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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCGAAGTGGAAGATTGCTGTTGGGCATCATACCATTAGGAGCGTCAGTGACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAGgttatacagaagttgcctcgatattaagttctgaaggatccacaaaaagagtacttccttatcactgtttcatggaatttcag

Basic information

species Oryza sativa
transcript LOC_Os03g13540.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g13540.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G152477_T03 (Zea mays), 5'ss of exon 4
AGCGAAGTGGAAGATTGCTGTTGGGCATCATACCATTAGGAGCGTCAGTGACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAGgtt----atacag---aagttgcctcgatattaagttc--tgaaggatccacaaa----aagagtacttccttatcactgtttcatggaatttcag----------------------------------
 |||  ||||||| |||| || || || |||||||| ||||| |||||||| |||||||||||||||||||| ||||| || || |||||||| ||  ||||     |||||    ||           || |    |   |  |  | |||||     | ||| |    |  |||   |  |    || |  |                                    
TGCGGCGTGGAAGGTTGCCGTGGGCCACCATACCATGAGGAGTGTCAGTGATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAGgtatacaatacaactcaaagcaagcaagcatcagcgccgtcgttgtcttcacaagttctatgagaaggaacggatcggagccttccagagtaacgtacggttcttccatggcatttggtttaatttccag
















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|27576382|gb|CA999076.1|CA999076
EST:     ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAG                         GTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
genomic: ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAGgttatacaga ... ggaatttcagGTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
EST: gi|9865081|gb|AU100831.1|AU100831
EST:     ACCATGGTGACACCAAGGACCTTCTGCANCTTCTACTTCCAGTTCTGAAG                         GTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
genomic: ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAGgttatacaga ... ggaatttcagGTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
EST: gi|86507744|gb|CI150377.1|CI150377
EST:     TCCAGTTCTGAAG                         GTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
genomic: TCCAGTTCTGAAGgttatacaga ... ggaatttcagGTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
EST: gi|88962486|gb|CI097638.1|CI097638
EST:     ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAG                         GTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
genomic: ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAGgttatacaga ... ggaatttcagGTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
EST: gi|109711830|gb|CI029000.1|CI029000
EST:     ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAG                         GTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
genomic: ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAGgttatacaga ... ggaatttcagGTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
EST: gi|89161610|gb|CI100770.1|CI100770
EST:     AAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAG                         GTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
genomic: AAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAGgttatacaga ... ggaatttcagGTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
EST: gi|88221310|gb|CI221266.1|CI221266
EST:     ACTTCCAGTTCTGAAG                         GTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
genomic: ACTTCCAGTTCTGAAGgttatacaga ... ggaatttcagGTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
EST: gi|86510427|gb|CI153060.1|CI153060
EST:     ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAG                         GTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
genomic: ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAGgttatacaga ... ggaatttcagGTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
EST: gi|27576775|gb|CA999469.1|CA999469
EST:     ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAG                         GTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
genomic: ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAGgttatacaga ... ggaatttcagGTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
EST: gi|89183251|gb|CI045816.1|CI045816
EST:     ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAG                         GTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
genomic: ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAGgttatacaga ... ggaatttcagGTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
EST: gi|89168999|gb|CI020539.1|CI020539
EST:     ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAG                         GTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
genomic: ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAGgttatacaga ... ggaatttcagGTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
EST: gi|86481343|gb|CI123976.1|CI123976
EST:     ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAG                         GTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
genomic: ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAGgttatacaga ... ggaatttcagGTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
EST: gi|89165522|gb|CI102612.1|CI102612
EST:     AAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAG                         GTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
genomic: AAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAGgttatacaga ... ggaatttcagGTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
EST: gi|89165032|gb|CI102120.1|CI102120
EST:     ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAG                         GTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
genomic: ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAGgttatacaga ... ggaatttcagGTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
EST: gi|8527438|gb|AU092253.1|AU092253
EST:     ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAG                         GTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
genomic: ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAGgttatacaga ... ggaatttcagGTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
EST: gi|87026542|gb|CI252496.1|CI252496
EST:     ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAG                         GTCAATAGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
genomic: ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAGgttatacaga ... ggaatttcagGTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
EST: gi|88984674|gb|CI009447.1|CI009447
EST:     ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAG                         GTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
genomic: ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAGgttatacaga ... ggaatttcagGTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
EST: gi|117234872|gb|CT847928.1|CT847928
EST:     ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAG                         GTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
genomic: ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAGgttatacaga ... ggaatttcagGTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
EST: gi|27577370|gb|CB000065.1|CB000065
EST:     ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAG                         GTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
genomic: ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAGgttatacaga ... ggaatttcagGTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
EST: gi|89164491|gb|CI101579.1|CI101579
EST:     CCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAG                         GTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
genomic: CCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAGgttatacaga ... ggaatttcagGTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
EST: gi|3766780|gb|AU030890.1|AU030890
EST:     CCCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAG                         GTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
genomic: ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAGgttatacaga ... ggaatttcagGTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
EST: gi|33660753|gb|CF291720.1|CF291720
EST:     ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAG                         GTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
genomic: ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAGgttatacaga ... ggaatttcagGTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
EST: gi|15850183|gb|BI798459.1|BI798459
EST:     CCAT-GTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAG                         GTCAAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACA
genomic: CCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAGgttatacaga ... ggaatttcagGTC-AATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACA
EST: gi|58592688|gb|CF990996.1|CF990996
EST:     ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAG                         GTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
genomic: ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAGgttatacaga ... ggaatttcagGTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
EST: gi|58691567|gb|CK080254.1|CK080254
EST:     ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAG                         GTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
genomic: ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAGgttatacaga ... ggaatttcagGTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
EST: gi|89165743|gb|CI102833.1|CI102833
EST:     ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAG                         GTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC
genomic: ACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAGgttatacaga ... ggaatttcagGTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 71 (upstream exon), 68 (downstream exon)
Score: 123

AGCGAAGTGGAAGATTGCTGTTGGGCATCATACCATTAGGAGCGTCAGTGACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAGgttatacaga ... ggaatttcagGTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACACATTAGCAGCAGAGACAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCGAAGTGGAAGATTGCTGTTGGGCATCATACCATTAGGAGCGTCAGTGACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAGgttatacagaagttgcctcgatattaagttctgaaggatccacaaaaagagtacttccttatcactgtttcatggaatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG