ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GCAGGCCTGCCGGGCGAAGAAGGGTGAGGACTTCGCGCTGCTCAAGCCCGCCTGCGAGCGACGCCCCGGCGCGCCGTCCACCTCCTTCTCCGCCTTCGCCgtaagcgctccccacctcgacccactccgtcttccctgtcccaatgttagcatgctactatgctctggaggctcgttctcagaaaggcgccccgcgcccccgcccgtgtctggcctcgtccgctctcgcag

Basic information

species	Zea mays
transcript	GRMZM2G044382_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G044382_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os04g37660.2 (Oryza sativa), 5'ss of exon 1

---GCAGGCCTGCCGGGCGAAGAAGGGTGAGGACTTCGCGCTGCTCAAGCCCGCCTGCGAGCGACGCCCCGGCGCGCCGTCCACCTCCTTCTCCGCCTTCGCCgtaagcgctccccacctcgacccactccgtcttccctgtcc-caatgttagcatgctactatgctctggaggctcgttctcagaaaggcgccccgcgcccccgcccgtgtctggcctcgtccgctctcgcag---------------------------
   |||||| ||  |||| |||||||| ||||||||||||||||||||||| ||||||||||| |  ||||||  || |  | || ||||||||||||||||||| || ||||    | ||    | |  |  || |  || |  |   |   ||    ||    | || |    ||      |      ||||  | ||| | |   |  | | ||   ||    |||                                 
GGGGCAGGCGTGTAGGGCTAAGAAGGGGGAGGACTTCGCGCTGCTCAAGCCGGCCTGCGAGCGCC-TCCCGGCCGGCGG--CGCCCCCTTCTCCGCCTTCGCCgtgagtgctcgtgtcgtcccgtctcctccactgcaatgactacgccgcgtgcggtttatctcgttccgcgatctgcgctgcgctgccgcgctgcccgctcgcttgcacgaccgggggcggattctcagatgagtttttcggttttggttttggttgcag

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|149071130|gb|EE159529.2|EE159529

EST:     CCTGCGAGCGACGCCCCGGCGCGCCGTCCACCTCCTTCTCCGCCTTCGCC                         CTGTTCGATGGGCACAACGGGAGCGCCGCCGCGGTGTACGCCAAGGAGCAC
genomic: CCTGCGAGCGACGCCCCGGCGCGCCGTCCACCTCCTTCTCCGCCTTCGCCgtaagcgctc ... gctctcgcagCTGTTCGATGGGCACAACGGGAGCGCCGCCGCGGTGTACGCCAAGGAGCAC

EST: gi|148971590|gb|EE022306.2|EE022306

EST:     CCTGCGAGCGACGCCCCGGCGCGCCGTCCACCTCCTTCTCCGCCTTCGCC                         CTGTTCGATGGGCACAACGGGAGCGCCGCCGCGGTGTACGCCAAGGAGCAC
genomic: CCTGCGAGCGACGCCCCGGCGCGCCGTCCACCTCCTTCTCCGCCTTCGCCgtaagcgctc ... gctctcgcagCTGTTCGATGGGCACAACGGGAGCGCCGCCGCGGTGTACGCCAAGGAGCAC

EST: gi|148993132|gb|EE033731.2|EE033731

EST:     CCTGCGAGCGACGCCCCGGCGCGCCGTCCACCTCCTTCTCCGCCTTCGCC                         CTGTTCGATGGGCACAACGGGAGCGCCGCCGCGGTGTACGCCAAGGAGCAC
genomic: CCTGCGAGCGACGCCCCGGCGCGCCGTCCACCTCCTTCTCCGCCTTCGCCgtaagcgctc ... gctctcgcagCTGTTCGATGGGCACAACGGGAGCGCCGCCGCGGTGTACGCCAAGGAGCAC

EST: gi|148939724|gb|EC884406.2|EC884406

EST:     CCTGCGAGCGACGCCCCGGCGCGCCGTCCACCTCCTTCTCCGCCTTCGCC                         CTGTTCGATGGGCACAACGGGAGCGCCGCCGCGGTGTACGCCAAGGAGCAC
genomic: CCTGCGAGCGACGCCCCGGCGCGCCGTCCACCTCCTTCTCCGCCTTCGCCgtaagcgctc ... gctctcgcagCTGTTCGATGGGCACAACGGGAGCGCCGCCGCGGTGTACGCCAAGGAGCAC

EST: gi|88747035|gb|DY531176.1|DY531176

EST:     CCTGCGAGCGACGCCCCGGCGCGCCGTCCACCTCCTTCTCCGCCTTCGCC                         CTGTTCGATGGGCACAACGGGAGCGCCGCCGCGGTGTACGCCAAGGAGCAC
genomic: CCTGCGAGCGACGCCCCGGCGCGCCGTCCACCTCCTTCTCCGCCTTCGCCgtaagcgctc ... gctctcgcagCTGTTCGATGGGCACAACGGGAGCGCCGCCGCGGTGTACGCCAAGGAGCAC

EST: gi|89249221|gb|DY621007.1|DY621007

EST:     CCTGCGAGCGACGCCCCGGCGCGCCGTCCACCTCCTTCTCCGCCTTCGCC                         CTGTTCGATGGGCACAACGGGAGCGCCGCCGCGGTGTACGCCAAGGAGCAC
genomic: CCTGCGAGCGACGCCCCGGCGCGCCGTCCACCTCCTTCTCCGCCTTCGCCgtaagcgctc ... gctctcgcagCTGTTCGATGGGCACAACGGGAGCGCCGCCGCGGTGTACGCCAAGGAGCAC

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), 48 (downstream exon)
Score: 161

GCAGGCCTGCCGGGCGAAGAAGGGTGAGGACTTCGCGCTGCTCAAGCCCGCCTGCGAGCGACGCCCCGGCGCGCCGTCCACCTCCTTCTCCGCCTTCGCCgtaagcgctc ... gctctcgcagCTGTTCGATGGGCACAACGGGAGCGCCGCCGCGGTGTACGCCAAGGAGCACCTCCTCGGCAACGTGCTCAGCTGCGTCCCGACCGATCTGGCCTGGGACG

Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 70

Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 87