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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttatcttgaatgatttgcattattactccttcttcatgattgcataattgcttctatctttctttacctttttcaattccttttccatttgactagGTGATATCTGGTAAACTATATGCTGGCCCTGAAGTTGATGTGTGGAGTTGTGGTGTTATTCTTTATGCTCTTCTTTGTGGTACCCTTCCATTTGATGACG

Basic information

species Oryza sativa
transcript LOC_Os05g45420.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g45420.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G077278_T01 (Zea mays), 3'ss of exon 4
gtatttatcttgaatgatttgcattattactccttcttcatgattgcataattgcttctatctttctttacctttttcaattccttttccatttgactagGTGATATCTGGTAAACTATATGCTGGCCCTGAAGTTGATGTGTGGAGTTGTGGTGTTATTCTTTATGCTCTTCTTTGTGGTACCCTTCCATTTGATGACG
||||  |||| | || |||| ||  ||||  | | ||||||| ||||||  || | | |||      || || |      || || |   ||||   ||||| ||||||||||||||||||||||| ||||||||||| || ||||| ||||| |||||||||||||||||||||||||| || || |||||||| || |
gtatc-atctagcataatttaca--attag-cgtccttcatggttgcat--ttacatatataa---cttgccatgacacgtttctgtcttattttcttagGTCATATCTGGTAAACTATATGCTGGTCCTGAAGTTGACGTCTGGAGCTGTGGAGTTATTCTTTATGCTCTTCTTTGTGGCACTCTCCCATTTGACGATG

upper sequence: LOC_Os05g45420.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 4
--------------------------------gtatttatcttga-atgatttgcattattactccttcttcatgattgcataattgcttctatctttctttacctttt---tcaa---ttccttttccatttgactagGTGATATCTGGTAAACTATATGCTGGCCCTGAAGTTGATGTGTGGAGTTGTGGTGTTATTCTTTATGCTCTTCTTTGTGGTACCCTTCCATTTGATGACG
                                 ||||  | || |  | |||   ||||||| |   ||   |    ||     || | | || ||   | |   |  |   ||||   |    | |   |||    |||| || ||||| ||| | |||||||| || ||||| ||||| ||||| |||||||| ||| | ||||||||||| ||||| || ||||| |||||||| |
gtttgtaaataattaaattgtaacggaataggatattattattaatgttattattattattattatatcactacttctgagactttacatttacctccttgtgattaataaatcaaggataaactgttgtttttcacagGTTATCTCTGGAAAATTGTATGCTGGACCAGAAGTAGATGTCTGGAGCTGTGGTGTAATTTTATATGCTCTTCTCTGTGGCACTCTTCCTTTTGATGATG

upper sequence: LOC_Os05g45420.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA18G49770.1 (Glycine max), 3'ss of exon 5
gtatttatcttgaatgatttgcattattactccttcttcatgattgcataattgcttctatctttctttacctttttcaattccttttccatttgactagGTGATATCTGGTAAACTATATGCTGGCCCTGAAGTTGATGTGTGGAGTTGTGGTGTTATTCTTTATGCTCTTCTTTGTGGTACCCTTCCATTTGATGACG
   ||| |  || |  ||   |   |  | |  || || | |||   |||  ||  | | | | ||||           |  | |||||  |||    |||| || ||||| ||| | |||||||| |||||||| ||||| ||||| |||||||| ||| | ||||| ||||||||||| |||||||| |||||||| |
--gtttgtaatgga--atacacggcaacaattattgttgaggat-atatatgtgtgtgtgtgtgtcttggtt-------acactttttcatttttcacagGTTATCTCTGGGAAATTGTATGCTGGACCTGAAGTGGATGTCTGGAGCTGTGGTGTAATTTTATATGCCCTTCTTTGTGGCACCCTTCCTTTTGATGATG

upper sequence: LOC_Os05g45420.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA08G26180.1 (Glycine max), 3'ss of exon 4
gtatttatcttg-aatgatttgcattattactccttcttcatgattgcataattgcttctatctttctttacctttttcaattccttttccatttgactagGTGATATCTGGTAAACTATATGCTGGCCCTGAAGTTGATGTGTGGAGTTGTGGTGTTATTCTTTATGCTCTTCTTTGTGGTACCCTTCCATTTGATGACG
   ||| |  || |||   | ||   | |  |  ||    ||   |  ||| |  ||  | |  ||| |     ||    |  | |||||  |||    |||| || ||||| ||||| |||||||| |||||||| ||||| ||||| |||||||| ||| | ||||| ||||||||||| || ||||| |||||||| |
--gtttgtaatggaatacatggcgaaaattattgttgaggatatatatatattgtctcttgtgattcatatttcttggttacactttttcatttttcacagGTTATCTCTGGGAAACTGTATGCTGGACCTGAAGTGGATGTCTGGAGCTGTGGTGTAATTTTATATGCGCTTCTTTGTGGCACTCTTCCTTTTGATGATG

upper sequence: LOC_Os05g45420.3 (Oryza sativa), 3'ss of exon 4
lower sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 4
gtatttatcttgaatgatttgcattattactccttcttcatgattgcataattgcttctatctttctttacctttttcaattc---cttttccatttgactagGTGATATCTGGTAAACTATATGCTGGCCCTGAAGTTGATGTGTGGAGTTGTGGTGTTATTCTTTATGCTCTTCTTTGTGGTACCCTTCCATTTGATGACG
          | | || ||  ||    |      |||     ||   ||||||     | | |    | |    ||  | |       | |  |||     |||| || || || ||  ||||||||||||||||||| ||||| ||||| |||||||| || || || |||||||| ||||| || |||||||||||||| |
---------gtaagtgctt--cagccctcaggtatctgaggaatactataattaggcttgtttcaaatgataggttatagtcgagatctataaattgtttcagGTAATTTCGGGCAAGTTATATGCTGGCCCTGAAGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATG

upper sequence: LOC_Os05g45420.3 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv08s0040g00720.t01 (Vitis vinifera), 3'ss of exon 5
gtatttatcttgaatgatttgcattattactccttcttcatgattgcataattgcttctatctttctttacctttttca-attccttttccatttgactagGTGATATCTGGTAAACTATATGCTGGCCCTGAAGTTGATGTGTGGAGTTGTGGTGTTATTCTTTATGCTCTTCTTTGTGGTACCCTTCCATTTGATGACG
                 | ||  | |  |||  || |  |   ||||  |    ||| |   |   | | |  | |  | | |    | |   |||   |||| || ||||   |||||||| |||| ||||| |||||||| |||||||||||||| ||| | | ||||||||| ||||| |  ||||| |||||||  |
----------------gtatgggtca--acttgttatata-agttgccaatgaacttgtgaataattatgctctgtgtacaatgaaatactgcttgtgcagGTTATTTCTGAACAACTATATTCTGGTCCTGAGGTTGATGTTTGGAGTTGTGGTGTCATTTTATTTGCTCTTCTCTGTGGAAGGCTTCCTTTTGATGCTG

upper sequence: LOC_Os05g45420.3 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 4
---------------------------------gtatttatcttgaat---gatttgcattattactccttcttcatgattgcataattgcttctatctttctttacctttttcaattccttttccatttgactagGTGATATCTGGTAAACTATATGCTGGCCCTGAAGTTGATGTGTGGAGTTGTGGTGTTATTCTTTATGCTCTTCTTTGTGGTACCCTTCCATTTGATGACG
                                  |  | || ||   |   ||  ||  |||  |  | ||||  |  ||   || ||      |    ||  | |  || |  ||||  | | |||||| | ||||| |||||||| | | | || || || ||||| || ||||| ||||| || ||||||||| | || ||||||||||||||||| |||||||||||||| |
gtaaggagtttgcagcattataatataagacaattcctaatttttggttgagagatgagttacaatactttct--aatatatgatgataatggttgaaatttctaaggttct--aattagtgtcccatttta-tagGTTATATCTGGAAGATTGTACGCAGGACCTGAGGTGGATGTATGGAGCTGCGGTGTTATTTTGTACGCTCTTCTTTGTGGTACTCTTCCATTTGATGATG

upper sequence: LOC_Os05g45420.3 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S28_12V6.1 (Physcomitrella patens), 3'ss of exon 3
--------------------------------------------------gtatttatcttgaatgatttgcattattactccttcttcatga------ttgcataattgct----tctatctttctttacctttttcaattccttttccatttgac---tagGTGATATCTGGTAAACTATATGCTGGCCCTGAAGTTGATGTGTGGAGTTGTGGTGTTATTCTTTATGCTCTTCTTTGTGGTACCCTTCCATTTGATGACG
                                                  ||  || | |   ||| ||    ||  |        | | |||      ||| |   || ||     |   |   ||    ||| || | |     |    ||  ||    |||| || || || ||  ||||||| || || || || ||||||||||| ||||| |||||||| ||||||||| | |||||| |  | || ||||| ||||
gttttgctctatgcctgattgccttgtttgacactgttttaattcgtcatgtgattgtgtcacatgtttctgttttctgtgttgggtgcctgaaccaagttgtaggttttctgtgcccggacacactcctgcttgttgactgttgatattgttgaacatgcagGTCATTTCAGGGAAGTTATATGCCGGTCCCGAGGTGGATGTGTGGAGCTGTGGCGTTATTCTGTATGCTCTTTTGTGTGGTTCTTTACCCTTTGACGACG

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|2317299|gb|C22353.1|C22353
EST:     GTCACTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCAGCACCTGAG                         GTGATATCTGGTAAACTATATGCTGGCCCTGGAAGTTGATGTGTGGAGTTG
genomic: GTCACTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCAGCACCTGAGgtatttatct ... atttgactagGTGATATCTGGTAAACTATATGCTGGCCCTG-AAGTTGATGTGTGGAGTTG
EST: gi|33676412|gb|CF304651.1|CF304651
EST:     GTCACTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCAGCACCTGAG                         GTGATATCTGGTAAACTATATGCTGGCCCTGAAGTTGATGTGTGGAGTTGT
genomic: GTCACTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCAGCACCTGAGgtatttatct ... atttgactagGTGATATCTGGTAAACTATATGCTGGCCCTGAAGTTGATGTGTGGAGTTGT
EST: gi|27576377|gb|CA999071.1|CA999071
EST:     GTCACTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCAGCACCTGAG                         GTGATATCTGGTAAACTATATGCTGGCCCTGAAGTTGATGTGTGGAGTTGT
genomic: GTCACTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCAGCACCTGAGgtatttatct ... atttgactagGTGATATCTGGTAAACTATATGCTGGCCCTGAAGTTGATGTGTGGAGTTGT
EST: gi|27554019|gb|CA997919.1|CA997919
EST:     GTCACTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCAGCACCTGAG                         GTGATATCTGGTAAACTATATGCTGGCCCTGAAGTTGATGTGTGGAGTTGT
genomic: GTCACTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCAGCACCTGAGgtatttatct ... atttgactagGTGATATCTGGTAAACTATATGCTGGCCCTGAAGTTGATGTGTGGAGTTGT
EST: gi|58663248|gb|CK051934.1|CK051934
EST:     GTCACTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCAGCACCTGAG                         GTGATATCTGGTAAACTATATGCTGGCCCTGA
genomic: GTCACTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCAGCACCTGAGgtatttatct ... atttgactagGTGATATCTGGTAAACTATATGCTGGCCCTGA
EST: gi|13420631|gb|AU174721.1|AU174721
EST:     GTCACTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCAGCACCTGAG                         GTGATATCTGGTAAACTATATGCTGGCCCTGAAGTTGATGTGTGGAGTTGT
genomic: GTCACTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCAGCACCTGAGgtatttatct ... atttgactagGTGATATCTGGTAAACTATATGCTGGCCCTGAAGTTGATGTGTGGAGTTGT
EST: gi|66924039|gb|CX110887.1|CX110887
EST:     GTCACTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCAGCACCTGAG                         GTGATATCTGGTAAACTATATGCTGGCCCTGAAGTTGATGTGTGGAGTTGT
genomic: GTCACTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCAGCACCTGAGgtatttatct ... atttgactagGTGATATCTGGTAAACTATATGCTGGCCCTGAAGTTGATGTGTGGAGTTGT
EST: gi|29680933|gb|CB677208.1|CB677208
EST:     GTCACTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCAGCACCTGAG                         GTGATATCTGGTAAACTATATGCTGGCCCTGAAGTTGATGTGTGGAGTTGT
genomic: GTCACTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCAGCACCTGAGgtatttatct ... atttgactagGTGATATCTGGTAAACTATATGCTGGCCCTGAAGTTGATGTGTGGAGTTGT

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: 73 (upstream exon), 70 (downstream exon)
Score: 39

ATGCAATGTTAAGATTGCAGACTTTGGCTTGAGTAATGTTATGCGTGATGGTCACTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCAGCACCTGAGgtatttatct ... atttgactagGTGATATCTGGTAAACTATATGCTGGCCCTGAAGTTGATGTGTGGAGTTGTGGTGTTATTCTTTATGCTCTTCTTTGTGGTACCCTTCCATTTGATGACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcataattgcttctatctttctttacctttttcaattccttttccatttgactagGTGATATCTGGTAAACTATATGCTGGCCCTGAAGTTGATGTGTGGAGTTGTGGTGTTATTCTTTATGCTCTTCTTTGTGGTACCCTTCCATTTGATGACG
         cttctatctttcttta  CT-rich tract
                           tttttcaatt  TA-rich tract