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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtttgtgacttgtctgatgtgattccttgatacatatgtaacgtgtctcttttttccgcatatagGATGTTTCAAGGGAGTTCAGGAGCACTCTTGAACGAGAAATTGGACTTGATGAAGTTCCCCCATCAATGAACTACAGGCCCCCGACCATGAATAATAGTC

Basic information

species Oryza sativa
transcript LOC_Os11g37130.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g37130.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G151529_T02 (Zea mays), 3'ss of exon 3
gttggtttgtgacttgtctgatgtgat-tccttgatacatatg-----taacgtgtctcttttttccgcatatagGATGTTTCAAGGGAGTTCAGGAGCACTCTTGAACGAGAAATTGGACTTGATGAAGTTCCCCCATCAATGAACTACAGGCCCCCGACCATGAATAATAGTC
||||||   | | |||| || ||  || |  ||||      ||     ||| |        |||   |||  |||||||| ||||||||||||||||||||||||||||||||||| ||| ||||||| ||| |||  || | ||| || |  ||| ||||||||||||| |  |
gttggtcctttatttgt-tgttgcaatatgtttgacgatcttgcttcgtaatgcaatatgatttgatgcacttagGATGTATCAAGGGAGTTCAGGAGCACTCTTGAACGAGAAATCGGAATTGATGAGGTTTCCCAGTCGACGAATTATACACCCACGACCATGAATAACAACC

upper sequence: LOC_Os11g37130.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G898735_T02 (Zea mays), 3'ss of exon 3
gttggtttgtgacttgtc-tgatgtgattccttgatacat-atgtaacgtgtctcttttttccgcatatagGATGTTTCAAGGGAGTTCAGGAGCACTCTTGAACGAGAAATTGGACTTGATGAAGTTCCCCCATCAATGAACTACAGGCCCCCGACCATGAATAATAGTC
||||||   |   ||||    || || ||          | | || | ||       ||| | |||  |||||||| ||||||||||||||||||||||||||||||||||| ||| ||||||| ||| ||| ||||| |||||| |||||| | ||||||||||| |  |
gttggtccttagtttgttacaatatgtttgaggatcttgttacgttatgtaatatgatttgctgcacttagGATGTATCAAGGGAGTTCAGGAGCACTCTTGAACGAGAAATCGGAATTGATGAGGTTTCCCAATCAACGAACTATAGGCCCACAACCATGAATAACAACC

upper sequence: LOC_Os11g37130.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA10G37690.1 (Glycine max), 3'ss of exon 3
-------------gttggtttgtgacttgtctgatgtgattccttgatacatatg---taacgt-gtctctt----ttttccgcatatagGATGTTTCAAGGGAGTTCAGGAGCACTCTTGAACGAGAAATTGGACTTGATGA-AGTTC---CCCCATCAATGAACTACAGGCCCCCGACCATGAATAATAGTC
              ||     || | |  | |      |||||   | | | |||   ||| ||  |  |||    ||| || | | ||||||||||||||||| || | ||| ||||||||||| || ||||| |||||||| | ||     || | | |  |   | |     || || ||    ||||   
gttggtgctaaatattttcaagtaaatattttatgccaattccactacatagatgctttaatgttattgcttgccatttcccccctttagGATGTTTCAAGGGAATTTAAGAGTACTCTTGAACGGGAGATTGGTCTTGATGACAATTTAAGTCCAACCCAGAACACATACAATTCCAAC-ATACGCAATA---

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|88594632|gb|CI714590.1|CI714590
EST:     ATTTGGGGAAGACTTTGCGTGCTTTCCAGCCAACCATTAGAGAGCTACAG                         GATGTTTCAAGGGAGTTCAGGAGCACTCTTGAACGAGAAATTGGAC-T--T
genomic: ATTTGGGGAAGACTTTGCGTGCTTTCCAGCCAACCATTAGAGAGCTACAGgttggtttgt ... ccgcatatagGATGTTTCAAGGGAGTTCAGGAGCACTCTTGAACGAGAAATTGGACTTGAT
EST: gi|29663432|gb|CB659707.1|CB659707
EST:     ATTTGGGGAAGACTTTGCGTGCTTTCCAGCCAACCATTAGAGAGCTACAG                         GATGTTTCAAGGGAGTTCAGGAGCACTCTTGAACGAGAAATTGGACTTGAT
genomic: ATTTGGGGAAGACTTTGCGTGCTTTCCAGCCAACCATTAGAGAGCTACAGgttggtttgt ... ccgcatatagGATGTTTCAAGGGAGTTCAGGAGCACTCTTGAACGAGAAATTGGACTTGAT
EST: gi|88691337|gb|CI733921.1|CI733921
EST:     TTTGCGTGCTTTCCAGCCAACCATTAGAGAGCTACAG                         GATGTTTCAAGGGAGTTCAGGAGCACTCTTGAACGAGAAATTGGACTTGAT
genomic: TTTGCGTGCTTTCCAGCCAACCATTAGAGAGCTACAGgttggtttgt ... ccgcatatagGATGTTTCAAGGGAGTTCAGGAGCACTCTTGAACGAGAAATTGGACTTGAT
EST: gi|88594536|gb|CI714494.1|CI714494
EST:     ATTTGGGGAAGACTTTGCGTGCTTTCCAGCCAACCATTAGAGAGCTACAG                         GATGTTTCAAGGGAGTTCAGGAGCACTCTTGAACGAGAAATTGGAC-T--T
genomic: ATTTGGGGAAGACTTTGCGTGCTTTCCAGCCAACCATTAGAGAGCTACAGgttggtttgt ... ccgcatatagGATGTTTCAAGGGAGTTCAGGAGCACTCTTGAACGAGAAATTGGACTTGAT
EST: gi|88593428|gb|CI713382.1|CI713382
EST:     ATTTGGGGAAGACTTTGCGTGCTTTCCAGCCAACCATTAGAGAGCTACAG                         GATGTTTCAAGGGAGTTCAGGAGCACTCTTGAACGAGAAATTGGAC-T--T
genomic: ATTTGGGGAAGACTTTGCGTGCTTTCCAGCCAACCATTAGAGAGCTACAGgttggtttgt ... ccgcatatagGATGTTTCAAGGGAGTTCAGGAGCACTCTTGAACGAGAAATTGGACTTGAT
EST: gi|88689432|gb|CI733008.1|CI733008
EST:     TTTGCGTGCTTTCCAGCCAACCATTACAGAGCTACAG                         GATGTTTCAAGGGAGTTCAGGAGCACTCTTGAACGAGAAATTGGACTTGAT
genomic: TTTGCGTGCTTTCCAGCCAACCATTAGAGAGCTACAGgttggtttgt ... ccgcatatagGATGTTTCAAGGGAGTTCAGGAGCACTCTTGAACGAGAAATTGGACTTGAT

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: 44 (upstream exon), 60 (downstream exon)
Score: 14

GTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAGCCAACCATTAGAGAGCTACAGgttggtttgt ... ccgcatatagGATGTTTCAAGGGAGTTCAGGAGCACTCTTGAACGAGAAATTGGACTTGATGAAGTTCCCCCATCAATGAACTACAGGCCCCCGACCATGAATAATAGTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtctgatgtgattccttgatacatatgtaacgtgtctcttttttccgcatatagGATGTTTCAAGGGAGTTCAGGAGCACTCTTGAACGAGAAATTGGACTTGATGAAGTTCCCCCATCAATGAACTACAGGCCCCCGACCATGAATAATAGTC
                         atgtaac  putative branch site (score: 14)
                               cgtgtctcttttttcc  CT-rich tract
                   atacatat  TA-rich tract