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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgggccccattgtagtttcatttctttacattttttttagcttcctatcatgttaatcaatttgtctgtaaattaaaagaacatcttgttatcagGAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAGACGTAATTGACCTGAATCTTACTGGTGTTTTCCTCTGTACACAA

Basic information

species Oryza sativa
transcript LOC_Os04g30760.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g30760.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G099696_T01 (Zea mays), 3'ss of exon 5
gttgggccccattgtagtttcatttctt-tacattttttttagcttcctatcatgttaatcaa-tttgtctgtaaattaaaagaacatcttgttatcagGAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAGACGTAATTGACCTGAATCTTACTGGTGTTTTCCTCTGTACACAA
||  |  | ||   |    |  | | ||  || ||     |  |  | |  ||  ||  |  | ||||| ||| || ||||  || || || |||| ||| ||||| ||||||||||| || ||||||||||||||||| || ||||||||||||||||| |||||||||||||| || ||||| |||||||| 
gtatgttctcaacttcccatggtatattgcactttgccagttcccacttcccagtttggttgactttgtttgtcaaataaac-aatattttcttattagGGATTACACGAGACACATTGTTGATGAGGATGAAGAAATCTCAGTGGCAAGACGTAATTGATCTGAATCTTACTGGCGTCTTCCTTTGTACACAG

upper sequence: LOC_Os04g30760.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G351023_T01 (Zea mays), 3'ss of exon 5
gttgggccccattgtagtttcatttctttacattttttttagcttcctatcatgttaatcaatttgtctgtaaattaaaagaacatcttgttatcagGAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAGACGTAATTGACCTGAATCTTACTGGTGTTTTCCTCTGTACACAA
             |||  |||   | ||    |    |||  |  |   |  | | | | | ||||| ||  || ||||  || || || |||| ||||||||| |||||||||||||| ||||||||||||||||| || |||||||| |||||||| ||||||||||| || || | ||| |||||||| 
-------------gtatgttcccatgttagattgcactttgccagctccttgtttgattgactttgtttggcaaataaac-aatattttcttattagGAATTACACGAGACACATTATTGATGAGGATGAAGAAATCTCAGTGGCAAGATGTAATTGATCTGAATCTTACAGGCGTCTGCCTGTGTACACAG

upper sequence: LOC_Os04g30760.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA08G10760.1 (Glycine max), 3'ss of exon 4
---gttgggccccattgtagtttcatttctttacattttttttagcttcctatc-atgttaatcaatttgtctgtaaattaaaagaacatcttgttatcagGAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAGACGTAATTGACCTGAATCTTACTGGTGTTTTCCTCTGTACACAA
   | | ||    ||  ||  || |   |||     |  | |||  ||  |||  || |||||  |    |   ||  | |||  || ||| ||   ||||||||||| |||||    || |||||||| |||||||||||||||||||| || || ||||| |||||||| ||||||||||| || || |  || 
gtagcttggataaataataaattaagcacttg----tgctattacttttttatttattttaatttaagatttcatac-taaaataaatatcatgggttcagGAATTACTCGAGATGGTTTGTTAATGAGAATGAAGAAATCACAATGGCAGGAAGTTATTGATCTGAATCTCACTGGTGTTTTTCTTTGCATGCAG

upper sequence: LOC_Os04g30760.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA09G26480.1 (Glycine max), 3'ss of exon 2
---gttgggccccattgtagtttcatttctttacattttttttagcttcctatcatgttaatcaatttgtctgtaaattaaaagaacatcttgttatcagGAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAGACGTAATTGACCTGAATCTTACTGGTGTTTTCCTCTGTACACAA
   | | |     ||  ||  || |   |||     |  | |||| |   |||  |  |  | |  ||   |   ||  | || || ||| ||   |||| |||||| | |||    || |||||||| |||||||||||||||||||| || || ||| | |||||||| ||| ||||||| || || |  || 
gtagcttgcataaataataaattaagcacttg----tgctattagttatttattttaatt-taagattccatactaaaaataaaaatatcatgggttcagTAATTACTCAAGATGGTTTGTTAATGAGAATGAAGAAATCACAATGGCAGGAAGTTATTAATCTGAATCTCACTAGTGTTTTTCTTTGCATGCAG

upper sequence: LOC_Os04g30760.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA11G37320.1 (Glycine max), 3'ss of exon 5
gttgggccccattgtagtttcatttctttacattttttttagcttcctatcatgttaatcaatttgtctgtaaattaaaagaacatcttgttatcagGAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAGACGTAATTGACCTGAATCTTACTGGTGTTTTCCTCTGTACACAA
             |||  ||       |  | | |  || ||||  || || | ||  || | |  |    || |   |   | ||  || | |||||||| ||  ||||    ||||||||||| ||||||||||| |||||||| || || ||||| || ||||| ||||||||||| || || || || 
-------------gtaagttggaaagct--cctgtgcttgagctctctctc-tctttctctaatcattctcaagt---agtcatattatgatttcagGAATAACTAGAGATGGTTTATTAATGAGAATGAAGAAATCTCAATGGCAGGATGTTATTGATCTAAATCTCACTGGTGTTTTTCTTTGCACCCAG

upper sequence: LOC_Os04g30760.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA18G01280.1 (Glycine max), 3'ss of exon 5
gttgggccccattgtagtttcatttctttacattttttttagcttcctatcatgttaatcaatttgtctgtaaattaaaagaacatcttgttatcagGAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAGACGTAATTGACCTGAATCTTACTGGTGTTTTCCTCTGTACACAA
||  |     |   |  | |  ||    ||   | | |    || ||  || | ||  || |    |    ||||   ||  | ||  || | |||||||| ||  ||||    ||||||||||| ||||||||||| |||||||| || || ||||| || ||||| ||||||||||| || || ||||| 
gtaagttggaaagctcctgtggttgagctaacctctctccctctccccctc-tttttctctaggcattctcaaat---aatcatattatgatttcagGAATAACAAGAGATGGTTTATTAATGAGAATGAAGAAATCTCAATGGCAGGATGTTATTGATCTAAATCTCACTGGTGTTTTTCTTTGCACACAG

upper sequence: LOC_Os04g30760.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S109_238V6.1 (Physcomitrella patens), 3'ss of exon 5
--gttgggcccca-ttgtagt-ttcatttctttacattttttttagcttcctatcatgttaatcaatttgtctgtaaattaaaagaacatcttgttatcagGAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAGACGTAATTGACCTGAATCTTACTGGTGTTTTCCTCTGTACACAA
  |||   |  |  || |||| || | |    || |   |    |  ||| |   ||  |  ||||  |    ||    |  |  |         | | |||||||||  | || || || || ||||||||||||||   ||||||||| || || |||||||| || || ||||| ||||||||||| || || 
acgttcttcatcggttttagtatttagtcagctataacgtgccaattttcatga-atacttttcaaggttgacgtctcatgtattagtggtgaaattttagGAATTACGAGGGATACTTTGTTGATGAGGATGAAGAAGGAACAATGGCAGGATGTCATTGACCTCAACCTCACTGGCGTTTTCCTCTGCACTCAG

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|14980713|gb|BI305391.1|BI305391
EST:     GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG                         GAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
genomic: GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAGgttgggcccc ... ttgttatcagGAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
EST: gi|23514981|gb|BU673887.1|BU673887
EST:     GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG                         GAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
genomic: GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAGgttgggcccc ... ttgttatcagGAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
EST: gi|30227133|gb|CB965025.1|CB965025
EST:     GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG                         GAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
genomic: GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAGgttgggcccc ... ttgttatcagGAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
EST: gi|30227817|gb|CB965709.1|CB965709
EST:     GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG                         GAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
genomic: GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAGgttgggcccc ... ttgttatcagGAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
EST: gi|23512833|gb|BU672855.1|BU672855
EST:     GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG                         GAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
genomic: GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAGgttgggcccc ... ttgttatcagGAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
EST: gi|30226632|gb|CB964524.1|CB964524
EST:     GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG                         GAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
genomic: GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAGgttgggcccc ... ttgttatcagGAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
EST: gi|30227770|gb|CB965662.1|CB965662
EST:     GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG                         GAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
genomic: GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAGgttgggcccc ... ttgttatcagGAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
EST: gi|87006512|gb|CI294895.1|CI294895
EST:     TGGGGAACAATTGATGTGCTGGTAAACAATGCAG                         GAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
genomic: TGGGGAACAATTGATGTGCTGGTAAACAATGCAGgttgggcccc ... ttgttatcagGAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
EST: gi|30228838|gb|CB966729.1|CB966729
EST:     GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG                         GAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
genomic: GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAGgttgggcccc ... ttgttatcagGAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
EST: gi|23514324|gb|BU673583.1|BU673583
EST:     GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG                         GAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
genomic: GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAGgttgggcccc ... ttgttatcagGAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
EST: gi|23513544|gb|BU673187.1|BU673187
EST:     GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG                         GAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
genomic: GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAGgttgggcccc ... ttgttatcagGAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG

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: 33 (upstream exon), 75 (downstream exon)
Score: 35

GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAGgttgggcccc ... ttgttatcagGAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAGACGTAATTGACCTGAATCTTACTGGTGTTTTCCTCTGTACACAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcctatcatgttaatcaatttgtctgtaaattaaaagaacatcttgttatcagGAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAGACGTAATTGACCTGAATCTTACTGGTGTTTTCCTCTGTACACAA
          tgttaat  putative branch site (score: 35)
                                           tcttgtt  putative PPT
                            taaattaaaagaacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgggccccattgtagtttcatttctttacattttttttagcttcctatcatgttaatcaatttgtctgtaaattaaaagaacatcttgttatcagGAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAGACGTAATTGACCTGAATCTTACTGGTGTTTTCCTCTGTACACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA