ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtacgtgtagtgtagtgcgtgcgtgcgtttctccccgcggatgggttcgactcaatctgatttggagttcctttgcgccgctgcagCTGGTGGACAAGGATCCGGAGAAGGCGATCGCGCTGTTCTGGAGTGCGATCAACGCCGGAGACCGCGTTGACAGCGCGCTCAAGGACATGGCCATCGTGA

Basic information

species	Zea mays
transcript	GRMZM2G000825_T02
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G000825_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os09g36740.1 (Oryza sativa), 3'ss of exon 1

gtacgtgtagtgtagtgcgtgcgtgcgtttctccccgcggatgggttcgactcaatctgatttggagttcctttgcgccgctgcagCTGGTGGACAAGGATCCGGAGAAGGCGATCGCGCTGTTCTGGAGTGCGATCAACGCCGGAGACCGCGTTGACAGCGCGCTCAAGGACATGGCCATCGTGA
|||||||      | |||| ||| |||||  |    | || | || | |     ||  | ||  ||      | | |   | ||||||||||||||||||||||||||||||||||||||||||||||   |||||||||||||| ||||| || |||||||||||||||||||||||||||||||
gtacgtg------attgcgagcgagcgttcttgatggtggtttggattgg---gattgggttgtgatggtggtggtgattcggcagCTGGTGGACAAGGATCCGGAGAAGGCGATCGCGCTGTTCTGGGCGGCGATCAACGCCGGCGACCGGGTGGACAGCGCGCTCAAGGACATGGCCATCGTGA

upper sequence: GRMZM2G000825_T02 (Zea mays), 3'ss of exon 1
lower sequence: EFJ08332 (Selaginella moellendorffii), 3'ss of exon 1

gtacgtgtagtgtagtgcgtgcgtgcgtttctccccgcggatgggttcgactcaatctgatttggagttcctttgcg---ccgct----gcagCTGGTGGACAAGGATCCGGAGAAGGCGATCGCGCTGTTCTGGAGTGCGATCAACGCCGGAGACCGCGTTGACAGCGCGCTCAAGGACATGGCCATCGTGA
|||   | |  | |     | | | || | |   |    ||| |||    | |  |||    | |  |  ||  | |   || ||    |||||||||||||||||| ||||| ||||| |||||||| ||||||   |||||||| || || |||||||| ||||||||||||||||||||||| |||||||
gtaaaagaaagggaccaattccatccgat-cgatcgatcgatcggtcgcgcactgtctcgcatcgcatctctgagagaacccccttttggcagCTGGTGGACAAGGAGCCGGACAAGGCCATCGCGCTCTTCTGGGCGGCGATCAATGCGGGCGACCGCGTGGACAGCGCGCTCAAGGACATGGCGATCGTGA

upper sequence: GRMZM2G000825_T02 (Zea mays), 3'ss of exon 1
lower sequence: EFJ30150 (Selaginella moellendorffii), 3'ss of exon 1

gtacgtgtagtgtagtgcgtgcgtgcgtttctccccgcggatgggttcgactcaatctgatttggagttcctttgcg---ccgct----gcagCTGGTGGACAAGGATCCGGAGAAGGCGATCGCGCTGTTCTGGAGTGCGATCAACGCCGGAGACCGCGTTGACAGCGCGCTCAAGGACATGGCCATCGTGA
|||   | |  | |     | | | || | |   |    ||| |||    | |  |||    | |  |  ||  | |   || ||    |||||||||||||||||| || || ||||| |||||||| ||||||   |||||||| || || ||||| || ||||||||||||||||||||||| |||||||
gtaaaagaaagggaccaattccatccgat-cgatcgatcgatcggtcgcgcactgtctcgcatcgcatctctgagagaacccccttttggcagCTGGTGGACAAGGAGCCCGACAAGGCCATCGCGCTCTTCTGGGCGGCGATCAATGCGGGCGACCGTGTGGACAGCGCGCTCAAGGACATGGCGATCGTGA

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|211337533|gb|FK986458.1|FK986458

EST:     ACAAGGTGCCGGTCGGCGACACGCCCTACGTGCGAGCCAAGCGCGTCCAG                         CTGGTGGACAAGGATCCGGAGAAGGCGATCGCGCTGTTCTGGAGTGCGATC
genomic: ACAAGGTGCCGGTCGGCGACACGCCCTACGTGCGAGCCAAGCGCGTCCAGgtacgtgtag ... gccgctgcagCTGGTGGACAAGGATCCGGAGAAGGCGATCGCGCTGTTCTGGAGTGCGATC

EST: gi|71309463|gb|DR791018.1|DR791018

EST:     ACAAGGTGCCGGTCGGCGACACGCCCTACGTGCGAGCCAAGCGCGTCCAG                         CTGGTGGACAAGGATCCGGAGAAGGCGATCGCGCTGTTCTGGAGTGCGATC
genomic: ACAAGGTGCCGGTCGGCGACACGCCCTACGTGCGAGCCAAGCGCGTCCAGgtacgtgtag ... gccgctgcagCTGGTGGACAAGGATCCGGAGAAGGCGATCGCGCTGTTCTGGAGTGCGATC

EST: gi|71441995|gb|DR823045.1|DR823045

EST:     ACAAGGTGCCGGTCGGCGACACGCCCTACGTGCGAGCCAAGCGCGTCCAG                         CTGGTGGACAAGGATCCGGAGAAGGCGATCGCGCTGTTCTGGAGTGCGATC
genomic: ACAAGGTGCCGGTCGGCGACACGCCCTACGTGCGAGCCAAGCGCGTCCAGgtacgtgtag ... gccgctgcagCTGGTGGACAAGGATCCGGAGAAGGCGATCGCGCTGTTCTGGAGTGCGATC

EST: gi|37421391|gb|CF648394.1|CF648394

EST:     ACAAGGTGCCGGTCGGCGACACGCCCTACGTGCGAGCCAAGCGCGTCCAG                         CTGGTGGACAAGGATCCGGAGAAGGCGATCGCGCTGTTCTGGAGTGCGATC
genomic: ACAAGGTGCCGGTCGGCGACACGCCCTACGTGCGAGCCAAGCGCGTCCAGgtacgtgtag ... gccgctgcagCTGGTGGACAAGGATCCGGAGAAGGCGATCGCGCTGTTCTGGAGTGCGATC

EST: gi|211337530|gb|FK986455.1|FK986455

EST:     ACAAGGTGCCGGTCGGCGACACGCCCTACGTGCGAGCCAAGCGCGTCCAG                         CTGGTGGACAAGGATCCGGAGAAGGCGATCGCGCTGTTCTGGAGTGCGATC
genomic: ACAAGGTGCCGGTCGGCGACACGCCCTACGTGCGAGCCAAGCGCGTCCAGgtacgtgtag ... gccgctgcagCTGGTGGACAAGGATCCGGAGAAGGCGATCGCGCTGTTCTGGAGTGCGATC

EST: gi|211431813|gb|FL298794.1|FL298794

EST:     ACAAGGTGCCGGTCGGCGACACGCCCTACGTGCGAGCCAAGCGCGTCCAG                         CTGGTGGACAAGGATCCGGAGAAGGCGATCGCGCTGTTCTGGAGTGCGATC
genomic: ACAAGGTGCCGGTCGGCGACACGCCCTACGTGCGAGCCAAGCGCGTCCAGgtacgtgtag ... gccgctgcagCTGGTGGACAAGGATCCGGAGAAGGCGATCGCGCTGTTCTGGAGTGCGATC

EST: gi|78108225|gb|DV526643.1|DV526643

EST:     ACAAGGTGCCGGTCGGCGACACGCCCTACGTGCGAGCCAAGCGCGTCCAG                         CTGGTGGACAAGGATCCGGAGAAGGCGATCGCGCTGTTCTGGAGTGCGATC
genomic: ACAAGGTGCCGGTCGGCGACACGCCCTACGTGCGAGCCAAGCGCGTCCAGgtacgtgtag ... gccgctgcagCTGGTGGACAAGGATCCGGAGAAGGCGATCGCGCTGTTCTGGAGTGCGATC

EST: gi|78085350|gb|DV513743.1|DV513743

EST:     ACAAGGTGCCGGTCGGCGACACGCCCTACGTGCGAGCCAAGCGCGTCCAG                         CTGGTGGACAAGGATCCGGAGAAGGCGATCGCGCTGTTCTGGAGTGCGATC
genomic: ACAAGGTGCCGGTCGGCGACACGCCCTACGTGCGAGCCAAGCGCGTCCAGgtacgtgtag ... gccgctgcagCTGGTGGACAAGGATCCGGAGAAGGCGATCGCGCTGTTCTGGAGTGCGATC

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 3 RNA-Seq libraries.

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 59

CATCAAGCCGCCGCCGGCGACCATGCTGCGGACTCACTTCCACGTCGCGCACAAGGTGCCGGTCGGCGACACGCCCTACGTGCGAGCCAAGCGCGTCCAGgtacgtgtag ... gccgctgcagCTGGTGGACAAGGATCCGGAGAAGGCGATCGCGCTGTTCTGGAGTGCGATCAACGCCGGAGACCGCGTTGACAGCGCGCTCAAGGACATGGCCATCGTGA

Block sizes: 46 (upstream exon), 27 (downstream exon)
Score: 6

Block sizes: 37 (upstream exon), 40 (downstream exon)
Score: 2

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tccccgcggatgggttcgactcaatctgatttggagttcctttgcgccgctgcagCTGGTGGACAAGGATCCGGAGAAGGCGATCGCGCTGTTCTGGAGTGCGATCAACGCCGGAGACCGCGTTGACAGCGCGCTCAAGGACATGGCCATCGTGA