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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatttccttgaacaatatagtacttctagagaaaagtgttgtaccaacacaacttgtgttatcactgttaagtgttgattttactaatcctgtttcttgtgctttacagCTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAAATATAAGATACAAGGGTTTGGTTCTTGAACCGGGAGGTGAGAGGTTCTA

Basic information

species Oryza sativa
transcript LOC_Os02g47850.3
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47850.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G147450_T03 (Zea mays), 3'ss of exon 11
gtacatttccttgaacaatatagtacttctagagaaaagtgttgtaccaacacaacttgtgttatcactgttaagt-gttgattttactaatcctgtttcttgtgctttacagCTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAAATATAAGATACAAGGGTT-----TGGTTCTTGAACCGGGAGGTGAGAGGTTCTA
|||||||| |||   | | |   | ||  |     |   || ||||  |||  |   ||   | | | ||| |  | | |||| |  | | ||  || | |||||||||||||| || ||||| ||||||||| | ||||||| |||||||||||||||        ||     ||| |||      | ||  | |  |      |    | |     
gtacattttcttttgctagaatcttctgttgatccaccatggtgtag-aacgta--ctgctatcttaatgtgatttagctgatgtctcgattc--gtcttttgtgctttacagCCTTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGGGAGGGGAGTACTG-GCAAAGGTCAACAATTGTCTTGGTGCTCTCTCGCAGCAAGC----
















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|88365911|gb|CI545770.1|CI545770
EST:     TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGG                         CTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
genomic: TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGGgtacatttcc ... tgctttacagCTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
EST: gi|88385064|gb|CI561720.1|CI561720
EST:     TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGG                         CTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
genomic: TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGGgtacatttcc ... tgctttacagCTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
EST: gi|89176288|gb|CI043309.1|CI043309
EST:     TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGG                         CTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
genomic: TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGGgtacatttcc ... tgctttacagCTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
EST: gi|58661834|gb|CK050514.1|CK050514
EST:     TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGG                         CTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
genomic: TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGGgtacatttcc ... tgctttacagCTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
EST: gi|88250235|gb|CI348465.1|CI348465
EST:     TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGG                         CTTTTGGTTAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
genomic: TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGGgtacatttcc ... tgctttacagCTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
EST: gi|25803551|gb|CA759512.1|CA759512
EST:     TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGG                         CTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
genomic: TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGGgtacatttcc ... tgctttacagCTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
EST: gi|86880519|gb|CI321005.1|CI321005
EST:     TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGG                         CTTTTGGTGAATTTATAGGAG-TGATGAAGAACAACAGATTGTGAGGCGCA
genomic: TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGGgtacatttcc ... tgctttacagCTTTTGGTGAATTTATA-GAGATGATGAAGAACAACAGATTGTGAGGCGCA
EST: gi|88468047|gb|CI517506.1|CI517506
EST:     TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGG                         CTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
genomic: TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGGgtacatttcc ... tgctttacagCTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
EST: gi|88274055|gb|CI394461.1|CI394461
EST:     CCATCCAGAGTCCTCACCCGGGCCGCATGATTCTTACTTGG                         CTTTT-GTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
genomic: CCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGGgtacatttcc ... tgctttacagCTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
EST: gi|88268554|gb|CI378489.1|CI378489
EST:     TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGG                         CTTGTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGGCA
genomic: TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGGgtacatttcc ... tgctttacagCTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCG-CA
EST: gi|88266357|gb|CI377259.1|CI377259
EST:     TCTTCACTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGG                         CTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
genomic: TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGGgtacatttcc ... tgctttacagCTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
EST: gi|88975138|gb|CI023389.1|CI023389
EST:     TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGG                         CTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
genomic: TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGGgtacatttcc ... tgctttacagCTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
EST: gi|88232225|gb|CI230683.1|CI230683
EST:     TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGG                         CTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
genomic: TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGGgtacatttcc ... tgctttacagCTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
EST: gi|88322108|gb|CI537691.1|CI537691
EST:     TCTTCAGTACCATCCAGAGTCCTCACCCGGNCCGCATGATTCTGACTTGG                         CTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
genomic: TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGGgtacatttcc ... tgctttacagCTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
EST: gi|86482764|gb|CI125397.1|CI125397
EST:     TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGG                         CTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
genomic: TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGGgtacatttcc ... tgctttacagCTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA

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: 69 (upstream exon), 73 (downstream exon)
Score: 101

AACGATAATAGCTGTGCCGGCCTTCAGTACCCTAAGATGAAACTTTTGTCTCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGGgtacatttcc ... tgctttacagCTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAAATATAAGATACAAGGGTTTGGTTCTTGAACCGGGAGGTGAGAGGTTCTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgttatcactgttaagtgttgattttactaatcctgtttcttgtgctttacagCTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAAATATAAGATACAAGGGTTTGGTTCTTGAACCGGGAGGTGAGAGGTTCTA
                           tactaat  putative branch site (score: 101)
                                      tttcttgt  putative PPT
                    ttgattttactaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatttccttgaacaatatagtacttctagagaaaagtgttgtaccaacacaacttgtgttatcactgttaagtgttgattttactaatcctgtttcttgtgctttacagCTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAAATATAAGATACAAGGGTTTGGTTCTTGAACCGGGAGGTGAGAGGTTCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG