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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggatactacatctcgtgcaaccaaacttgccttatgctctcaatgccctgatggatttgcttctgatgtagGTTGAGGCCACAGAAGTTTTCTTTGCAGTAACAAAGCTGTTCCAGTCCAAGGATGCTGGTCTTAGGCGGCTGGTGTATTTAATGATCAAAGAGCTTTCAC

Basic information

species Oryza sativa
transcript LOC_Os03g12590.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g12590.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G012501_T03 (Zea mays), 3'ss of exon 3
----------------------------------------------gtagg-atactacatctcgtgcaaccaaacttgccttat-gctctcaatgccctgatggatttgcttctgatgtagGTTGAGGCCACAGAAGTTTTCTTTGCAGTAACAAAGCTGTTCCAGTCCAAGGATGCTGGTCTTAGGCGGCTGGTGTATTTAATGATCAAAGAGCTTTCAC
                                              ||  | | ||       |    || ||||  ||  | || |     ||    |   ||    || ||||| |  ||||||||||||| ||||| |||||||||||||||||| | |||||||| |  ||||||||||||||| |||| ||||| |||||||||||||| ||||| |
gtaccgtagtaaaaaaatgcatagtagtaaaagttttgtagtttctgtgtgcacacatttgtacagagaagcaaaactgtttgattggggagaaaattcaattgtgcatgtttctgttacagGTTGAGGCCACGGAAGTCTTCTTTGCAGTAACAAAGTTATTCCAGTCTAGTGATGCTGGTCTTAGGAGGCTAGTGTACTTAATGATCAAAGAACTTTCTC

upper sequence: LOC_Os03g12590.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA06G01520.1 (Glycine max), 3'ss of exon 3
-------gtaggatactacatctcgtgcaacca--aacttgccttatg-----ctctcaatgccctgatggat--ttgcttctgatgtagGTTGAGGCCACAGAAGTTTTCTTTGCAGTAACAAAGCTGTTCCAGTCCAAGGATGCTGGTCTTAGGCGGCTGGTGTATTTAATGATCAAAGAGCTTTCAC
        |   || |  || |  |   |       | ||  |||| |     || | ||| || |  ||| |  ||   | |  | |||||||| |||||||||||||||||||| || || ||||| |||||||| || |||   ||  | ||| |  |||| ||  | ||||| || ||| | || |
gtctagaatgatatccatcaccatgcttatttgtggaattatcttagggatacctattaatccctttttgggtaattttattttttctagGTTGAAGCCACAGAAGTTTTCTTTGCTGTGACTAAGCTTTTCCAGTCTAAAGATATGGGATTAAGGAGAATGGTCTACCTGATGATAAAGGAGATCTCTC

upper sequence: LOC_Os03g12590.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA04G01470.1 (Glycine max), 3'ss of exon 3
--gtaggatacta--catc-tcgtgcaacc----aaacttgccttatg-----ctctcaatgccctgatggat--ttgcttctgatgtagGTTGAGGCCACAGAAGTTTTCTTTGCAGTAACAAAGCTGTTCCAGTCCAAGGATGCTGGTCTTAGGCGGCTGGTGTATTTAATGATCAAAGAGCTTTCAC
   ||| ||  ||  ||||  |||||          | ||| ||||       || | ||| || |  ||| |  ||   | |    |||||||| |||||||||||||||||||| || || ||||| |||||||| || ||| | ||  | ||| |  |||| ||  | ||||| || ||| | || |
gtatagaatgatatccatcaccgtgcttatttgtggaattgtcttagagacacctattaattcctttttgggtaattttatttttgctagGTTGAAGCCACAGAAGTTTTCTTTGCTGTGACTAAGCTTTTCCAGTCTAAAGATACGGGATTAAGGAGAATGGTCTACCTGATGATAAAGGAGATCTCTC

upper sequence: LOC_Os03g12590.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA12G04820.1 (Glycine max), 3'ss of exon 3
------------------------------------------gtaggatactacatctcgtgcaaccaaacttgcctta----tgctctcaatgccctgatgg--atttgcttctgatgtagGTT--------GAGGCCACAGAAGTTTTCTTTGCAGTAACAAAGCTGTTCCAGTCCAAGGATGCTGGTCTTAGGCGGCTGGTGTATTTAATGATCAAAGAGCTTTCAC
                                          || |     || |    |      || | ||   |||    || |   ||| || |       ||||| |  || ||||  ||        || |||||||||||||||||| | ||||| ||||| ||||||||   ||||  |||  | ||| |  |||| ||  | || || || ||||| || |
gtcaagaggtttttctttgtcttttctatttcatagatatttgtggttgtttatagaatggctttgcagaattatattagagttgttacgaatcccttttcaataatttgttcttgttgtaatttcatagACCGAAGCCACAGAAGTTTTCTTTTCTGTAACTAAGCTTTTCCAGTCTCGGGATCTTGGGTTAAGGAGAATGGTCTACCTGATCATAAAGGAGCTCTCCC

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|88692689|gb|CI736264.1|CI736264
EST:     TCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG                         GTTGAGGCCACAGAAGTTTTCTTTG
genomic: TCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAGgtaggatact ... tctgatgtagGTTGAGGCCACAGAAGTTTTCTTTG
EST: gi|88401623|gb|CI588564.1|CI588564
EST:     TCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG                         GTTGAGGCCACAGAAGTTTTCTTTGCAGTAACAAAGCTGTTCCAGTCCAAG
genomic: TCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAGgtaggatact ... tctgatgtagGTTGAGGCCACAGAAGTTTTCTTTGCAGTAACAAAGCTGTTCCAGTCCAAG
EST: gi|88388647|gb|CI683432.1|CI683432
EST:     TCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG                         GTTGAGGCCACAGAAGTTTTCTTTGCAGTAACAAAGCTGTTCCAGTCCAAG
genomic: TCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAGgtaggatact ... tctgatgtagGTTGAGGCCACAGAAGTTTTCTTTGCAGTAACAAAGCTGTTCCAGTCCAAG
EST: gi|88377051|gb|CI597835.1|CI597835
EST:     TCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGAGATTCACAAAG                         GTTGAGGCCACAGAAGTTTTCTTTGCAGTA
genomic: TCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAGgtaggatact ... tctgatgtagGTTGAGGCCACAGAAGTTTTCTTTGCAGTA
EST: gi|88443658|gb|CI591883.1|CI591883
EST:     TCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG                         GTTGAGGCCAAAGAAGTTTTCTTTGCAGTAACAAAGCTGTTCCAGTCCAAG
genomic: TCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAGgtaggatact ... tctgatgtagGTTGAGGCCACAGAAGTTTTCTTTGCAGTAACAAAGCTGTTCCAGTCCAAG
EST: gi|88414473|gb|CI691639.1|CI691639
EST:     TCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG                         GTTGAGGCCACAGAAGTTTTCTTTGCAGTAACAAAGCTGTTCCAGTCCAAG
genomic: TCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAGgtaggatact ... tctgatgtagGTTGAGGCCACAGAAGTTTTCTTTGCAGTAACAAAGCTGTTCCAGTCCAAG
EST: gi|88454333|gb|CI569905.1|CI569905
EST:     TCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG                         GTTGAGGCCACAGAAGTTTTCTTTGCAGTAACAAAGCTGTTCCAGTCCAAG
genomic: TCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAGgtaggatact ... tctgatgtagGTTGAGGCCACAGAAGTTTTCTTTGCAGTAACAAAGCTGTTCCAGTCCAAG
EST: gi|88333728|gb|CI643760.1|CI643760
EST:     TCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG                         GTTGAGGCCACAGAAGTTTTCTTTGCAGTAACAAAGCTGTTCCAGTCCAAG
genomic: TCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAGgtaggatact ... tctgatgtagGTTGAGGCCACAGAAGTTTTCTTTGCAGTAACAAAGCTGTTCCAGTCCAAG
EST: gi|88405887|gb|CI591282.1|CI591282
EST:     TCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG                         GTTGAGGCCACAGAAGTTTTCTTTGCAGTAACAAAGCTGTTCCAGTCCAAG
genomic: TCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAGgtaggatact ... tctgatgtagGTTGAGGCCACAGAAGTTTTCTTTGCAGTAACAAAGCTGTTCCAGTCCAAG
EST: gi|88328220|gb|CI651227.1|CI651227
EST:     TCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG                         GTTGAGGCCACAGAAGTTTTCTTTGCAGTAACAAAGCTGTTCCAGTCCAAG
genomic: TCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAGgtaggatact ... tctgatgtagGTTGAGGCCACAGAAGTTTTCTTTGCAGTAACAAAGCTGTTCCAGTCCAAG
EST: gi|88311189|gb|CI570263.1|CI570263
EST:     TCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG                         GTTGAGGCCACAGAAGTTTTCTTTGCAGTAACAAAGCTGTTCCAGTCCAAG
genomic: TCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAGgtaggatact ... tctgatgtagGTTGAGGCCACAGAAGTTTTCTTTGCAGTAACAAAGCTGTTCCAGTCCAAG
EST: gi|88370130|gb|CI585135.1|CI585135
EST:     TCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG                         GTTGAGGCCACAGAAGTTTTCTTTGCAGTAACAAAGCTGTTCCAGTCCAAG
genomic: TCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAGgtaggatact ... tctgatgtagGTTGAGGCCACAGAAGTTTTCTTTGCAGTAACAAAGCTGTTCCAGTCCAAG
EST: gi|88313845|gb|CI597476.1|CI597476
EST:     TCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG                         GTTGAGGCCACAGAAGTTTTCTTTGCAGTAACCAACGCTGTTCCAGTCCAA
genomic: TCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAGgtaggatact ... tctgatgtagGTTGAGGCCACAGAAGTTTTCTTTGCAGTAACAAA-GCTGTTCCAGTCCAA
EST: gi|88387536|gb|CI583054.1|CI583054
EST:     TCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG                         GTTGAGGCCACAGAAGTTTTCTTT
genomic: TCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAGgtaggatact ... tctgatgtagGTTGAGGCCACAGAAGTTTTCTTT
EST: gi|88574218|gb|CI665987.1|CI665987
EST:     TCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG                         GTTGAGGCCACAGAAGTTTTCTTTGCAGTAACAAAGCTGTTCCAGTCCAAG
genomic: TCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAGgtaggatact ... tctgatgtagGTTGAGGCCACAGAAGTTTTCTTTGCAGTAACAAAGCTGTTCCAGTCCAAG
EST: gi|88310289|gb|CI659079.1|CI659079
EST:     TCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAG                         GTTGAGGCCACAGAAGTTTTCTTTGCAGTAACAAAGCTGTTCCAGTCCAAG
genomic: TCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAGgtaggatact ... tctgatgtagGTTGAGGCCACAGAAGTTTTCTTTGCAGTAACAAAGCTGTTCCAGTCCAAG

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: 51 (upstream exon), 72 (downstream exon)
Score: 43

GTCATCACTAAGCTATTGTATTTACTCAACCAAGGGGAGACATTCACAAAGgtaggatact ... tctgatgtagGTTGAGGCCACAGAAGTTTTCTTTGCAGTAACAAAGCTGTTCCAGTCCAAGGATGCTGGTCTTAGGCGGCTGGTGTATTTAATGATCAAAGAGCTTTCAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaaccaaacttgccttatgctctcaatgccctgatggatttgcttctgatgtagGTTGAGGCCACAGAAGTTTTCTTTGCAGTAACAAAGCTGTTCCAGTCCAAGGATGCTGGTCTTAGGCGGCTGGTGTATTTAATGATCAAAGAGCTTTCAC
                                            ttctgat  putative branch site (score: 43)
                                       tttgcttct  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggatactacatctcgtgcaaccaaacttgccttatgctctcaatgccctgatggatttgcttctgatgtagGTTGAGGCCACAGAAGTTTTCTTTGCAGTAACAAAGCTGTTCCAGTCCAAGGATGCTGGTCTTAGGCGGCTGGTGTATTTAATGATCAAAGAGCTTTCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT