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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggttcctgatcgattgcgcctccctccccctcctcgtcgcgctctcccgctgcgcatctcaccatttcgttgcgatgtttttgctggtttctgattggtgggttgtggcgatgatgcagAAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACT

Basic information

species Oryza sativa
transcript LOC_Os05g41110.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g41110.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G044137_T02 (Zea mays), 3'ss of exon 1
gtaaggttcctgatcgattgcgcctccctccccctcc-tcgtcgcgctctcccgctgcgcatctcaccatttcgttgcgatgtttttgctggtttctgattggtgggttgtggcgatgatgcagAAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACT---
               |  ||  || |   |  ||||  | |   | |||| || || ||      |   |||   || ||||||  |  |||| ||   ||    ||||  |      ||||||||||||||||| || | ||||||||||||||||||||||||||||||||||||||||||||| || ||||||||||||||||||||||||||||||||||   
---------------gtatgaaccccaagcaacctcagttggtcctctcttccacttcggggtgaa---ttttcctgtgatgttgat--tggtctcccgtt----ggtttcgat--ctatgcagaagAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCA

upper sequence: LOC_Os05g41110.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G044137_T01 (Zea mays), 3'ss of exon 1
gtaaggttcctgatcgattgcgcctccctccccctcc-tcgtcgcgctctcccgctgcgcatctcaccatttcgttgcgatgtttttgctggtttctgattggtgggttgtggcgatgatgcagAAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACT
               |  ||  || |   |  ||||  | |   | |||| || || ||      |   |||   || ||||||  |  |||| ||   ||    ||||  |      ||||||||||||||||| || | ||||||||||||||||||||||||||||||||||||||||||||| || ||||||||||||||||||||||||||||||||||
---------------gtatgaaccccaagcaacctcagttggtcctctcttccacttcggggtgaa---ttttcctgtgatgttgat--tggtctcccgtt----ggtttcgat--ctatgcagAAGAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACT

upper sequence: LOC_Os05g41110.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv13s0064g00850.t01 (Vitis vinifera), 3'ss of exon 1
gtaaggttcctgatcgattgcgcctccctccccctcctcgtcgcgctctcccgctgcgcatctcaccatttcgttgcgatgtttttgctggtttctgattggtgggttgtggcgatgat-gcagAAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACT
       | | ||     |   | |   |||||   ||  |     ||  |  ||   |   |||  |    | ||  |||  |||  |  | | |||||  || |||||   |   ||  ||||||||||     || |||||||||||||||||    || ||||||||||||||||||||||||||||||||||||||||| |||||||  ||  | | ||
------gtacggacatcgtattcgttgttccccgatcttatt---ttcaacttctctacgattcaaga----gatgtaatgcatttcattttgtttgattt-tgtgttgttttggaaatcacagAAGAAGACTCAAGAAAACATCAACAACAAGCTCGCTCTCGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCT

upper sequence: LOC_Os05g41110.2 (Oryza sativa), 3'ss of exon 1
lower sequence: EDP06387 (Chlamydomonas reinhardtii), 3'ss of exon 1
----gtaaggttcctg-atcgattgcgcctccctccccctcctcgtcg------cgctctc-ccgctgcgcatct--caccatttcgttgcgatgtttttgctggtttctga--ttggtgggttgtg------gcgatgatgcagAAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACT
    ||| ||    || |         |   || |  ||  |    ||      |||   |  |||||  | ||   |   |  | | | | |  |     | ||| |   |  | ||| |   | |      | |     ||||||||||| |  ||| |||||||||  |   |||  ||||||||||||||| ||||||||||| || ||||||||||||  ||| ||||| ||||||    
gtgcgtagggcagatgcagtagcaaaactagccgcagccgtcaaaacggagagtcgccgccgtcgctggtcgtccagcgtaaggtggctacaaaatcaaatcaggtattgaacctcggtcgcgcgcgtactttgtgcacccgcagAAGAAGACCCAGGAGAACATCAACGCCCGTCTGGCGCTGGTGATGAAGAGTGGCAAGTACACTCTGGGCTACAAGACCTGCCTGAAGACCCTGCGCTCGG

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|88208991|gb|CI208840.1|CI208840
EST:     TCGATCACGATGGCTCCCACCAAGAAGGCG                         AAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: TCGATCACGATGGCTCCCACCAAGAAGGCGgtaaggttcc ... gatgatgcagAAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|30228744|gb|CB966634.1|CB966634
EST:     GCTCGATCACGATGGCTCCCACCAAGAAGGCG                         AAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: GCTCGATCACGATGGCTCCCACCAAGAAGGCGgtaaggttcc ... gatgatgcagAAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|14981077|gb|BI305768.1|BI305768
EST:     CGATCACGATGGGCTCCCACCAAGAAGGCG                         AAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: CGATCACGAT-GGCTCCCACCAAGAAGGCGgtaaggttcc ... gatgatgcagAAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|27578251|gb|CB000946.1|CB000946
EST:     GTCGTCGTCGCCGCGGCCGCTCGATCACGATGGCTCCCACCAAGAAGGCG                         AAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: GTCGTCGTCGCCGCGGCCGCTCGATCACGATGGCTCCCACCAAGAAGGCGgtaaggttcc ... gatgatgcagAAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|30228625|gb|CB966515.1|CB966515
EST:     GATCACGATGGCTCCCACCAAGAAGGCG                         AAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: GATCACGATGGCTCCCACCAAGAAGGCGgtaaggttcc ... gatgatgcagAAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|58594776|gb|CF993084.1|CF993084
EST:     GTCGTCGTCGCCGCGGCCGCTCGATCACGATGGCTCCCACCAAGAAGGCG                         AAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: GTCGTCGTCGCCGCGGCCGCTCGATCACGATGGCTCCCACCAAGAAGGCGgtaaggttcc ... gatgatgcagAAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|87032220|gb|CI262002.1|CI262002
EST:     GATGGCTCCCACCAAGAAGGCG                         AAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: GATGGCTCCCACCAAGAAGGCGgtaaggttcc ... gatgatgcagAAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|86593179|gb|CI255641.1|CI255641
EST:     GTCGTCGTCGACGCGGCCGCTCGATCACGATGGCTCCCACCAAGAAGGCG                         AAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: GTCGTCGTCGCCGCGGCCGCTCGATCACGATGGCTCCCACCAAGAAGGCGgtaaggttcc ... gatgatgcagAAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|53553193|gb|CO435745.1|CO435745
EST:     GTCGTCGTCGCCGCGGCCGCTCGATCACGATGGCTCCCACCAAGAAGGCG                         AAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: GTCGTCGTCGCCGCGGCCGCTCGATCACGATGGCTCCCACCAAGAAGGCGgtaaggttcc ... gatgatgcagAAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|29686201|gb|CB682476.1|CB682476
EST:     GCCGCGGCCGCTCGATCACGATGGCTCCCACCAAGAAGGCG                         AAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: GCCGCGGCCGCTCGATCACGATGGCTCCCACCAAGAAGGCGgtaaggttcc ... gatgatgcagAAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|86530215|gb|CI170421.1|CI170421
EST:     ACGATGGCTCCCACCAAGAAGGCG                         AAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: ACGATGGCTCCCACCAAGAAGGCGgtaaggttcc ... gatgatgcagAAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|58031073|gb|CX728616.1|CX728616
EST:     GTCGTCGTCGCCGCGGCCGCTCGATCACGATGGCTCCCACCAAGAAGGCG                         AAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: GTCGTCGTCGCCGCGGCCGCTCGATCACGATGGCTCCCACCAAGAAGGCGgtaaggttcc ... gatgatgcagAAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|87011660|gb|CI281362.1|CI281362
EST:     CGATCACGATGGCTCCCACCAAGAAGGCG                         AAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: CGATCACGATGGCTCCCACCAAGAAGGCGgtaaggttcc ... gatgatgcagAAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|88400326|gb|CI591016.1|CI591016
EST:     GTCGTCGTCGCCGCGGCCGCTCGATCACGATGGCTCCCACCAAGAAGGCG                         AAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: GTCGTCGTCGCCGCGGCCGCTCGATCACGATGGCTCCCACCAAGAAGGCGgtaaggttcc ... gatgatgcagAAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|55410942|gb|CV723318.1|CV723318
EST:     GTCGTCGTCGCCGCGGCCGCTCGATCACGATGGCTCCCACCAAGAAGGCG                         AAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: GTCGTCGTCGCCGCGGCCGCTCGATCACGATGGCTCCCACCAAGAAGGCGgtaaggttcc ... gatgatgcagAAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|86416886|gb|CI030897.1|CI030897
EST:     CGCCGCGGCCGCTCGATCACGATGGCTCCCACCAAGAAGGCG                         AAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: CGCCGCGGCCGCTCGATCACGATGGCTCCCACCAAGAAGGCGgtaaggttcc ... gatgatgcagAAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
EST: gi|88991955|gb|CI035093.1|CI035093
EST:     CCGCTCGATCACGATGGCTCCCACCAAGAAGGCG                         AAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGC
genomic: CCGCTCGATCACGATGGCTCCCACCAAGAAGGCGgtaaggttcc ... gatgatgcagAAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGC

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), 73 (downstream exon)
Score: 76

GCCGCCCATTCGCGCCGCCGCCGCAGAAGCCACCGCGCCCCGCAGCTCTCGTCGTCGTCGCCGCGGCCGCTCGATCACGATGGCTCCCACCAAGAAGGCGgtaaggttcc ... gatgatgcagAAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcgttgcgatgtttttgctggtttctgattggtgggttgtggcgatgatgcagAAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACT
                        ttctgat  putative branch site (score: 76)
          atgttttt  TA-rich tract