ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

...gcaacatgtcttgctgctgcattccaagtattcatgtttccagtcttgcaatttatgttctaagctctgtttttcgtttttcgttgttggttttgtgcagAAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATT

Basic information

species	Zea mays
transcript	GRMZM2G050460_T01
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G050460_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g16890.3 (Oryza sativa), 3'ss of exon 1

---------------------------gcaacatgtcttgctgctgcattccaagtattcatgtttccag--tcttgcaatttatgtt---ctaag----ctctgtttttcgtttt------tcgttgttggttttgt--gcagAAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATT
                            |  |||  | |    | ||    ||||    |  |    |    || |||| ||    |    ||||     |||||||  ||||  |        | || ||||| |||  |||||||||||||||||||||||||||||||||||| ||||| |||||||||||||||||||||||||||||||||||||| |||||||||||||||||||| |
gtaacgttgtcctcctcccggtctctccctccatcacctcggtccgccgcgcaagcgagcgagcgagcgagatcctgcatttctcatggcgctaacgcctctctgttcgtcgtggtgatggtgtgatggtggttgtgtttgcagAAGAAGTCCACGGACAACATCAACAACAAGCTGCAGCTCGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACT

upper sequence: GRMZM2G050460_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv13s0064g00850.t01 (Vitis vinifera), 3'ss of exon 1

------gcaacatgtc--ttgctgctgcattccaagtattcatgtttccagtcttgcaatttatgttctaagctctgtttttcgtttttcgttgttggttttg----tgcagAAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATT
       || | | |   ||| | |   ||   |  | ||||  ||  |     | |||   ||||  |    |   ||||   |  ||   ||||| ||| |      ||||||||| |    || |||||||||||||||||    || |||||||||||||||||||||||||||||||||||||| || |||| || |||||| |  |
gtacggacatcgtattcgttgttccccgatctta--ttttcaacttctctacgattcaagagatgtaatgcatttcattttgtttgattttgtgttgttttggaaatcacagAAGAAGACTCAAGAAAACATCAACAACAAGCTCGCTCTCGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCT

upper sequence: GRMZM2G050460_T02 (Zea mays), 3'ss of exon 1
lower sequence: EDP06387 (Chlamydomonas reinhardtii), 3'ss of exon 1

------------------gcaacatgtcttgctgctgcattccaagt----attcat----gtttccagtcttgcaatttatgtt--cta-------agctctgtttttcgtttttcgttgttggt----tttgtgca------gAAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATT
                  | | ||   || || || ||  || ||      | ||      ||  |  ||| | ||   || | |  |||       |  || | | ||     |  || |   |     ||||||||      ||||||| ||  ||| |||||||||  |   ||   ||| ||||||||||| ||||||||||| || |||||||||||   ||| | ||||||  |     
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|211445721|gb|FL164466.1|FL164466

EST:     GCAACCATGGTGGCCGCAAAGAAGACG                         AAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC
genomic: GCAACCATGGTGGCCGCAAAGAAGACGgtaacgatca ... ttttgtgcagAAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC

EST: gi|15590487|gb|BI675103.1|BI675103

EST:     TCAACGCCGTCACTCCTCGGGGCGCAACCATGGTGGCCGCAAAGAAGACG                         AAGAAGTCCACGGACAACATCAACAACCAGCTTCAGCTTGTGATGAAGAGC
genomic: TCGACGCCGTCACTCATCGGGGCGCAACCATGGTGGCCGCAAAGAAGACGgtaacgatca ... ttttgtgcagAAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC

EST: gi|18164616|gb|BM334455.1|BM334455

EST:     ATCGGGGCGCAACCATGGTGGCCGCAAAGAAGACG                         AAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC
genomic: ATCGGGGCGCAACCATGGTGGCCGCAAAGAAGACGgtaacgatca ... ttttgtgcagAAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC

EST: gi|211447832|gb|FL164470.1|FL164470

EST:     TCGACGCCGTCACTCATCGGGGCGCAACCATGGTGGCCGCAAAGAAGACG                         AAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC
genomic: TCGACGCCGTCACTCATCGGGGCGCAACCATGGTGGCCGCAAAGAAGACGgtaacgatca ... ttttgtgcagAAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC

EST: gi|60354341|gb|DN221314.1|DN221314

EST:     TCGACGCCGTCACTCATCGGGGCGCAACCATGGTGGCCGCAAAGAAGACG                         AAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC
genomic: TCGACGCCGTCACTCATCGGGGCGCAACCATGGTGGCCGCAAAGAAGACGgtaacgatca ... ttttgtgcagAAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC

EST: gi|44900176|gb|CK826721.1|CK826721

EST:     TCAACGCCGTCACTCCTCGGGGCGCAACCATGTTGGCCGCAAAGAAGACG                         AAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC
genomic: TCGACGCCGTCACTCATCGGGGCGCAACCATGGTGGCCGCAAAGAAGACGgtaacgatca ... ttttgtgcagAAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC

EST: gi|60358040|gb|DN225013.1|DN225013

EST:     TCGACGCCGTCACTCATCGGGGCGCAACCATGGTGGCCGCAAAGAAGACG                         AAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC
genomic: TCGACGCCGTCACTCATCGGGGCGCAACCATGGTGGCCGCAAAGAAGACGgtaacgatca ... ttttgtgcagAAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC

EST: gi|18649989|gb|BM498808.1|BM498808

EST:     TCGACGCCG-CACTCATCGGGGCGCAACCATGGTGGCCGCAAAGAAGACG                         AAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC
genomic: TCGACGCCGTCACTCATCGGGGCGCAACCATGGTGGCCGCAAAGAAGACGgtaacgatca ... ttttgtgcagAAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC

EST: gi|4887277|gb|AI677376.1|AI677376

EST:     TCATCGGGGCGCAACCATGGTGGCCGCAAAGAAGACG                         AAGAAGTCCNCGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC
genomic: TCATCGGGGCGCAACCATGGTGGCCGCAAAGAAGACGgtaacgatca ... ttttgtgcagAAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC

EST: gi|15554273|gb|BI644271.1|BI644271

EST:     TCAACGCCGTCACTCCTCGGGGCGCAACCATGGTGGCCGCAAAGAAGACG                         AAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC
genomic: TCGACGCCGTCACTCATCGGGGCGCAACCATGGTGGCCGCAAAGAAGACGgtaacgatca ... ttttgtgcagAAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC

EST: gi|71772654|gb|DR970582.1|DR970582

EST:     TCGACGCCGTCACTCATCGGGGCGCAACCATGGTGGCCGCAAAGAAGACG                         AAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC
genomic: TCGACGCCGTCACTCATCGGGGCGCAACCATGGTGGCCGCAAAGAAGACGgtaacgatca ... ttttgtgcagAAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC

EST: gi|45567674|gb|CK985687.1|CK985687

EST:     TCAACGCCGTCACTCCTCGGGGCGCAACCATGGTGGCCGCAAAGAAGACG                         AAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC
genomic: TCGACGCCGTCACTCATCGGGGCGCAACCATGGTGGCCGCAAAGAAGACGgtaacgatca ... ttttgtgcagAAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC

EST: gi|32912640|gb|CF017452.1|CF017452

EST:     TCAACGACGTCACTCCTCGGGGCGCAACCATGGTGGCCGCAAAGAAGACG                         AAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC
genomic: TCGACGCCGTCACTCATCGGGGCGCAACCATGGTGGCCGCAAAGAAGACGgtaacgatca ... ttttgtgcagAAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC

EST: gi|45848107|gb|CN072050.1|CN072050

EST:     TCAACGCCGTCACTCCTCGGGGCGCAACCATGGTGGCCGCAAAGAAGACG                         AAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC
genomic: TCGACGCCGTCACTCATCGGGGCGCAACCATGGTGGCCGCAAAGAAGACGgtaacgatca ... ttttgtgcagAAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC

EST: gi|9794654|gb|BE552962.1|BE552962

EST:     TCGACGCCGTCACTCATCGGGGCGCAACCATGGTGGCCGCAAAGAAGACG                         AAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC
genomic: TCGACGCCGTCACTCATCGGGGCGCAACCATGGTGGCCGCAAAGAAGACGgtaacgatca ... ttttgtgcagAAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC

EST: gi|19822553|gb|BQ048577.1|BQ048577

EST:     TCGACGCCGTCACTCATCGGGGCGCAACCATGGTGGCCGCAAAGAAGACG                         AAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC
genomic: TCGACGCCGTCACTCATCGGGGCGCAACCATGGTGGCCGCAAAGAAGACGgtaacgatca ... ttttgtgcagAAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC

EST: gi|71439472|gb|DR820522.1|DR820522

EST:     TCGACGCCGTCACTCATCGGGGCGCAACCATGGTGGCCGCAAAGAAGACG                         AAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC
genomic: TCGACGCCGTCACTCATCGGGGCGCAACCATGGTGGCCGCAAAGAAGACGgtaacgatca ... ttttgtgcagAAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC

EST: gi|78027496|gb|DV495883.1|DV495883

EST:     TAGACGCCGTCACTCATCGGGGCGCAACCATGGTGGCCGCAAAGAAGACG                         AAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC
genomic: TCGACGCCGTCACTCATCGGGGCGCAACCATGGTGGCCGCAAAGAAGACGgtaacgatca ... ttttgtgcagAAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC

EST: gi|7227589|gb|AW566230.1|AW566230

EST:     TCGACGCCGTCACTCATCGGGGCGCAACCATGGTGGCCGCAAAGAAGACG                         AAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC
genomic: TCGACGCCGTCACTCATCGGGGCGCAACCATGGTGGCCGCAAAGAAGACGgtaacgatca ... ttttgtgcagAAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC

EST: gi|15590488|gb|BI675104.1|BI675104

EST:     TCGGGGCGCAACCATGGTGGCCGCAAAGAAGACG                         AAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC
genomic: TCGGGGCGCAACCATGGTGGCCGCAAAGAAGACGgtaacgatca ... ttttgtgcagAAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC

EST: gi|37378408|gb|CF625893.1|CF625893

EST:     TCAACGCCGTCACTCCTCGGGGCGCAACCATGGTGGCCGCAAAGAAGACG                         AAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC
genomic: TCGACGCCGTCACTCATCGGGGCGCAACCATGGTGGCCGCAAAGAAGACGgtaacgatca ... ttttgtgcagAAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC

EST: gi|211445724|gb|FL164469.1|FL164469

EST:     GACGCCGTCACTCATCGGGGCGCAACCATGGTGGCCGCAAAGAAGACG                         AAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC
genomic: GACGCCGTCACTCATCGGGGCGCAACCATGGTGGCCGCAAAGAAGACGgtaacgatca ... ttttgtgcagAAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC

EST: gi|211445722|gb|FL164467.1|FL164467

EST:     TCAACGCCGTCACTCCTCGGGGCGCAACCATGGTGGCCGCAAAGAAGACG                         AAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC
genomic: TCGACGCCGTCACTCATCGGGGCGCAACCATGGTGGCCGCAAAGAAGACGgtaacgatca ... ttttgtgcagAAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGC

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 4 RNA-Seq libraries.

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 164

TTCCGCCCCGCAGTCATCCCCGAGAAGAGCCGCCGCCGCGCAAAGCCGCTTCGACGCCGTCACTCATCGGGGCGCAACCATGGTGGCCGCAAAGAAGACGgtaacgatca ... ttttgtgcagAAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATT

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 137

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 215

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 64

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttgcaatttatgttctaagctctgtttttcgtttttcgttgttggttttgtgcagAAGAAGTCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATT