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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataaatggaatcatgtttgaacatcctaattctgttggcatggagtgctttgacattttgatgtgctacagttgtgaataactgaatttccttttcccagGTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATGAAGGATATGCTCTCCCCCATGCTATCCTTCGTCTCGACCTTGCTGGGCG

Basic information

species Oryza sativa
transcript LOC_Os03g50885.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g50885.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G152328_T02 (Zea mays), 3'ss of exon 2
ataaatggaatcatgtttgaacatcctaattctgttggcatggagtgctttgacattttgatgtgctacagttgtgaataactgaatttccttttcccagGTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATGAAGGATATGCTCTCCCCCATGCTATCCTTCGTCTCGACCTTGCTGGGCG
 | |   || ||   | |   | |   |||| |        |   ||||    || |  | | | ||  | |     ||   ||  || || | || ||||||| ||| | ||||| || |||||||| |||||||| ||||||||||| || ||||| || |||||||| || ||||||||||| ||||| || || ||
gtgagctgattccgttctctgcttaacaatt-tccaaatccgatttgctcctgcagtccgttat-ctctaat-----atctgtggcttcccctctctcagGTATCGTGCTCGACTCGGGAGATGGTGTGAGCCACACCGTCCCCATCTACGAGGGATACGCCCTCCCCCACGCCATCCTTCGTCTTGACCTGGCCGGTCG

upper sequence: LOC_Os03g50885.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G047055_T04 (Zea mays), 3'ss of exon 3
ataaatggaatcatgtttgaacatcctaattctgttggcatggagtgctttgacattttgatgtgctacagttgtgaataactgaatttccttttcccagGTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATGAAGGATATGCTCTCCCCCATGCTATCCTTCGTCTCGACCTTGCTGGGCG----------------------------------------------
                                          ||      |||   || | |    | ||  | | | |  ||    |      || ||||||| ||| | ||||| || ||||||||||||||||||||||||||||| || ||||| || |||||||| || ||||||||||||||||| ||||| ||                                              
------------------------------------------gaaattagtgat-cttcgctaattttcaaatctcatttgct---ctcttgcctctcaggtatcgtgctcgactcgggagatggtgtcagccacactgtccccatCTACGAGGGATACGCCCTCCCCCACGCCATCCTTCGTCTCGACCTGGCTGGCCGCGACCTCACCGACTACCTCATGAAGATCCTGACTGAACGCGGCTAC

upper sequence: LOC_Os03g50885.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G047055_T01 (Zea mays), 3'ss of exon 3
ataaatggaatcatgtttgaacatcctaattctgttggcatggagtgctttgacattt--tgatgtgctacagttgtgaa---taactgaatttcct-tttcccagGTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATGAAGGATATGCTCTCCCCCATGCTATCCTTCGTCTCGACCTTGCTGGGCG
 | |   || ||   || ||   |  |   ||   ||    |       |||  | ||  |||| | |   | || | ||   | | |   | || |   || ||||||| ||| | ||||| || ||||||||||||||||||||||||||||| || ||||| || |||||||| || ||||||||||||||||| ||||| ||
gtgagctgattcg-attcgattctatt--ctccactgaaccgtttccacttggaaattagtgatcttcgctaattttcaaatctcatttgctctcttgcctctcagGTATCGTGCTCGACTCGGGAGATGGTGTCAGCCACACTGTCCCCATCTACGAGGGATACGCCCTCCCCCACGCCATCCTTCGTCTCGACCTGGCTGGCCG

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|58601004|gb|CK011532.1|CK011532
EST:     CGTCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAG                         GTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATG
genomic: CGTCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAGgtgagcacat ... cttttcccagGTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATG
EST: gi|58671237|gb|CK059923.1|CK059923
EST:     CGTCGGCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAG                         GTATTGTGTTGGACTCTGGTGATGGTGTCA
genomic: CGTCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAGgtgagcacat ... cttttcccagGTATTGTGTTGGACTCTGGTGATGGTGTCA
EST: gi|58657067|gb|CK045747.1|CK045747
EST:     CGTCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAG                         GTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATG
genomic: CGTCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAGgtgagcacat ... cttttcccagGTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATG
EST: gi|58671902|gb|CK060588.1|CK060588
EST:     CGTCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAG                         GTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATG
genomic: CGTCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAGgtgagcacat ... cttttcccagGTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATG
EST: gi|58599400|gb|CK009928.1|CK009928
EST:     CGTCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAG                         GTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTTGTCCCCATCTAT
genomic: CGTCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAGgtgagcacat ... cttttcccagGTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACT-GTCCCCATCTAT
EST: gi|58677367|gb|CK066054.1|CK066054
EST:     CGTCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAG                         GTATCGTGTCGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATG
genomic: CGTCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAGgtgagcacat ... cttttcccagGTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATG
EST: gi|27576180|gb|CA998874.1|CA998874
EST:     CGTCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAG                         GTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATG
genomic: CGTCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAGgtgagcacat ... cttttcccagGTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATG
EST: gi|27578311|gb|CB001006.1|CB001006
EST:     CGTCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAG                         GTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATG
genomic: CGTCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAGgtgagcacat ... cttttcccagGTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATG
EST: gi|58610538|gb|CK038250.1|CK038250
EST:     CGTCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAG                         GTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATG
genomic: CGTCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAGgtgagcacat ... cttttcccagGTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATG
EST: gi|58659164|gb|CK047844.1|CK047844
EST:     TCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAG                         GTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATG
genomic: TCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAGgtgagcacat ... cttttcccagGTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATG
EST: gi|66947394|gb|AU312238.1|AU312238
EST:     CGTCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAG                         GTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATG
genomic: CGTCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAGgtgagcacat ... cttttcccagGTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATG
EST: gi|58589384|gb|CF987692.1|CF987692
EST:     CGTCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAG                         GTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATG
genomic: CGTCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAGgtgagcacat ... cttttcccagGTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATG
EST: gi|58596324|gb|CK006852.1|CK006852
EST:     CGTCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAG                         GTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATG
genomic: CGTCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAGgtgagcacat ... cttttcccagGTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATG
EST: gi|58675220|gb|CK063907.1|CK063907
EST:     CGTCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAG                         GTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATG
genomic: CGTCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAGgtgagcacat ... cttttcccagGTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATG
EST: gi|58653290|gb|CK041970.1|CK041970
EST:     CGTCGACATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAG                         GTATTGTGTTGGACTCTGGTGATGGTGT
genomic: CGTCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAGgtgagcacat ... cttttcccagGTATTGTGTTGGACTCTGGTGATGGTGT
EST: gi|396941638|gb|HO188295.1|HO188295
EST:     CGTCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAG                         GTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATG
genomic: CGTCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAGgtgagcacat ... cttttcccagGTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATG
EST: gi|66947175|gb|AU312019.1|AU312019
EST:     CGTCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAG                         GTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATG
genomic: CGTCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAGgtgagcacat ... cttttcccagGTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATG
EST: gi|66913140|gb|CX099988.1|CX099988
EST:     CGTCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAG                         GTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATG
genomic: CGTCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAGgtgagcacat ... cttttcccagGTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATG
EST: gi|58602094|gb|CK012622.1|CK012622
EST:     CGTCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAG                         GTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATG
genomic: CGTCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAGgtgagcacat ... cttttcccagGTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATG

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: 75 (upstream exon), 73 (downstream exon)
Score: 138

GAGAAGATGACCCAGATCATGTTTGAGACCTTCAACACCCCTGCTATGTACGTCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAGgtgagcacat ... cttttcccagGTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATGAAGGATATGCTCTCCCCCATGCTATCCTTCGTCTCGACCTTGCTGGGCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctttgacattttgatgtgctacagttgtgaataactgaatttccttttcccagGTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATGAAGGATATGCTCTCCCCCATGCTATCCTTCGTCTCGACCTTGCTGGGCG
                              gaataac  putative branch site (score: 138)
                                         tttccttttccc  putative PPT
         attttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataaatggaatcatgtttgaacatcctaattctgttggcatggagtgctttgacattttgatgtgctacagttgtgaataactgaatttccttttcccagGTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATGAAGGATATGCTCTCCCCCATGCTATCCTTCGTCTCGACCTTGCTGGGCG

- - - - -atcatgt
- - - - - - - - ttgaaca
- - - - - - - - - - - - - - -ttctgtt
- - - - - - - - - - - - - - - - - - -gcatgga
- - - - - - - - - - - - - - - - - - - - - - -tgctttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgctac