ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gtgagtgttaaacccatttgatagttctactaacctgtgtcataatccatattaactaattgatcaattctgttgcatgaaacagATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAG

Basic information

species	Oryza sativa
transcript	LOC_Os02g07870.1
intron #	16
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 13

--------------gtgagtgttaaacccatttgatagttctactaacctgtgtc-ataatccatattaactaatt--gatcaattctgttgcatgaaacagATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAG
               | |   ||       ||  |   ||||||| |  | | || ||  |   | |||| |||||  ||  | |  ||||  ||  |  |||||||||||||  ||||||||||||||||| ||||||||||||||||| |||||||| ||||||||||||||||  |||
atactagaccaaaaatcaagattttgggtgttacaattttctactcatatttctccattttattttttaaataattctgacaagtgttgtttaat--attagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAG

upper sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 16

gtgagtgttaaacccatttga-------tagttct-actaacctgtgtcataatccatattaactaattgatcaattctgttgcatgaaacagATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAG
||||||     ||  |||| |       |  | || | |   ||   | ||| |  | | ||  |  ||||  | | |||||  || | | |||||||||||||  ||||||||||||||||| |||||||||||||||||||||||||| ||||||||||||||||  |||
gtgagtcccctacttatttcaacacatttgatgctcatttttctccattatatttta-agtatttttttgacaagtgctgtttaattatatagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACATTATTCACTTCAACACATTGGCAAATCAG

upper sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 17

gtgagtgttaaacccatttgatagttctactaacctgtgtcataat-ccatattaactaattgatcaattctgt-tgcatgaaacagATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAG
|| || |        ||| | ||  |    |||| | | | ||| |    | ||      ||| |   |||||| ||  ||  | ||||||||||| | |||||| |||||||| |||||||||||||||||||||||||| |||||| |||  |||||||  |||
gtaagggcccttgtaattggttaacttctttaacatttattatattattgtgttcttatgttggtaccttctgtgtggctgtgatagATATGATAAATTTTGCCCCTTCTACAAGTCTGTTTGGATGATGCGCAACATTATCCATTTCTACAATTTGGCAAATCAG

upper sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 17

------------gtgagtgttaaacccatttgatagttctactaacctgtgtcataatccatattaactaattgatcaattctgttgcatgaaacagATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAG
            || | || | |||   ||| |||  | |  ||   |   |  || |   | |||  |   |      || ||| || ||  | |||||||| || |  ||||| |||||||| |||||||||||||||||||||||||| |||||| |||  |||||||  |||
gtaagggaccttgtaattggttaacttctttaatatgtattatattattgtttttatttgttcttatgttggtacctttttgtgtggc-tgtgatagATATGACAAATTCTGCCCCTTCTACAAGTCTGTTTGGATGATGCGCAACATTATCCATTTCTACAATTTGGCAAATCAG

upper sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 16
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 17

--------gtgagtgttaaacccatttga--tagttctactaacctgtgtcataatccatattaactaat-tgatcaat--tctgttgcatga--aacagATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAG
        || | |||   ||  |  ||   || || |  | || |       |||    |||| ||    |||| | |  | | |||  ||    |||||||||| |||| ||| || || ||||| || |||||||||||| | ||||||||||||||| | |  ||||| |  |||
cactcttagtcactgtaggactgacatgggttattttttgttacttccaatcaaattttcattatcttccatgattattgattttttggttggttgacagATATGACAAGTTTTGTCCCTTTTACAAGTCAGTTTGGATGATGAGGAACATTATTCATTTCTATAATTTGGCCAATCAG

upper sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 16
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 17

-----------------------------------------------------gtgagtgttaaacccatttgatagttctactaacctg-tgtcataatccatatt--aactaattgatcaattctgt-tgcatgaaacagATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAG
                                                      |   |  ||   || | || |     |  ||  ||| | |   ||| | | ||  |  ||||  ||  ||    | ||  ||  |||||||||||||||  ||||| |||||||| || ||||||||||||||||| ||||| |||||| | |  ||||| |  |||
gtaagtcccagattaagtttttgattcaaattttcgtcctttttaatttttgtttacttactatttccttatgttcccctttttatgctggtctagaaattctttttccacttaatatatgtatctcatgtggctgtgacagATATGATAAGTTCTGCCCCTTCTACAAGTCGGTTTGGATGATGCGCAATATTATCCATTTCTATAATTTGGCCAATCAG

upper sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 16
lower sequence: PP1S44_102V6.1 (Physcomitrella patens), 3'ss of exon 17

-------gtgagtgttaaacccatttg----atagt-tctactaacct---gtgtcataatccatattaactaattgat-caattctgttgcatgaaacagATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAG
        |  |  || ||   ||| |    | ||| || ||  ||||    ||| ||  | ||| |    ||  |||        |||     |   ||| |||||||| | ||||||||| || || || || |||||||||||||||||| | || ||||||||  | || |  |||
cgatgcactttgccttgaatagattgggggtagagtgtcaacataccttgaatgtgattttgcatgt-gcgtatctgacatgggcttgtcatgggtggcagTTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAG

upper sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 16
lower sequence: PP1S10_201V6.1 (Physcomitrella patens), 3'ss of exon 17

-----------------gtgagtgttaaacccatttgatagttctactaacctgtgtcataatccatattaactaattgatcaattctgttgcatgaaacagATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAG
                  |   |   |        ||| || |   |||| || ||      || ||   |      ||     | ||  ||  ||   ||| ||||||||||  ||||||||||| ||||| || |||||||||||||| ||| | || || |||||  | || |  |||
ttatgcatttcgttataatagattgcagttgtggatgacagcttgcctaatctatggatgtttctatccaagtctgatgtgggttcctcatgggtgg--cagTTATGATAAGTTCTGCCCATTCTATAAATCAGTATGGATGATGCGCAATATTGTCCACTTTAACACTCTTGCCAATCAG

upper sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 16
lower sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 17

----------------------------------gtgagtgttaaacccatttgatagttctactaacctgtgtcataatc-catattaactaat---tgat-caattctgttgcatgaaacagATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAG
                                   ||   | || |    ||| ||  ||||     |||||   |  ||    | ||     ||   |||| |  | || |   | |  |||| ||||| || |  |||||||||||||| ||||| ||||||||||| || ||| | || ||||||||  | ||||  |||
gtgagctttgttgaaattttgttgtgtaggatgtttgttgggtagatgtttttcattattctgtgtccctgttcgacgattgtgtgtttctccatgtctgattcggtcctctcatacgtgacagTTATGACAAATTCTGCCCATTCTACAAGTCTGTGTGGATGATGCGTAATATTGTCCACTTCAACACTCTTGCAAATCAG

upper sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 16
lower sequence: EFJ33015 (Selaginella moellendorffii), 3'ss of exon 16

gtgagtgttaaacccatttgatagttctactaacctgtgtcataatccatattaactaattgatcaattctgttg-catgaaacagATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAG
                                    ||  | |  |||    |  ||  ||| | |   ||       ||   |||||| ||||||| ||| || |||||||| || |||||||||||||| |||||  ||||||||  |    || | || |||
------------------------------------gta-cgtgttccgggcttgctc-ttgtttatcgctaacaatctgctccagATACGATAAGTTTTGTCCGTTCTACAAGTCCGTTTGGATGATGCGAAACATCGTTCATTTCTGCGACCTGTCCACTCAG

upper sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 16
lower sequence: EFJ30330 (Selaginella moellendorffii), 3'ss of exon 17

gtgagtgttaaacccatttgatagttctactaacctgtgtcataatccatattaactaattgatcaattctgttg-catgaaacagATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAG
                                    ||  | |  |||    |  ||  ||| | |   ||       ||   |||||| ||||||| ||| || |||||||| || |||||||||||||| |||||  | ||||||  |    || | || |||
------------------------------------gta-cgtgttccgggcttgctc-ttgtttatcgctaacaatctgctccagATACGATAAGTTTTGTCCGTTCTACAAGTCCGTTTGGATGATGCGAAACATCGTCCATTTCTGCGACCTGTCCACTCAG

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|66925761|gb|CX112609.1|CX112609

EST:     ACAGCGAAACTTCTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCC                         ATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACAT
genomic: ACAGCAAAACTTCTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCCgtgagtgtta ... catgaaacagATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACAT

EST: gi|86829584|gb|CI286768.1|CI286768

EST:     ATTTGGCACAAAATGCATTCACCCC                         ATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACAT
genomic: ATTTGGCACAAAATGCATTCACCCCgtgagtgtta ... catgaaacagATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACAT

EST: gi|89198392|gb|CI007452.1|CI007452

EST:     GCATTCACCCC                         ATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACAT
genomic: GCATTCACCCCgtgagtgtta ... catgaaacagATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACAT

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), 75 (downstream exon)
Score: 25

CTTGTTGGTAAAGACGCACTGGCAGAATCTGACAAGATTACACTGGAGACAGCAAAACTTCTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCCgtgagtgtta ... catgaaacagATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAG

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

taacctgtgtcataatccatattaactaattgatcaattctgttgcatgaaacagATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAG