGCCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAG                         CCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG
genomic: ACTGGGATATTCTGCCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAGgtattttgca ... atgattacagCCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG
EST: gi|88691187|gb|CI735266.1|CI735266
EST:     ACTGGGATATTCTGCCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAG                         CCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG
genomic: ACTGGGATATTCTGCCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAGgtattttgca ... atgattacagCCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG
EST: gi|58656433|gb|CK045113.1|CK045113
EST:     ACTGGGATATTCTGCCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAG                         CCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG
genomic: ACTGGGATATTCTGCCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAGgtattttgca ... atgattacagCCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG
EST: gi|29675242|gb|CB671517.1|CB671517
EST:     ACTGGGATATTCTGCCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAG                         CCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG
genomic: ACTGGGATATTCTGCCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAGgtattttgca ... atgattacagCCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG
EST: gi|33793940|gb|CF322858.1|CF322858
EST:     ACTGGGATATTCTGCCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAG                         CCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG
genomic: ACTGGGATATTCTGCCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAGgtattttgca ... atgattacagCCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG
EST: gi|58596614|gb|CK007142.1|CK007142
EST:     ACTGGGATATTCTGCCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAG                         CCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG
genomic: ACTGGGATATTCTGCCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAGgtattttgca ... atgattacagCCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG
EST: gi|88690114|gb|CI734193.1|CI734193
EST:     ACTGGGATATTCTGCCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAG                         CCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG
genomic: ACTGGGATATTCTGCCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAGgtattttgca ... atgattacagCCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG
EST: gi|88730078|gb|CI753693.1|CI753693
EST:     ACTGGGATATTCTGCCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAG                         CCAGAGGACTGGGATGACAAGGAGTACATTCCTGACGCTGAGGACAAGAAG
genomic: ACTGGGATATTCTGCCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAGgtattttgca ... atgattacagCCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG
EST: gi|66915891|gb|CX102739.1|CX102739
EST:     ACTGGGATATTCTGCCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAG                         CC-GAGGACTGGGATGACAAGGAGTACATTCCTGACCCCGAGGACAAGAAG
genomic: ACTGGGATATTCTGCCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAGgtattttgca ... atgattacagCCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG
EST: gi|8856749|gb|AU094067.1|AU094067
EST:     ACTGGGATATTCTGCCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAG                         CCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG
genomic: ACTGGGATATTCTGCCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAGgtattttgca ... atgattacagCCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG
EST: gi|29660493|gb|CB656768.1|CB656768
EST:     AAGCAAATCAAGGACCCAGAAGCTAAGAAG                         CCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG
genomic: AAGCAAATCAAGGACCCAGAAGCTAAGAAGgtattttgca ... atgattacagCCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG
EST: gi|29629338|gb|CB634349.1|CB634349
EST:     CTGCCTCCGAAGCACATCAAGGACCCAGAAGCTAAGAAG                         CCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCCGAGGACAAGAAG
genomic: CTGCCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAGgtattttgca ... atgattacagCCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG
EST: gi|58679227|gb|CK067914.1|CK067914
EST:     ACTGGGATATTCTGCCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAG                         CCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG
genomic: ACTGGGATATTCTGCCTCCGAAGCAAATCAAGGACCCAGAAGCTAAGAAGgtattttgca ... atgattacagCCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaatgccttgcttttgtgtctcttgaatgttaagatattaccttatgattacagCCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAG
                          aatgttaagatatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattttgcatattcctagctttcttggaatgccttgcttttgtgtctcttgaatgttaagatattaccttatgattacagCCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAG

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