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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacctcttgtccaataatagtatcattctattaggttatattcacatctcactccttttgtttggggaaccatattaaattctaatttttgttcaaacagGAGCCCGTTATACCAGGATGCTTCCTACGAGCAAAGGCCATTGGTCTCATGCCTATGATTGACCAG

Basic information

species Oryza sativa
transcript LOC_Os05g02310.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g02310.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA10G05130.1 (Glycine max), 3'ss of exon 5
tacctcttgtccaataatag--tatcattctattaggttatattcacatctcactccttttgtttggggaaccatattaaattctaatttt---tgttcaaacagGAGCCCGTTATACCAGGATGCTTCCTACGAGCAAAGGCCATTGGTCTCATGCCTATGATTGACCAG
    |  | | || || ||   ||| | ||||||||||  |  ||   | | |    ||| || |   |    ||  |||    |  | ||   || |   ||||||||| ||| | ||||| ||||| ||||| || || || ||||| ||||||||||||||||| |||
---attatcttcagtagtatgttattaatctattaggtact--tcttgttttatgtttttagtgttttgtgtgatgctaacccttcgtcttacttggttggacagGAGCCAGTTCTTCCAGGTTGCTTTCTACGGGCCAAAGCTATTGGACTCATGCCTATGATTGATCAG

upper sequence: LOC_Os05g02310.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv08s0040g02470.t01 (Vitis vinifera), 3'ss of exon 5
tacctcttgtccaataatagtatcattctattaggttatattcacatctcactccttttgtttggggaaccatattaaattctaatttttgttcaaaca------gGAGCCCGTTATACCAGGATGCTTCCTACGAGCAAAGGCCATTGGTCTCATGCCTATGATTGACCAG
 |  | |||        | || ||    ||||     ||||| |||   || |  || |   |||  |  |  ||  | | || ||   | ||||||||      ||| || ||| | ||||||||||| || || || || || ||||||||||||||||||||||| |||
aattttttggatgtgcttggtttctgaatatt---ccatatt-acaaagcaatggttataaatggaaactctcat--attccttatggcttttcaaacatttacagGAACCAGTTCTTCCAGGATGCTTTCTCCGGGCTAAAGCTATTGGTCTCATGCCTATGATTGATCAG
















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|8859734|gb|AU097052.1|AU097052
EST:     ACGCTGTTGTGAAGAAAGTGAATCCGTTGGATGTNCTGGTTATAATGCAG                         GAGCCCCGTTATACCCAGGATGCTTCCTACGAGCAAAGGCCATTGGNCTCA
genomic: ACGCTG-TGTGAAGACAGTG-ATCCGTTGGATGTGCTGGTTATAATGCAGgtatgtcttt ... gttcaaacagGAG-CCCGTTATA-CCAGGATGCTTCCTACGAGCAAAGGCCATTGGTCTCA
EST: gi|4878573|gb|AU062872.1|AU062872
EST:     GCACGCTGTGTGAAGACAGTGATCCGTTGGATGTGCTNGTTATAATGCAG                         GAGCCCGTTATACCAGGGTGCTTCCTACGAGCAAAGGC-ATTGGGCTCATG
genomic: GCACGCTGTGTGAAGACAGTGATCCGTTGGATGTGCTGGTTATAATGCAGgtatgtcttt ... gttcaaacagGAGCCCGTTATACCAGGATGCTTCCTACGAGCAAAGGCCATTGGTCTCATG
EST: gi|8594726|gb|AU093264.1|AU093264
EST:     GCACGCTGTGTGAAGACAGTGATCCGTTGGATGTGCTGGTTATAATGCAG                         GAGCCCGTTATACCAGGATGCTTCCTACGAGCAAAGGCCATTGGTCTCATG
genomic: GCACGCTGTGTGAAGACAGTGATCCGTTGGATGTGCTGGTTATAATGCAGgtatgtcttt ... gttcaaacagGAGCCCGTTATACCAGGATGCTTCCTACGAGCAAAGGCCATTGGTCTCATG
EST: gi|3761138|gb|C98386.1|C98386
EST:     GCACGCTGTGTGANGACAGTGATCCGTTGGATGTGCTGGTTATAATGCAG                         GAGCCCGTTATACCAGGATGCTTCCTACGAGCAAAGGCCATTGGTCTCATG
genomic: GCACGCTGTGTGAAGACAGTGATCCGTTGGATGTGCTGGTTATAATGCAGgtatgtcttt ... gttcaaacagGAGCCCGTTATACCAGGATGCTTCCTACGAGCAAAGGCCATTGGTCTCATG
EST: gi|33663513|gb|CF294480.1|CF294480
EST:     CACGCTGTGTGAAGACAGTGATCCGTTGGATGTGCTGGTTATAATGCAG                         GAGCCCGTTACACCAGGATGCTTCCTACGAGCAAAGGCCATTGGTCTCATG
genomic: CACGCTGTGTGAAGACAGTGATCCGTTGGATGTGCTGGTTATAATGCAGgtatgtcttt ... gttcaaacagGAGCCCGTTATACCAGGATGCTTCCTACGAGCAAAGGCCATTGGTCTCATG
EST: gi|33663512|gb|CF294479.1|CF294479
EST:     GCACGCTGTGTGAAGACAGTGATCCGTTGGATGTGCTGGTTATAATGCAG                         GAGCCCGTTACACCAGGATGCTTCCTACGAGCAAAGGCCATTGGTCTCATG
genomic: GCACGCTGTGTGAAGACAGTGATCCGTTGGATGTGCTGGTTATAATGCAGgtatgtcttt ... gttcaaacagGAGCCCGTTATACCAGGATGCTTCCTACGAGCAAAGGCCATTGGTCTCATG
EST: gi|3763568|gb|AU030320.1|AU030320
EST:     GCACGCTGTGTGAAGACAGTGATCCGTTGGATGTGCTGGTTATAATGCAG                         GAGCCCGTTATACCAGGATGCTTCCTACGAGCAAAGGCCATTGGTCTCATG
genomic: GCACGCTGTGTGAAGACAGTGATCCGTTGGATGTGCTGGTTATAATGCAGgtatgtcttt ... gttcaaacagGAGCCCGTTATACCAGGATGCTTCCTACGAGCAAAGGCCATTGGTCTCATG
EST: gi|88425227|gb|CI564744.1|CI564744
EST:     GCACGCTGTGTGAAGACAGTGATCCGTTGGATGTGCTGGTTATAATGCAG                         GAGCCCGTTATAC-AGGATGC
genomic: GCACGCTGTGTGAAGACAGTGATCCGTTGGATGTGCTGGTTATAATGCAGgtatgtcttt ... gttcaaacagGAGCCCGTTATACCAGGATGC
EST: gi|117243396|gb|CT843443.1|CT843443
EST:     GCACGCTGTGTGAAGACAGTGATCCGTTGGATGTGCTGGTTATAATGCAG                         GAGCCCGTTATACCAGGATGCTTCCTACGAGCAAAGGCCATTGGTCTCATG
genomic: GCACGCTGTGTGAAGACAGTGATCCGTTGGATGTGCTGGTTATAATGCAGgtatgtcttt ... gttcaaacagGAGCCCGTTATACCAGGATGCTTCCTACGAGCAAAGGCCATTGGTCTCATG
EST: gi|163918065|gb|EG713993.1|EG713993
EST:     GCACGCTGTGTGAAGACAGTGATCCGTTGGATGTGCTGGTTATAATGCAG                         GAGCCCGTTATACCAGGATGCTTCCTACGAGCAAAGGCCATTGGTCTCATG
genomic: GCACGCTGTGTGAAGACAGTGATCCGTTGGATGTGCTGGTTATAATGCAGgtatgtcttt ... gttcaaacagGAGCCCGTTATACCAGGATGCTTCCTACGAGCAAAGGCCATTGGTCTCATG
EST: gi|87039980|gb|CI194602.1|CI194602
EST:     GCACGCTGTGTGAAGACAGTGATCCGTTGGATGTGCTGGTTATAATGCAG                         GAGCCCGTTATACCAGGATGCTTCCTACGAGCAAAGGCCATTGGTCTCATG
genomic: GCACGCTGTGTGAAGACAGTGATCCGTTGGATGTGCTGGTTATAATGCAGgtatgtcttt ... gttcaaacagGAGCCCGTTATACCAGGATGCTTCCTACGAGCAAAGGCCATTGGTCTCATG

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: 72 (upstream exon), 66 (downstream exon)
Score: 35

TGTGCTCTATTCATCAGTTGTGTACCCTCACAACTATGGATTCATTCCTCGCACGCTGTGTGAAGACAGTGATCCGTTGGATGTGCTGGTTATAATGCAGgtatgtcttt ... gttcaaacagGAGCCCGTTATACCAGGATGCTTCCTACGAGCAAAGGCCATTGGTCTCATGCCTATGATTGACCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctcactccttttgtttggggaaccatattaaattctaatttttgttcaaacagGAGCCCGTTATACCAGGATGCTTCCTACGAGCAAAGGCCATTGGTCTCATGCCTATGATTGACCAG
                                  ttctaat  putative branch site (score: 35)
                                        tttttgttc  CT-rich tract
                          atattaaattctaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacctcttgtccaataatagtatcattctattaggttatattcacatctcactccttttgtttggggaaccatattaaattctaatttttgttcaaacagGAGCCCGTTATACCAGGATGCTTCCTACGAGCAAAGGCCATTGGTCTCATGCCTATGATTGACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaccata