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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagggctccagaggaaccttttcggctgacagtttgatcattatgtttccgctctgacaaaatgatatttgaatctttgtagTGTGCCACTGCTGATCCTGATGGCCGTAAGAGAGCTCTTCTCATTGGAGGTGGTATAGCGAACTTCACTGATGTCGCTGCTACATTCAGTGGCATCATTC

Basic information

species Oryza sativa
transcript LOC_Os12g37870.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g37870.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G034083_T01 (Zea mays), 3'ss of exon 8
gtaagggctccagaggaaccttttcggctgacagttt-----gatcattatgtttccgctctgacaaaatgatatttgaatctttgtagTGTGCCACTGCTGATCCTGATGGCCGTAAGAGAGCTCTTCTCATTGGAGGTGGTATAGCGAACTTCACTGATGTCGCTGCTACATTCAGTGGCATCATTC
|||||  |   ||  |||||||| | |||| |  | |     | || |||  | |    |     || |||   ||| ||    || |||| || ||  ||||||||||||||||||||||||| ||||| || ||||| || || || |||||||| ||||| ||| ||||||| |||||||||||||
gtaagaac---agtagaaccttt-cagctgtctatcttttctgttcgttacatatatctttcatgaatatgt--tttcaactcgtgcagTGCGCTACCTCTGATCCTGATGGCCGTAAGAGAGCCCTTCTAATCGGAGGAGGAATCGCTAACTTCACAGATGTTGCTTCTACATTTAGTGGCATCATTC

upper sequence: LOC_Os12g37870.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT1G09430.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaagggctccagaggaacct----tttcggctgacagttt--gatcattatgtttccgct-ctgacaaaatga-tatttgaatctttgtagTGTGCCACTGCTGATCCTGATGGCCGTAAGAGAGCTCTTCTCATTGGAGGTGGTATAGCGAACTTCACTGATGTCGCTGCTACATTCAGTGGCATCATTC
|| ||   |    | |||| |    |||    | |  ||||      || |  |||  |    | ||| |   |   || |    ||   ||||||||||| |||||||||| || |||||  |||||||||| |||||||| || || || || ||||||||||| || ||||| ||||  || |||||||
gtgagtcatggcaaagaacttggccttttccttaattgtttctatctataaaattttagagattcacagaccaaacgttcgggctttctcagTGTGCCACTACTGATCCTGACGGGCGTAAACGAGCTCTTCTAATTGGAGGAGGCATTGCCAATTTCACTGATGTGGCAGCTACTTTCAACGGTATCATTC

upper sequence: LOC_Os12g37870.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv14s0060g00550.t01 (Vitis vinifera), 3'ss of exon 9
-------gtaagggctccagaggaaccttttcggctgacagtttgatcattatgttt-ccgctctgacaaaatgatatttg--------------aatctttgtagTGTGCCACTGCTGATCCTGATGGCCGTAAGAGAGCTCTTCTCATTGGAGGTGGTATAGCGAACTTCACTGATGTCGCTGCTACATTCAGTGGCATCATTC
        | | |      |    ||||||| ||||  ||| |   |  | |  ||| | |||   |  || |   |||||              | |||||  ||||||| |||||||| |||||||||||||||||||| |||||||||||||| ||||| || |||||||||||||| ||||| || |||| ||| ||  | |
gtaagaaattatgaactttggcataccttttgggctt-cagctctttgttaaaatttgctgcttaaaataattttcatttgttgtggaacaatatactctttacagTGTGCTACTGCTGACCCTGATGGCCGTAAGAGAGCCCTTCTCATTGGAGGGGGTATTGCTAACTTCACTGATGTTGCTGCCACTTTCAATGGGATTGTCC

upper sequence: LOC_Os12g37870.1 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S7_156V6.2 (Physcomitrella patens), 3'ss of exon 10
------------------------------------------------------------------------------------------------gtaagggctccagaggaaccttttcggctgacagtttgatcattatgtttccgctctgacaaaatgatatttgaatctttgtagTGTGCCACTGCTGATCCTGATGGCCGTAAGAGAGCTCTTCTCATTGGAGGTGGTATAGCGAACTTCACTGATGTCGCTGCTACATTCAGTGGCATCATTC
                                                                                                   |    |   || | | || |   ||   |  |||| | |    |  || || ||          || ||   | | | ||||||  ||||||  |||||||||| ||    ||||| ||  || |||||||||| || || ||||||||||| || ||||||||||||| ||| || ||||
gtaagttctttcataacatacatgaaaccacctagcccactagtatgagctatgactagtagtaagtctgtctcgcagagaaaatcaatctaatcaactacaaattttgacgtatctgtgaagc-atctatttgttta--gaggatcagccctagttctgacctagttctttttgt-tagTGTTGCACTGCAAATCCTGATGGACGCCGAAGAGCGCTAGTCGTTGGAGGTGGAATTGCCAACTTCACTGACGTTGCTGCTACATTCAATGGTATTATTC

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|27577556|gb|CB000251.1|CB000251
EST:     CGCTCCCAACGAGGAGGAGGTTCTGCACTATGCTAGAGTGGTTTTTGGAT                         TGTGCCACTGCTGATCCTGATGGCCGT
genomic: CGCTCCCAACGAGGAGGAGGTTCTGCAGTATGCTAGAGTGGTTTT-GGATgtaagggctc ... atctttgtagTGTGCCACTGCTGATCCTGATGGCCGT
EST: gi|33807858|gb|CF329821.1|CF329821
EST:     GCGCTCCCAACGAGGAGGAGGTTCTGCAGTATGCTAGAGTGGTTTTGGAT                         TGTGCCACTGCTGATCCTGATGGCCGTAAGAGAGCTCTTCTCATTG
genomic: GCGCTCCCAACGAGGAGGAGGTTCTGCAGTATGCTAGAGTGGTTTTGGATgtaagggctc ... atctttgtagTGTGCCACTGCTGATCCTGATGGCCGTAAGAGAGCTCTTCTCATTG
EST: gi|88248192|gb|CI248041.1|CI248041
EST:     GAGGAGGTTCTGCAGTATGCTAGAGTGGTTTTGGAT                         TGTGCCACTGCTGATCCTGATGGCCGTAAGAGAGCTCTTCTCATTGGAGGT
genomic: GAGGAGGTTCTGCAGTATGCTAGAGTGGTTTTGGATgtaagggctc ... atctttgtagTGTGCCACTGCTGATCCTGATGGCCGTAAGAGAGCTCTTCTCATTGGAGGT
EST: gi|88974793|gb|CI023089.1|CI023089
EST:     GCGCTCCCAACGAGGAGGAGGTTCTGCAGTATGCTAGAGTGGTTTTGGAT                         TGTGCCACTGCTGATCCTGATGGCCGTAAGAGAGCTCTTCTCATTGGAGGT
genomic: GCGCTCCCAACGAGGAGGAGGTTCTGCAGTATGCTAGAGTGGTTTTGGATgtaagggctc ... atctttgtagTGTGCCACTGCTGATCCTGATGGCCGTAAGAGAGCTCTTCTCATTGGAGGT
EST: gi|33807860|gb|CF329822.1|CF329822
EST:     GCTCCCAACGAGGAGGAGGTTCTGCAGTATGCTAGAGTGGTTTTGGAT                         TGTGCCACTGCTGATCCTGATGGCCGTAAGAGAGCTCTTCTCATTGGAGGT
genomic: GCTCCCAACGAGGAGGAGGTTCTGCAGTATGCTAGAGTGGTTTTGGATgtaagggctc ... atctttgtagTGTGCCACTGCTGATCCTGATGGCCGTAAGAGAGCTCTTCTCATTGGAGGT
EST: gi|87021578|gb|CI275977.1|CI275977
EST:     AGTGGTTTTGGAT                         TGTGCCACTGCTGATCCTGATGCCCGTAAGAGAGCTCTTCTCATTGGAGGT
genomic: AGTGGTTTTGGATgtaagggctc ... atctttgtagTGTGCCACTGCTGATCCTGATGGCCGTAAGAGAGCTCTTCTCATTGGAGGT
EST: gi|29662348|gb|CB658623.1|CB658623
EST:     GCGCTCCCAACGAGGAGGAGGTTTTGCAGTATGCTAGAGTGGTTTTGGAT                         TGTGCCACTGCTGATCCTGATGGCCGTAAGAGAGCTCTTCTCATTGGAGGT
genomic: GCGCTCCCAACGAGGAGGAGGTTCTGCAGTATGCTAGAGTGGTTTTGGATgtaagggctc ... atctttgtagTGTGCCACTGCTGATCCTGATGGCCGTAAGAGAGCTCTTCTCATTGGAGGT
EST: gi|29680113|gb|CB676388.1|CB676388
EST:     GCGCTCCCAACGAGGAGGAGGTTCTGCAGTATGCTAGAGTGGTTTTGGAT                         TGTGCCACTGCTGATCCTGATGGCCGTAAGAGAGCTCTTCTCATTGGAGGT
genomic: GCGCTCCCAACGAGGAGGAGGTTCTGCAGTATGCTAGAGTGGTTTTGGATgtaagggctc ... atctttgtagTGTGCCACTGCTGATCCTGATGGCCGTAAGAGAGCTCTTCTCATTGGAGGT
EST: gi|29638061|gb|CB643070.1|CB643070
EST:     GCGCTCCCAACGAGGAGGAGGTTCTGCAGTATGCTAGAGTGGTTTTGGAT                         TGTGCCACTGCTGATCCTGATGGCCGTAAGAGAGCTCTTCTCATTGGAGGT
genomic: GCGCTCCCAACGAGGAGGAGGTTCTGCAGTATGCTAGAGTGGTTTTGGATgtaagggctc ... atctttgtagTGTGCCACTGCTGATCCTGATGGCCGTAAGAGAGCTCTTCTCATTGGAGGT
EST: gi|29669994|gb|CB666269.1|CB666269
EST:     GCGCTCCCAACGAGGAGGAGGTTTTGCAGTATGCTAGAGTGGTTTTGGAT                         TGTGCCCCTGCTGATCCTGATGGCCGTAAGAGAGCTCTTTTCATTGGAGGT
genomic: GCGCTCCCAACGAGGAGGAGGTTCTGCAGTATGCTAGAGTGGTTTTGGATgtaagggctc ... atctttgtagTGTGCCACTGCTGATCCTGATGGCCGTAAGAGAGCTCTTCTCATTGGAGGT
EST: gi|88248053|gb|CI246671.1|CI246671
EST:     AGGTTCTGCAGTATGCTAGAGTGGTTTTGGAT                         TGTGCCACTGCTGATCCTGATGGCCGTAAGAGAGCTCTTCTCATTGGAGGT
genomic: AGGTTCTGCAGTATGCTAGAGTGGTTTTGGATgtaagggctc ... atctttgtagTGTGCCACTGCTGATCCTGATGGCCGTAAGAGAGCTCTTCTCATTGGAGGT
EST: gi|86908638|gb|CI318965.1|CI318965
EST:     AGAGTGGTTTTGGAT                         T-TCCCACTGCTGATCCTGATGGCCGTAAGAGAGCTCTTCTCATTGGAGGT
genomic: AGAGTGGTTTTGGATgtaagggctc ... atctttgtagTGTGCCACTGCTGATCCTGATGGCCGTAAGAGAGCTCTTCTCATTGGAGGT

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), 72 (downstream exon)
Score: 63

TGGAGATTTGGGATATGCGTCAGAGCTTGGAAATTATGCAGAATACAGCGGCGCTCCCAACGAGGAGGAGGTTCTGCAGTATGCTAGAGTGGTTTTGGATgtaagggctc ... atctttgtagTGTGCCACTGCTGATCCTGATGGCCGTAAGAGAGCTCTTCTCATTGGAGGTGGTATAGCGAACTTCACTGATGTCGCTGCTACATTCAGTGGCATCATTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacagtttgatcattatgtttccgctctgacaaaatgatatttgaatctttgtagTGTGCCACTGCTGATCCTGATGGCCGTAAGAGAGCTCTTCTCATTGGAGGTGGTATAGCGAACTTCACTGATGTCGCTGCTACATTCAGTGGCATCATTC
                        ctctgac  putative branch site (score: 63)
                                              tctttgt  putative PPT
                               aaaatgatatttgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagggctccagaggaaccttttcggctgacagtttgatcattatgtttccgctctgacaaaatgatatttgaatctttgtagTGTGCCACTGCTGATCCTGATGGCCGTAAGAGAGCTCTTCTCATTGGAGGTGGTATAGCGAACTTCACTGATGTCGCTGCTACATTCAGTGGCATCATTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT