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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatacttctacttctctgatctctctttcctgcagtggaattgttcttttcgttgagcgagactagagtagaattctgaatatccaacctgacgctcatgctatcttcttaaacatcaacagGGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCATCCTTTGGGTGCCAGAGACAAAAGGAAGAACTCTCGAAGAGATACAATG

Basic information

species Oryza sativa
transcript LOC_Os05g49270.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g49270.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G028570_T01 (Zea mays), 3'ss of exon 9
gtacatacttctacttctctgatctctctttcctgcagtggaattgttctttt-cgttgagcgagactagagtagaattctgaatatccaacctgacgctcatgctatcttcttaaacatcaacagGGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCATCCTTTGGGTGCCAGAGACAAAAGGAAGAACTCTCGAAGAGATACAATG
                                     ||  |  | | | |||  ||||  |||   |  |  |     |  |  ||   ||  |   |     || | || | |||  |   |||| || ||||  |  |||||| | ||||||||||||||  |||| ||||||||||||||||||||||||||||| |||| ||| ||||| |||||||||||
-------------------------------------gtccatatatacatttgtgttggtcgatcgtttatgaactacccaaccatatgacaggttac-----ctttgttttcaaat-tgtgcagGTACATTTGCCTTGTACATGATGGTGAGTGCTTTCACGGTCGTCTTCGTCATCCTTTGGGTGCCAGAGACAAAGGGAAAAACCCTCGAGGAGATACAATG

upper sequence: LOC_Os05g49270.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G160430_T02 (Zea mays), 3'ss of exon 1
gtacatacttctacttctctgatctctctttcctgcagtggaattgttcttttcgttgagcgagactagagtagaattctgaatatccaacc---tgac--gctcatgctatcttcttaaacatca-acagGGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCATCCTTTGGGTGCCAGAGACAAAAGGAAGAACTCTCGAAGAGATACAATG
                              |||  |  |  |  |||     ||  |     ||  |||||| | ||    | || | ||||    |||  | |  ||   | |  ||    |||   |||| || ||||  ||||||||| | |||||||||||||| ||||| ||||||||||||||||| |||||||| || |||||||| || ||||||||||| ||
-----------------------------gtccatctatacatctgtgtccatcactagtgtagggtagagtcgtatatgaactaccaaaccatgcgacaggttggtgacctttgtttcctaatcgtgcagGTACATTTGCCTCCTACATGATGGTGAGTGCTTTCACTCTCGTCTTCGTCATCCTTTGGGTACCAGAGACGAAGGGAAGAACCCTTGAAGAGATACAGTG

upper sequence: LOC_Os05g49270.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G160460_T02 (Zea mays), 3'ss of exon 16
gtacatacttctacttctctgatctctctttcctgcagtggaattgttcttttcgttgagcgagactagagtagaattctgaatatccaacctgacgctcatgctatcttc---ttaaacatcaacagGGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCATCCTTTGGGTGCCAGAGACAAAAGGAAGAACTCTCGAAGAGATACAATG
                                ||| | | || |||| |   |  |    || |  |||||||| |     |  |||   ||| || | || | || | |    |  ||  |  ||||| || |||   ||||||||| | |||||||| ||||| ||||||||||| ||| ||||||||||||||||||| |||||||| |||||||||||||||||
------------------------------gtctgta-tagatttgtgcagcttatc--tcgtgtatagagtaggag---aaccatcagcccttacacacaggttacccttgtttccaaactgtacagGTACGTTTACCTCCTACATGATTGTGAGTGCCTTCACTCTCGTGTTCGTAATCGTTTGGGTGCCAGAGACAAAGGGAAGAACCCTCGAAGAGATACAATG

upper sequence: LOC_Os05g49270.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G160504_T01 (Zea mays), 3'ss of exon 16
gtacatacttctacttctctgatctctctttcctgcagtggaattgttcttttcgttgagcga--gactagagtagaattctgaat-atccaacctgacgctcatgctatcttcttaaacatcaacagGGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCATCCTTTGGGTGCCAGAGACAAAAGGAAGAACTCTCGAAGAGATACAATG
                             | |   ||      |||| |||    |    ||   || |||  ||| ||| ||||  ||  || |||| ||   |  | |||| |      |   |||| || ||| | || |||||||| ||||| || |||||| |||| || ||  ||||||||||||| ||||| || || |||||||| || |||||||||| 
----------------------------gtccacacaacacctttgtgcttcagctctgacgtctgaataggataggattatgaaccatggaagctgatgca-gttttttcttttcttttctgggcagGCACTTTTCTCTCGTACATGGTTGTGAGCGCCTTCACCATCGTTTTTGTTGTCCTTTGGGTGCCGGAGACGAAGGGGAGAACTCTAGAGGAGATACAATT

upper sequence: LOC_Os05g49270.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G077546_T02 (Zea mays), 3'ss of exon 15
gtacatacttctacttctctgatctctctttcctgcagtggaattgttcttttcgttgagcgagactagagtagaattctgaatatccaacctgacgctcatgctatcttcttaaacatcaacagGGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCATCCTTTGGGTGCCAGAGACAAAAGGAAGAACTCTCGAAGAGATACAATG
                                     ||  |  | | | | || | | |  ||| |||  | | || | ||| | | ||||| |||    |||     | |  ||     ||||| || ||||  |||||||||||||||||||| ||||| ||  ||||||||||||| |||||||||||||| || |||||||| || || |||||||| ||
-------------------------------------gtccatatatacatctc-tcgtgt-agattaggatggtatac-gaacaacaaaccttacgacactgcctctgtttccaaatcgtacagGCACATTTGCCTCCTACATGGTCGTGAGTGCGTTCACTCTAATGTTCGTCATCCTCTGGGTGCCAGAGACGAAGGGAAGAACCCTTGAGGAGATACAGTG

upper sequence: LOC_Os05g49270.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G098679_T01 (Zea mays), 3'ss of exon 16
gtacatacttctacttctctgatctctctttcctgcagtggaattgttcttttcgttgagcgagactagagtagaattctgaatatccaacctgacgc-tcatgctatcttcttaaacatcaacagGGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCATCCTTTGGGTGCCAGAGACAAAAGGAAGAACTCTCGAAGAGATACAATG
                           | |   |||| | |  | | ||| || ||  || |    |||  | | ||    | || | ||||| ||   | |   |   |||  || | |   |||| || ||||  | ||||||| | |||||||||||||| ||||| || ||||||||||||||||| |||||||| |||||||||||||| |||||||||||
------------------------gtccatatatgcatttgtgtcggtctctt-gtgtagtg----taggatcgcatatgaattaccaaaccttacaagttacatttgtttccaaatcgt--gcagGTACATTTGCCTTCTACATGATGGTGAGTGCTTTCACTCTCGTCTTTGTCATCCTTTGGGTGCCGGAGACAAAGGGAAGAACTCTCGAGGAGATACAATG

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|87009920|gb|CI277421.1|CI277421
EST:     CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAG                         GGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
genomic: CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAGgtacatactt ... acatcaacagGGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
EST: gi|88956974|gb|CI095026.1|CI095026
EST:     CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAG                         GGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
genomic: CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAGgtacatactt ... acatcaacagGGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
EST: gi|58682760|gb|CK071447.1|CK071447
EST:     CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAG                         GGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
genomic: CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAGgtacatactt ... acatcaacagGGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
EST: gi|88966437|gb|CI352989.1|CI352989
EST:     CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAG                         GGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
genomic: CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAGgtacatactt ... acatcaacagGGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
EST: gi|88257732|gb|CI360318.1|CI360318
EST:     CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAG                         GGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
genomic: CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAGgtacatactt ... acatcaacagGGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
EST: gi|86541299|gb|CI181505.1|CI181505
EST:     CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAG                         GGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
genomic: CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAGgtacatactt ... acatcaacagGGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
EST: gi|86501749|gb|CI144382.1|CI144382
EST:     CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAG                         GGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
genomic: CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAGgtacatactt ... acatcaacagGGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
EST: gi|86546848|gb|CI187054.1|CI187054
EST:     CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAG                         GGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
genomic: CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAGgtacatactt ... acatcaacagGGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
EST: gi|88262958|gb|CI366732.1|CI366732
EST:     CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAG                         GGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
genomic: CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAGgtacatactt ... acatcaacagGGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
EST: gi|87021810|gb|CI277977.1|CI277977
EST:     CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAG                         GGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
genomic: CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAGgtacatactt ... acatcaacagGGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
EST: gi|86842154|gb|CI338494.1|CI338494
EST:     GATGCTTAGCTGGAGTGCTGGAG                         GGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
genomic: GATGCTTAGCTGGAGTGCTGGAGgtacatactt ... acatcaacagGGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
EST: gi|86890215|gb|CI321392.1|CI321392
EST:     CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAG                         GGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
genomic: CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAGgtacatactt ... acatcaacagGGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
EST: gi|88838225|gb|CI373585.1|CI373585
EST:     CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAG                         GGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
genomic: CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAGgtacatactt ... acatcaacagGGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
EST: gi|88281786|gb|CI403182.1|CI403182
EST:     CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAG                         GGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
genomic: CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAGgtacatactt ... acatcaacagGGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
EST: gi|29687040|gb|CB683315.1|CB683315
EST:     CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAG                         GGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
genomic: CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAGgtacatactt ... acatcaacagGGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
EST: gi|88502203|gb|CI429709.1|CI429709
EST:     CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAG                         GGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
genomic: CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAGgtacatactt ... acatcaacagGGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
EST: gi|86887575|gb|CI294209.1|CI294209
EST:     CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAG                         GGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
genomic: CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAGgtacatactt ... acatcaacagGGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
EST: gi|88975788|gb|CI024039.1|CI024039
EST:     CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAG                         GGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
genomic: CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAGgtacatactt ... acatcaacagGGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
EST: gi|86903200|gb|CI313563.1|CI313563
EST:     CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAG                         GGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
genomic: CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAGgtacatactt ... acatcaacagGGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
EST: gi|8857545|gb|AU094863.1|AU094863
EST:     TTTGGAATAACAATGACAGCAAA-TTGATGCTTAGCTCGGAGTGCTGGAG                         GGACTTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
genomic: TTTGGAATAACAATGACAGCAAACTTGATGCTTAGCT-GGAGTGCTGGAGgtacatactt ... acatcaacagGGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
EST: gi|86890239|gb|CI321416.1|CI321416
EST:     CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAG                         GGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA
genomic: CTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAGgtacatactt ... acatcaacagGGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCA

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: 68 (upstream exon), 60 (downstream exon)
Score: 19

ATCAAGAGTCTCGCAGGAAGCTTTGCGACGCTCGCCAACTGGCTTACATCCTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAGgtacatactt ... acatcaacagGGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCATCCTTTGGGTGCCAGAGACAAAAGGAAGAACTCTCGAAGAGATACAATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtagaattctgaatatccaacctgacgctcatgctatcttcttaaacatcaacagGGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCATCCTTTGGGTGCCAGAGACAAAAGGAAGAACTCTCGAAGAGATACAATG
                   acctgac  putative branch site (score: 19)
                                      ttcttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatacttctacttctctgatctctctttcctgcagtggaattgttcttttcgttgagcgagactagagtagaattctgaatatccaacctgacgctcatgctatcttcttaaacatcaacagGGACCTTTGTGTCCTACATGGTCGTGAGTGCTTTCACCCTCGTGTTCGTCATCCTTTGGGTGCCAGAGACAAAAGGAAGAACTCTCGAAGAGATACAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA