ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gcgtgtggccctctctacctgcgatgtttctctcgcgagaaaatcttcccttcggctgccaaattcttagagctttttctttggcttacggatcggcggtggtgggtggctgcagCCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCGATGCACGCCGAGAGCGGGTACTGGCGGCCCCGCCCTGACGGCTCCGTCG

Basic information

species	Zea mays
transcript	GRMZM2G092152_T02
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G092152_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g48760.1 (Oryza sativa), 3'ss of exon 1

gcgtgtggccctctctacctgcgatgtt-tctctcgcgagaaaatcttcccttcggctgccaaattcttagagctttttctttggcttacggatcggcggtggtgggtggctgcagCCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCGATGCACGCCGAGAGCGGGTACTGGCGGCCCCGCCCTGACGGCTCCGTCG
                     |||  |  || |  |       || |  | ||||   ||||||        |||||| | ||  ||       || |  ||  |   |    ||||| ||||||||||||||||||| |||||||||| ||||||| ||||||||||||||||||||||| |||||||||||||||||||| |||||||||||||
----------------gtaaacgacctcctcgcctgtatctgtatatctctttcgctcgccaaa--------gcttttaccttttct-------cgaccatgccgcacg----cagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCGATGCACGCCGAGAGTGGGTACTGGCGGCCCCGCCCCGACGGCTCCGTCG

upper sequence: GRMZM2G092152_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv19s0085g01130.t01 (Vitis vinifera), 3'ss of exon 1

gcgtgtggccctctctacctgcgatgtttctctcgcgagaaaatcttcccttcg-gctgccaaattcttagagctttttctttggcttacggatcggcggtggtgggtggctgcagCCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCGATGCACGCCGAGAGCGGGTACTGGCGGCCCCGCCCTGACGGCTCCGTCG
    ||   ||| | |  ||       | ||  |         |||||  ||   | ||   ||  |   ||  |||||||||   ||     || |   |  |  || |    |||| |||||  |||| |  |||| ||| |||||   |   || |||||||| ||||||||||||||||| || ||||||||    || |||||  || |||
----gtactcctttttctctttctaaatacttcc---------tcttcttttgatgatgatgaagacgatgacttttttctttccttttt---tctgtttttctttgttgaaaaagCCGGTGATTGCGTATAGCCAGAGGACTTGGAAATTGAGCTCCGGCGAGCCTATGCACGCCGAGAGCGGCTATTGGCGGCCTAAACCCGACGGTACCATCG

upper sequence: GRMZM2G092152_T02 (Zea mays), 3'ss of exon 1
lower sequence: EFJ33662 (Selaginella moellendorffii), 3'ss of exon 1

gcgtgtggccctctctacctgcgatgtttctctcgcgagaaaatcttcccttcggctgccaaattcttagagcttt--ttctttggctta--cggatcggcggtggtgggtggctgcagCCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCGATGCACGCCGAGAGCGGGTACTGGCGGCCCCGCCCTGACGGCTCCGTCG
            |  | | |||| | ||  ||| |   |      |||  | |   |    |||| ||   ||  |  ||  || ||| |  |||  |  || |||        | |||||||||||  | |||||||| ||||| |||||| |  |||| || ||||| |||||||||||||| || |||||| ||||| | || || |||||  |||
------------cagtgcttgcg-ttttcttcttgtttg------ttctttgcatttttttaattttttttgccatgatttgtttgctcatccggtactacgatggacttgttttccagCCAGTGATGGCCTACACGCAAAAGACATGGAAGGCATCGTCCGGGGAGCCTATGCACGCCGAGAGTGGCTACTGGAGGCCCAGGCCCGATGGCTCGCTCG

upper sequence: GRMZM2G092152_T02 (Zea mays), 3'ss of exon 1
lower sequence: EFJ37014 (Selaginella moellendorffii), 3'ss of exon 1

gcgtgtggccctctctacctgcgatgtttctctcgcgagaaaatcttcccttcggctgccaaattcttagagctttttctttggctta--cggatcggcggtggtgggtggctgcagCCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCGATGCACGCCGAGAGCGGGTACTGGCGGCCCCGCCCTGACGGCTCCGTCG
           ||  | | |||| | ||  ||| |   |    ||||  | |    |   |  || || |   |  ||  || ||| |  |||  |  || |||        | |||||||||||  | |||||||| ||||| |||||| |  |||| || ||||| |||||||||||||| || |||||| ||||| | || || |||||  |||
-----------tcagtgcttgcg-ttttcttcttgtttg---ttctttgcatt--tttttattttttttgccatgatttgtttgctcatccggtactacgatggacttgttttccagCCAGTGATGGCCTACACGCAAAAGACATGGAAGGCATCGTCCGGGGAGCCTATGCACGCCGAGAGTGGCTACTGGAGGCCCAGGCCCGATGGCTCGCTCG

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|5804510|gb|AI979480.1|AI979480

EST:     CCTCC-TCCGGTACGGCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAG                         CCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCG
genomic: CCTCCTTCCGGTACGGCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAGgcgtgtggcc ... gtggctgcagCCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCG

EST: gi|78021667|gb|DV490054.1|DV490054

EST:     CCTCCTTCCGGTACGGCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAG                         CCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCG
genomic: CCTCCTTCCGGTACGGCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAGgcgtgtggcc ... gtggctgcagCCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCG

EST: gi|60338639|gb|DN205612.1|DN205612

EST:     CCTCCTTCCGGTACGGCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAG                         CCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCG
genomic: CCTCCTTCCGGTACGGCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAGgcgtgtggcc ... gtggctgcagCCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCG

EST: gi|32909568|gb|CF014380.1|CF014380

EST:     TACGGCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAG                         CCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCG
genomic: TACGGCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAGgcgtgtggcc ... gtggctgcagCCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCG

EST: gi|211489357|gb|FL110823.1|FL110823

EST:     CCTCCTTCCGGTAC-GCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAG                         CCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCG
genomic: CCTCCTTCCGGTACGGCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAGgcgtgtggcc ... gtggctgcagCCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCG

EST: gi|9732493|gb|BE511245.1|BE511245

EST:     TCTCGCATCATCCCTCCAAG                         CCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCG
genomic: TCTCGCATCATCCCTCCAAGgcgtgtggcc ... gtggctgcagCCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCG

EST: gi|211489363|gb|FL110829.1|FL110829

EST:     CCTCCTTCCGGTACGGCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAG                         CCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCG
genomic: CCTCCTTCCGGTACGGCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAGgcgtgtggcc ... gtggctgcagCCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCG

EST: gi|211489356|gb|FL110822.1|FL110822

EST:     CCTCCTTCCGGTACGGCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAG                         CCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCG
genomic: CCTCCTTCCGGTACGGCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAGgcgtgtggcc ... gtggctgcagCCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCG

EST: gi|211486489|gb|FL110821.1|FL110821

EST:     CCTCCTTCCGGTACGGCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAG                         CCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCG
genomic: CCTCCTTCCGGTACGGCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAGgcgtgtggcc ... gtggctgcagCCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCG

EST: gi|211489365|gb|FL110831.1|FL110831

EST:     CCTCCTTCCGGTACGGCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAG                         CCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCG
genomic: CCTCCTTCCGGTACGGCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAGgcgtgtggcc ... gtggctgcagCCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCG

EST: gi|32909569|gb|CF014381.1|CF014381

EST:     CCTCCTTCCGGTACGGCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAG                         CCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCG
genomic: CCTCCTTCCGGTACGGCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAGgcgtgtggcc ... gtggctgcagCCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCG

EST: gi|17932025|gb|BM268985.1|BM268985

EST:     CCTCCTTCCGGTACGGCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAG                         CCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCG
genomic: CCTCCTTCCGGTACGGCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAGgcgtgtggcc ... gtggctgcagCCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCG

EST: gi|211489360|gb|FL110826.1|FL110826

EST:     CCTCCTTCCGGTACGGCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAG                         CCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCG
genomic: CCTCCTTCCGGTACGGCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAGgcgtgtggcc ... gtggctgcagCCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCG

EST: gi|211489362|gb|FL110828.1|FL110828

EST:     CCTCCTTCCGGTAC-GCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAG                         CCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCG
genomic: CCTCCTTCCGGTACGGCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAGgcgtgtggcc ... gtggctgcagCCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCG

EST: gi|9732494|gb|BE511246.1|BE511246

EST:     CCTCCTTCCGGTACGGCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAG                         CCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCG
genomic: CCTCCTTCCGGTACGGCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAGgcgtgtggcc ... gtggctgcagCCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCG

EST: gi|211489359|gb|FL110825.1|FL110825

EST:     CCTCCTTCCGGTACGGCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAG                         CCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCG
genomic: CCTCCTTCCGGTACGGCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAGgcgtgtggcc ... gtggctgcagCCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCG

EST: gi|14243770|gb|BG841433.2|BG841433

EST:     CCTCCTTCCGGTACGGCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAG                         CCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCG
genomic: CCTCCTTCCGGTACGGCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAGgcgtgtggcc ... gtggctgcagCCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCG

EST: gi|211489366|gb|FL110832.1|FL110832

EST:     CCTCCTTCCGGTACGGCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAG                         CCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCG
genomic: CCTCCTTCCGGTACGGCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAGgcgtgtggcc ... gtggctgcagCCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCG

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: 45 (upstream exon), 49 (downstream exon)
Score: 40

CCTACTGGGGAAGTGGCGCGGGGAAGGCGAGGGCAGCTTCCCCACCATATCCTCCTTCCGGTACGGCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAGgcgtgtggcc ... gtggctgcagCCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCGATGCACGCCGAGAGCGGGTACTGGCGGCCCCGCCCTGACGGCTCCGTCG

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 53

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 99

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 102

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

aaattcttagagctttttctttggcttacggatcggcggtggtgggtggctgcagCCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCGATGCACGCCGAGAGCGGGTACTGGCGGCCCCGCCCTGACGGCTCCGTCG