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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcatatgttatttaaaaggtttcgacgtaatcattgtgctgatataatagtaaattgatatgttatctgtcattctgatactaactgtacctttttgtatcaattttagGTGTTTGATTTTGTTAAACTAACAGAATTGTACTATGCTGGTAGCCATGGAATGGACATCATGGGTCCAGTTGGGGAACATGATTCAGTTACTAACCATA

Basic information

species Oryza sativa
transcript LOC_Os07g30160.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g30160.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA17G14780.1 (Glycine max), 3'ss of exon 3
gtgcatatgttatttaaaaggtttcgacgtaatcattgtgctgatataatagtaaattgatatgttatctgtcattctgat--actaact-gta----cctttttgtatcaatttt-agGTGTTTGATTTTGTTAAACTAACAGAATTGTACTATGCTGGTAGCCATGGAATGGACATCATGGGTCCAGTTGGGGA-ACATGATTCAGTTACTAACCATA
||   || | |  | |  || |||  |   | | |||| | | | ||| ||  | ||| || | || | |||   || |||  ||||| |  ||    | |  ||   ||| |||| |||| |||||||| ||||||||||||||| | ||||| |||||||| ||||| |||||||| || || || ||| | || || |  | ||   |  | |||  
gtatctaggatgatcattagttttacat-catttattgagttaa-atagtaa-atattaat-tattttttgtttatcagatttactaagtcataaagccatggttacttcatttttcagGTTTTTGATTTAGTTAAACTAACAGAACTCTACTACGCTGGTAGTCATGGGATGGACATTATTGGCCCTGTTAGTGAGACTTTGTCCAAAAATCACCCAA-

upper sequence: LOC_Os07g30160.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA12G00790.1 (Glycine max), 3'ss of exon 4
----------------------------------gtgcatatgttatttaaaaggtt-tcgacgtaatcattgtgctgatataatagtaaattgatatg--ttatctgtcatt--ctgatactaactgt--acctttttgtatcaattttagGTGTTTGATTTTGTTAAACTAACAGAATTGTACTATGCTGGTAGCCATGGAATGGACATCATGGGTCCAGTTGGGGAACATGATTCAGTTACTAACCATA
                                   |  || | || || |     || || |  | | ||      | ||| | |  |   || |      ||   ||||  |  ||  | |||||| |  |  |     | |    |  |||| | | | |||||   |||||||||| | || ||||||||||| ||||||||||||||||| || || ||| |  ||  ||  || | || | |||  |
gtagttgaacaatttttataaaaaacagacaattttctatctctttttaattcccttatctatctgagcaccac-ttcatacactcctgctttcaagaagcttccttgtcggttgctcgttctaactttcgaattacccctgttggctc-agGTATATCAATTTGTAGGACTAACAGAACTCTATTATGCTGGTAGTCATGGAATGGACATCATTGGGCCTGTTAGACAATCTGTATCTGATAATCACCCAA

upper sequence: LOC_Os07g30160.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA09G36570.2 (Glycine max), 3'ss of exon 3
-----------------------------------gtgcatatgttatttaaaaggtt-tcgacgtaatcattg-tgctgatataatagtaaattgatatgttatctgtcatt--ctgatactaactgt-acctttttgtatcaattttagGTGTTTGATTTTGTTAAACTAACAGAATTGTACTATGCTGGTAGCCATGGAATGGACATCATGGGTCCAGTTGGGGAACATGATTCAGTTACTAACCATA
                                    |  || | || || |     || || |  | | ||    |||  | |     |         |  ||   ||||| |  ||| | |||||| |    ||   |        | |||| | | | |||||   |||||||||| | || || |||||||| ||||||||||||||||| || || ||| |  ||  ||  || | || | |||  |
gtagttgaacaatttttagaaaaacacatacaattttctatctctttttaattcccttatctatctgagcaccactgcatacactcctgctcccaagaagcttccttgtcagttgctggttctaactttcgtattaccgctgttggctcagGTATATCAATTTGTAGGACTAACAGAACTTTATTACGCTGGTAGTCATGGAATGGACATCATTGGCCCTGTTAGACAATCTGTATCTGATAATCACCTAA

upper sequence: LOC_Os07g30160.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv16s0022g00660.t01 (Vitis vinifera), 3'ss of exon 3
-------------------gtgcata-tgttatttaaaaggtttcgacgtaat--cattgtgctgatat-aatagtaaattgatatgttatctgtcattctgat--actaactgtacctttttgtatcaattttagGTGTTTGATTTTGTTAAACTAACAGAATTGTACTATGCTGGTAGCCATGGAATGGACATCATGGGTCCAGTTGGGGAACATGATTC-AGTTACTAACCATA
                   |||  |  | |||||| |||    |    | |||  | |     | |||| | |  |   |  |||  |  | | ||||  | |   |||   |        |  |||  |||| |||||| | |||||||   |||||||||  | ||||| |||||||| ||||| |||||||||||||| || ||  |  |      ||| | | || | |||  
gtaattggcaggcttttgagtgtgtgctattattttaaaatcattatggcaatttcctcccatttatatcagttttccttctatagatggtttttcatcttcactgacttgttacgtaacctactattcattt-agGTGTATAATTTTGTGGGACTAACAGAGCTCTACTACGCTGGTAGTCATGGGATGGACATCATGGGCCCTGTCAGACACTCCATTTCTAATGACCATCCAA-

upper sequence: LOC_Os07g30160.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S47_110V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------------------------------------------gtgcatatgttatttaaaaggtttcgacgtaat-cattgtgctgatataatagtaaattgatatgttatctgtcattctgatac--taactgtacctt-tttgtatcaattttagGTGTTTGATTTTGTTAAACTAACAGAATTGTACTATGCTGGTAGCCATGGAATGGACATCATGGGTCCAGTTGGGGAACATGATTCAGTTACTAACCATA-
                                                          || | || ||  || ||    | ||| | |  | | | ||  |  | |  |  |   ||  | | || |   | |   | |  |  || | ||   || || |  ||      |||| |  ||||||||  || |  | || |||||||||||||| || ||||||||||| || |||||||| |      |     | |   ||   |  ||   
gtgagtctttggtccgtcgtttctctatgtagtcgaaaacgttgtgtggatgaccattgtacttaagtctttcaattattctcggcattttgcttcgttttttttttttcttttttttttttttttttgctgaacataacccaatatcggtgaattgttcgattctgaaacagGTTTACGATTTTGTGCAATTGTCGGAGTTGTACTATGCTGGAAGTCATGGAATGGATATAATGGGTCCTGC-AAAAAGTTCAAGTGGTTTTAAAGTCAACG

upper sequence: LOC_Os07g30160.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S201_97V6.1 (Physcomitrella patens), 3'ss of exon 3
gtgcatatgttatttaaaaggtttcgacgtaatcattgtgctgatataatagt---aaattgatatgt-tatctgtcattctgatactaactgtacctttttgtatcaattttagGTGTTTGATTTTGTTAAACTAACAGAATTGTACTATGCTGGTAGCCATGGAATGGACATCATGGGTCCAGT---TGGGGAACATGATTCAGTTACTAACCATA
||    ||| | || ||||   ||       ||| |||      | |    ||          | ||| | | ||| | |     |   | |  |   |||| |||  |    |||| |  || |||||  ||||  | || ||||||||||| || || |||||||||||||| |||||||| |    | | | |  || ||     |  ||     
gtcagcatgatcttcaaaactgttttctaccatccttgaaaacgttttgaggtctggggcctgtgtgtgtgtgtgtgaattgagcatggatta-attgttttatattgaaac-agGTCTACGAATTTGTGCAACTGTCCGAGTTGTACTATGCGGGAAGTCATGGAATGGACATAATGGGTCCTGCAAATAGCGCAAGTGTTTTCAAGATCAATG---

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|27546591|gb|CA764571.2|CA764571
EST:     CTGCCTTGCATCTACCCACTGCGATTATCAGTGGAAGGTCTCGTGATAAG                         GTGTTTGATTTTGTTAAACTAACAGAATTGTACTATGCTGGTAGCCATGGA
genomic: CTGCCTTGCATCTACCCACTGCGATTATCAGTGGAAGGTCTCGTGATAAGgtgcatatgt ... tcaattttagGTGTTTGATTTTGTTAAACTAACAGAATTGTACTATGCTGGTAGCCATGGA




















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: 43 (upstream exon), 33 (downstream exon)
Score: 1

ATGCGCGAGGTGGTGAGGAATGCTGCCTTGCATCTACCCACTGCGATTATCAGTGGAAGGTCTCGTGATAAGgtgcatatgt ... tcaattttagGTGTTTGATTTTGTTAAACTAACAGAATTGTACTATGCTGGTAGCCATGGAATGGACATCATGGGTCCAGTTGGGGAACATGATTCAGTTACTAACCATA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatatgttatctgtcattctgatactaactgtacctttttgtatcaattttagGTGTTTGATTTTGTTAAACTAACAGAATTGTACTATGCTGGTAGCCATGGAATGGACATCATGGGTCCAGTTGGGGAACATGATTCAGTTACTAACCATA
                        tactaac  putative branch site (score: 1)
                                     tttttgtatcaatttt  TA-rich tract