ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

AGCGACCCATGGCCGCGCATCTCGCAGGGCGCCAAGGACCTCGTCAGGAAGATGCTCAACCCTGACCCCAAGCAGCGGATTTCTGCATACGACGTCCTCAgtgagcgtttgcttctttctttttttctctctctctctctctcgtttgtttgttcctgaacatcagaaacagcagcagcatgacagattgacagtgagtactgaaacggccggtggtgcctctctgtggcgttcgtgcag

Basic information

species	Zea mays
transcript	GRMZM2G340224_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G340224_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g41270.1 (Oryza sativa), 5'ss of exon 3

AGCGACCCATGGCCGCGCATCTCGCAGGGCGCCAAGGACCTCGTCAGGAAGATGCTCAACCCTGACCCCAAGCAGCGGATTTCTGCATACGACGTCCTCAgtgagcgtttgcttctttctttttttctctctctctctctctcgtttgtttgttcctgaacatcagaaacagcagcagcatgacagattgacagtgagtactgaaacggccggtggtgcctctctgtggcgttcgtgcag
||||| |||||| ||||||||||||| |||||||||||||| ||||||  ||||||| |  |||||||||||||| ||||||||||||| ||||| |||||||||      ||||  | |    |   |   |    ||| ||           ||||||  |      |||  | |  |||     ||     |  || | |                                     
AGCGAGCCATGGTCGCGCATCTCGCATGGCGCCAAGGACCTTGTCAGGCGGATGCTCCATTCTGACCCCAAGCAGAGGATTTCTGCATATGACGTGCTCAgtgagtacc--cttcactttacgctgaacatcccaaatctttcaaca------ccctgaattttt----caggtgaatgatgctgtttttgttttctgtccag-------------------------------------

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|21481043|gb|BQ577726.1|BQ577726

EST:     CTGCATACGACGTCCTCA                         ACCATCCGTGGATCAAGGAGGACGGCGAGGCGCCGGACACGCCGCTGGACA
genomic: CTGCATACGACGTCCTCAgtgagcgttt ... gttcgtgcagACCATCCGTGGATCAAGGAGGACGGCGAGGCGCCGGACACGCCGCTGGACA

EST: gi|50324131|gb|CO519257.1|CO519257

EST:     GATGCTCAACCCTGACCCCAAGCAGCGGATTTCTGCATACGACGTCCTCA                         ACCATCCGTGGATCAAGGAGGACGGCGAGGCGCCGGACACGCCGCTGGACA
genomic: GATGCTCAACCCTGACCCCAAGCAGCGGATTTCTGCATACGACGTCCTCAgtgagcgttt ... gttcgtgcagACCATCCGTGGATCAAGGAGGACGGCGAGGCGCCGGACACGCCGCTGGACA

EST: gi|21480881|gb|BQ577564.1|BQ577564

EST:     CTGCATACGACGTCCTCA                         ACCATCCG-GGATC-AGGAGGACGGCGAGGCGCCGGACACGCCGCTGGACA
genomic: CTGCATACGACGTCCTCAgtgagcgttt ... gttcgtgcagACCATCCGTGGATCAAGGAGGACGGCGAGGCGCCGGACACGCCGCTGGACA

EST: gi|21390432|gb|BQ528481.1|BQ528481

EST:     CTGCATACGACGTCCTCA                         ACCATCCG-GGATCAAGGAGGACGGCGAGGCGCCGGACACGCCGCTGGACA
genomic: CTGCATACGACGTCCTCAgtgagcgttt ... gttcgtgcagACCATCCGTGGATCAAGGAGGACGGCGAGGCGCCGGACACGCCGCTGGACA

EST: gi|87154477|gb|DY399266.1|DY399266

EST:     CTGCATACGACGTCCTCA                         ACCATCCGTGGATCAAGGAGGACGGCGAGGCGCCGGACACGCCGCTGGACA
genomic: CTGCATACGACGTCCTCAgtgagcgttt ... gttcgtgcagACCATCCGTGGATCAAGGAGGACGGCGAGGCGCCGGACACGCCGCTGGACA

EST: gi|21330105|gb|BQ485486.1|BQ485486

EST:     CTGCATACGACGTCCTCA                         ACCATCCGTGGATCAAGGAGGACGGCGAGGCGCCGGACACGCCGCTGGACA
genomic: CTGCATACGACGTCCTCAgtgagcgttt ... gttcgtgcagACCATCCGTGGATCAAGGAGGACGGCGAGGCGCCGGACACGCCGCTGGACA

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 2 RNA-Seq libraries.

Block sizes: 27 (upstream exon), 23 (downstream exon)
Score: 1

AGCGACCCATGGCCGCGCATCTCGCAGGGCGCCAAGGACCTCGTCAGGAAGATGCTCAACCCTGACCCCAAGCAGCGGATTTCTGCATACGACGTCCTCAgtgagcgttt ... gttcgtgcagACCATCCGTGGATCAAGGAGGACGGCGAGGCGCCGGACACGCCGCTGGACAACGCGGTCCTCGGCCGGCTGAAGCAGTTCAGGGCCATGAACCAGTTCAA