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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggcttcattccaacatttacaaagtccagcgaaatgctattctgatccccatgtttctattctgaccccatgtttgtttgaacagGGAGAGGCAGATGACAAGATTATTGCCGTTTGTGCTGATGATCCTGAGTACAAGCATTACAATGATATCAAGGAGCTCCCACCTCACCGCTTGGCTGAAA

Basic information

species Oryza sativa
transcript LOC_Os05g02310.1
intron # 6
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 6
lower sequence: GRMZM2G137930_T02 (Zea mays), 3'ss of exon 6
gtttggcttcattccaacatttacaaagtccagcgaaatgctattctgatccccatgtttctattctgaccc---catgtttgtttgaacagGGAGAGGCAGATGACAAGATTATTGCCGTTTGTGCTGATGATCCTGAGTACA--AGCATTA---CAATGAT--ATCAAGGAGCTCCCACCTCACCGCTTGGCTGAAA------
        | | | | |    |  |    ||||  |  | | |||    |    |  |  ||| || |   |    ||||    |   ||            | ||     ||||  | |  |||        | |  ||  ||   || |||   | |||||  |||| ||||   | |  | ||    |   || |       
----actgttacttccaagcatgtaggagccagtcattttccatttctgtttatagttgcctagtcgggaacatgtatgtaaactgttacttccgtgcatgcagGAGCCTGTTATCCCAGGCTGTTTCCTACGTGCGAAGGCCATCGGCCTTATGCCGATGATTGATCAGGGAGAGGC-AGATGACAAGATCATTGCAGTGTGCG

upper sequence: LOC_Os05g02310.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA10G05130.1 (Glycine max), 3'ss of exon 6
--gtttggcttcattccaacatttacaaagtcc-agcgaaatgctattctgatcccca-----tgtttctatt-ctgaccccatgtttgtt----tgaa---cagGGAGAGGCAGATGACAAGATTATTGCCGTTTGTGCTGATGATCCTGAGTACAAGCATTACAATGATATCAAGGAGCTCCCACCTCACCGCTTGGCTGAAA
   | |    |  | ||    |  ||||||    |||      || || |  || | |     | |||  |||  ||| |     ||  ||    ||||   ||||| |||  |||||||||||| ||||| || |||||||||||||||||||| | ||||||||||||||||||||| || || |||||||| || |||||||
gtatgttagatattccctttttccacaaagcaagagcctctctctctttttctctctagcagttcttttgattattgatcaaccattaattgtgatgaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTATAGGCATTACAATGATATCAAGGACCTTCCTCCTCACCGTTTAGCTGAAA

upper sequence: LOC_Os05g02310.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA03G33000.6 (Glycine max), 3'ss of exon 8
---gtttggcttcattccaacatttacaaagtccagcgaaatgctattctgatccccatgtttctattctgaccccatgtttgtttgaacagGGAGAGGCAGATGACAAGATTATTGCCGTTTGTGCTGATGATCCTGAGTACAAGCATTACAATGATATCAAGGAGCTCCCACCTCACCGCTTGGCTGAAA
     ||     | | ||| ||||| | |        ||| | || || ||||    |   ||  ||    ||    ||      |  | |||| |||  |||||| ||||| ||||| || |||||||||||||| |||||    ||||||||||||||||||||||| || || || || || |||||||
gtaaattaaacac-tcccaccatttcccacacggcaagaactcctcttttgatgttgaatattgaataaccacttattgcgctgatataaagGGGGAGAAAGATGATAAGATAATTGCTGTCTGTGCTGATGATCCCGAGTATCGACATTACAATGATATCAAGGAGCTTCCTCCACATCGTTTAGCTGAAA

upper sequence: LOC_Os05g02310.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA13G19500.2 (Glycine max), 3'ss of exon 6
-------------------------------------------------------------------gtttggcttcattccaacatttacaaa---gtccagcgaaatgctattctgatccccatgtttctattctgaccccatgtttgtttgaa--cagGGAGAGGCAGATGACAAGATTATTGCCGTTTGTGCTGATGATCCTGAGTACAAGCATTACAATGATATCAAGGAGCTCCCACCTCACCGCTTGGCTGAAA
                                                                    | |  ||  ||    | || || | |    |  |   | ||  |   | | ||      ||  |  |||  |   |  | || |  ||  ||||| |||  |||||||||||| ||||| || |||||||||||||||||||| | |||||||||||||||||||||||| || || ||||| || |||||||
gtatattagacattccctttttccacaaagcaagagcctctctctctctctctctctctctctctctctctctctatatatatatatatatatatatatatatatatatatttagcagttcttttgattattgatctaccattaattgtgatcaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTATAGGCATTACAATGATATCAAGGAGCTTCCTCCACACCGTTTAGCTGAAA

upper sequence: LOC_Os05g02310.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA19G35710.2 (Glycine max), 3'ss of exon 8
gtttggcttcattccaacatttacaaagtccagcgaaatgctattctgatccccatgt-ttctattctgaccccatgtttgtttgaacagGGAGAGGCAGATGACAAGATTATTGCCGTTTGTGCTGATGATCCTGAGTACAAGCATTACAATGATATCAAGGAGCTCCCACCTCACCGCTTGGCTGAAA
  |    |  |  |   ||||| |          ||| | || || ||||       |  |  ||    ||    |||     || | |||| |||  |||||| || |||||||| || |||||||||||||||||||| |  ||||||||||||||||| ||||| || || || || || |||||||
-gtaaattaaaccctctcatttcccgcaaggcaagaactcctcttttgattattgaatactgaataaccactaattgtgctgatgtaaagGGGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCTGAGTATAGACATTACAATGATATCAAAGAGCTTCCTCCACATCGTTTAGCTGAAA

upper sequence: LOC_Os05g02310.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv08s0040g02470.t01 (Vitis vinifera), 3'ss of exon 6
gtttggcttcattccaacatttacaaagtccagcgaaatgctattctgatccccatgtttctattctgaccccatgtttgtttgaacagGGAGAGGCAGATGACAAGATTATTGCCGTTTGTGCTGATGATCCTGAGTACAAGCATTACAATGATATCAAGGAGCTCCCACCTCACCGCTTGGCTGAAA
||        ||  ||| || ||     ||   | || | ||  ||| | ||   ||  |  ||  |||||     ||  ||   ||||||||||  |||||||||||| ||||| ||||||||||||||||||||||||   || |||| ||||||||| |||||||| || ||||| |||||||| |
gtagaaaaagatgacaagatatatttcctctc-ccaattact--tctaaacct--tgaattaatcttgacc-----ttgattaacacagGGAGAGAAAGATGACAAGATAATTGCAGTTTGTGCTGATGATCCTGAGTACCGACACTACACTGATATCAATGAGCTCCCTCCGCACCGTTTGGCTGAGA

upper sequence: LOC_Os05g02310.1 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ27171 (Selaginella moellendorffii), 3'ss of exon 4
gtttggcttcattccaacatttacaaagtccagcgaaatgct-attctgatccccatgtttctattctgaccccatgtttgtttgaacagGGAGAGGCAGATGACAAGATTATTGCCGTTTGTGCTGATGATCCTGAGTACAAGCATTACAATGATATCAAGGAGCTCCCACCTCACCGCTTGGCTGAAA
                               ||| || || | |   |  |  |   |||||| |        ||  | | | ||| ||||| |||   || || ||||| || || || || ||||||||||| ||||||||||||| ||  || |||||| ||||||| |||||| |  | || || |
-----------------------------gtagcaaagtgtttacattcttttcagcgtttctctaagagtgtca--tctatctgatcagGGGGAGAAGGACGATAAGATCATAGCAGTGTGCGCTGATGATCCAGAGTACAAGCATTGCACGGACATCAAGCAGCTCCCGCCTCACAGGCTAGCAGAGA

upper sequence: LOC_Os05g02310.1 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ33488 (Selaginella moellendorffii), 3'ss of exon 5
gtttggcttcattccaacatttacaaagtccagcgaaatgctattctgatccccatgtttctattctgaccccatgtttgtttgaacagGGAGAGGCAGATGACAAGATTATTGCCGTTTGTGCTGATGATCCTGAGTACAAGCATTACAATGATATCAAGGAGCTCCCACCTCACCGCTTGGCTGAAA
                               ||| ||||| |    |  |   ||   || |  |  ||       | | | ||| ||||| |||   || || ||||| || || || || ||||||||||| ||||||||||||| ||  || |||||| ||||||| |||||| |  | || || |
-----------------------------gtagcaaaatgtttacatccttttcagcgtttttctaagagtgt-catctatctgatcagGGGGAGAAGGACGATAAGATCATAGCAGTGTGCGCTGATGATCCAGAGTACAAGCATTGCACGGACATCAAGCAGCTCCCGCCTCACAGGCTAGCGGAGA

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:     GATGCTTCCTACGAGCAAAGGCCATTGGNCTCATGCCTATGATTGACCAG                         GGAGAGGCAGATGACAAGATTATTGCCGTTTGTGCTGATGATCCTGAGTAC
genomic: GATGCTTCCTACGAGCAAAGGCCATTGGTCTCATGCCTATGATTGACCAGgtttggcttc ... gtttgaacagGGAGAGGCAGATGACAAGATTATTGCCGTTTGTGCTGATGATCCTGAGTAC
EST: gi|88981027|gb|CI021154.1|CI021154
EST:     TCTCATGCCTATGATTGACCAG                         GGAGAGGCAGATGACAAGATTATTGCCGTTTGTGCTGATGATCCTGAGTAC
genomic: TCTCATGCCTATGATTGACCAGgtttggcttc ... gtttgaacagGGAGAGGCAGATGACAAGATTATTGCCGTTTGTGCTGATGATCCTGAGTAC
EST: gi|8594726|gb|AU093264.1|AU093264
EST:     GATGCTTCCTACGAGCAAAGGCCATTGGTCTCATGCCTATGATTGACCAG                         GGAGAGGCAGATGACAAGATTATTGCCGTTTGTGCTGATGATCCTGAGTAC
genomic: GATGCTTCCTACGAGCAAAGGCCATTGGTCTCATGCCTATGATTGACCAGgtttggcttc ... gtttgaacagGGAGAGGCAGATGACAAGATTATTGCCGTTTGTGCTGATGATCCTGAGTAC
EST: gi|3761138|gb|C98386.1|C98386
EST:     GATGCTTCCTACGAGCAAAGGCCATTGGTCTCATGCCTATGATTGACCAG                         GGAGAGGCAGATGACAAGATTATTGCCGTTTGTGCTGATGATCCTGAGTAC
genomic: GATGCTTCCTACGAGCAAAGGCCATTGGTCTCATGCCTATGATTGACCAGgtttggcttc ... gtttgaacagGGAGAGGCAGATGACAAGATTATTGCCGTTTGTGCTGATGATCCTGAGTAC
EST: gi|33663513|gb|CF294480.1|CF294480
EST:     GATGCTTCCTACGAGCAAAGGCCATTGGTCTCATGCCTATGATTGACCAG                         GGAGAGGCAGATGACAAGATTATTGCCGTTTGTGCTGATGATCCTGAGTAC
genomic: GATGCTTCCTACGAGCAAAGGCCATTGGTCTCATGCCTATGATTGACCAGgtttggcttc ... gtttgaacagGGAGAGGCAGATGACAAGATTATTGCCGTTTGTGCTGATGATCCTGAGTAC
EST: gi|33663512|gb|CF294479.1|CF294479
EST:     GATGCTTCCTACGAGCAAAGGCCATTGGTCTCATGCCTATGATTGACCAG                         GGAGAGGCAGATGACAAGATTATTGGCCGTTTGTGCTGATGATCCTGAGTA
genomic: GATGCTTCCTACGAGCAAAGGCCATTGGTCTCATGCCTATGATTGACCAGgtttggcttc ... gtttgaacagGGAGAGGCAGATGACAAGATTATTG-CCGTTTGTGCTGATGATCCTGAGTA
EST: gi|3763568|gb|AU030320.1|AU030320
EST:     GATGCTTCCTACGAGCAAAGGCCATTGGTCTCATGCCTATGATTGACCAG                         GGAGAGGCNGATGACAAGATTATTGCCGTTTGTGCTGATGATCCTGAGTAC
genomic: GATGCTTCCTACGAGCAAAGGCCATTGGTCTCATGCCTATGATTGACCAGgtttggcttc ... gtttgaacagGGAGAGGCAGATGACAAGATTATTGCCGTTTGTGCTGATGATCCTGAGTAC
EST: gi|117243396|gb|CT843443.1|CT843443
EST:     GATGCTTCCTACGAGCAAAGGCCATTGGTCTCATGCCTATGATTGACCAG                         GGAGAGGCAGATGACAAGATTATTGCCGTTTGTGCTGATGATCCTGAGTAC
genomic: GATGCTTCCTACGAGCAAAGGCCATTGGTCTCATGCCTATGATTGACCAGgtttggcttc ... gtttgaacagGGAGAGGCAGATGACAAGATTATTGCCGTTTGTGCTGATGATCCTGAGTAC
EST: gi|163918065|gb|EG713993.1|EG713993
EST:     GATGCTTCCTACGAGCAAAGGCCATTGGTCTCATGCCTATGATTGACCAG                         GGAGAGGCAGATGACA
genomic: GATGCTTCCTACGAGCAAAGGCCATTGGTCTCATGCCTATGATTGACCAGgtttggcttc ... gtttgaacagGGAGAGGCAGATGACA
EST: gi|87039980|gb|CI194602.1|CI194602
EST:     GATGCTTCCTACGAGCAAAGGCCATTGGTCTCATGCCTATGATTGACCAG                         GGAGAGGCAGATGACAAGATTATTGCCGTTTGTGCTGATGATCCTGAGTAC
genomic: GATGCTTCCTACGAGCAAAGGCCATTGGTCTCATGCCTATGATTGACCAGgtttggcttc ... gtttgaacagGGAGAGGCAGATGACAAGATTATTGCCGTTTGTGCTGATGATCCTGAGTAC

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: 66 (upstream exon), 29 (downstream exon)
Score: 62

GAGCCCGTTATACCAGGATGCTTCCTACGAGCAAAGGCCATTGGTCTCATGCCTATGATTGACCAGgtttggcttc ... gtttgaacagGGAGAGGCAGATGACAAGATTATTGCCGTTTGTGCTGATGATCCTGAGTACAAGCATTACAATGATATCAAGGAGCTCCCACCTCACCGCTTGGCTGAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaatgctattctgatccccatgtttctattctgaccccatgtttgtttgaacagGGAGAGGCAGATGACAAGATTATTGCCGTTTGTGCTGATGATCCTGAGTACAAGCATTACAATGATATCAAGGAGCTCCCACCTCACCGCTTGGCTGAAA
                             ttctgac  putative branch site (score: 62)
                                          tttgttt  putative PPT
                       tttctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttggcttcattccaacatttacaaagtccagcgaaatgctattctgatccccatgtttctattctgaccccatgtttgtttgaacagGGAGAGGCAGATGACAAGATTATTGCCGTTTGTGCTGATGATCCTGAGTACAAGCATTACAATGATATCAAGGAGCTCCCACCTCACCGCTTGGCTGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT