ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TCGACCACATCGAGCACCACCGCATCCACGGCCTCGTCTACTTCGCCGACGAGGACAACGTGTACTCCCTTGACCTCTTCGACCAGCTTCGCGGCATAAGgtaaaggcgcacatcgtacctctcttagtttccccccactcgcgtttacgtacacgcattcgcgaccctgtttccgattggaattgattgggtcaattctgtactggaatttgaaacccattatgatcgatgttgcgttacatag

Basic information

species	Zea mays
transcript	GRMZM2G179504_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G179504_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os10g13810.1 (Oryza sativa), 5'ss of exon 1

TCGACCACATCGAGCACCACCGCATCCACGGCCTCGTCTACTTCGCCGACGAGGACAACGTGTACTCCCTTGACCTCTTCGACCAGCTTCGCGGCATAAGgtaaag----gcgcacatcgtacctctctta-gtttccccccactcgcgtttacgtacacgcattcgcgaccctgtttccgattggaattgattgggtcaattctgtactggaattt--------gaaacccattatgatcgat-gttg--cgttacatag---------------
| || |||||||||||||||||| | |||||| |||||||||||||||||||||||||||| |||||||||||||||||| |||| ||||||| ||| |||| |||    ||   |||     | | |||  |         |||    |||   ||  |  ||| |   ||  ||  |   || || |   | |    |||||  || |||| |||        ||||| ||||     | || | ||  |  |  |                  
TGGATCACATCGAGCACCACCGCCTACACGGCATCGTCTACTTCGCCGACGAGGACAACGTCTACTCCCTTGACCTCTTCTACCATCTTCGCGACATTAGgtgaagtgtagctatcatgacgtcacacttctgacaatttagactgttcttttgatatcctgattggaatccaagt--caatttagattacgtcgtactaattcgttattggagtttcggtacacgaaactcattggtgccaattggtgaacactgaacgatattctggtgtttag

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|50332431|gb|CO527557.1|CO527557

EST:     GAGGACAACGTGTACTCCCTTGACCTCTTCGACCAGCTTCGCGGCATAAG                         GAGTTTTGGCACCTGGCCAGTCGCAATGCTGGGCGTGGGGAAGAGCAAGAC
genomic: GAGGACAACGTGTACTCCCTTGACCTCTTCGACCAGCTTCGCGGCATAAGgtaaaggcgc ... cgttacatagGAGTTTTGGCACCTGGCCAGTCGCAATGCTGGGCGTGGGGAAGAGCAAGAC

EST: gi|71772175|gb|DR970112.1|DR970112

EST:     GAGGACAACGTGTACTCCCTTGACCTCTTCGACCAGCTTCGCGGCATAAG                         GAGTTTTGGCACCTGGCCAGTCGCAATGCTGGGCGTGGGGAAGAGCAAGAC
genomic: GAGGACAACGTGTACTCCCTTGACCTCTTCGACCAGCTTCGCGGCATAAGgtaaaggcgc ... cgttacatagGAGTTTTGGCACCTGGCCAGTCGCAATGCTGGGCGTGGGGAAGAGCAAGAC

EST: gi|71772174|gb|DR970111.1|DR970111

EST:     CAGCTTCGCGGCATAAG                         GAGTTTTGGCACCTGGCCAGTCGCAATGCTGGGCGTGGGGAAGAGCAAGAC
genomic: CAGCTTCGCGGCATAAGgtaaaggcgc ... cgttacatagGAGTTTTGGCACCTGGCCAGTCGCAATGCTGGGCGTGGGGAAGAGCAAGAC

EST: gi|76019947|gb|DT947117.1|DT947117

EST:     GAGGACAACGTGTACTCCCTTGACCTCTTCGACCAGCTTCCCGGCATAAG                         GAGTTTTGGCACCTGGCCAGTCGCAATGCTGGGCGTGGGGAAGAGCAAGAC
genomic: GAGGACAACGTGTACTCCCTTGACCTCTTCGACCAGCTTCGCGGCATAAGgtaaaggcgc ... cgttacatagGAGTTTTGGCACCTGGCCAGTCGCAATGCTGGGCGTGGGGAAGAGCAAGAC

EST: gi|50337294|gb|CO532420.1|CO532420

EST:     GAGGACAACGTGTACTCCCTTGACCTCTTCGACCAGCTTCGCGGCATAAG                         GAGTTTTGGCACCTGGCCAGTCGCA
genomic: GAGGACAACGTGTACTCCCTTGACCTCTTCGACCAGCTTCGCGGCATAAGgtaaaggcgc ... cgttacatagGAGTTTTGGCACCTGGCCAGTCGCA

EST: gi|76932469|gb|DV173052.1|DV173052

EST:     GAGGACAACGTGTACTCCCTTGACCTCTTCGACCAGCTTCGCGGCATAAG                         GAGTTTTGGCACCTGGCCAGTCGCAATGCTGGGCGTGGGGAAGAGCAAGAC
genomic: GAGGACAACGTGTACTCCCTTGACCTCTTCGACCAGCTTCGCGGCATAAGgtaaaggcgc ... cgttacatagGAGTTTTGGCACCTGGCCAGTCGCAATGCTGGGCGTGGGGAAGAGCAAGAC

EST: gi|76012484|gb|DT939654.1|DT939654

EST:     GAGGACAACGTGTACTCCCTTGACCTCTTCGACCAGCTTCGCGGCATAAG                         GAGTTTTGGCACCTGGCCAGTCGCAATGCTGGGC
genomic: GAGGACAACGTGTACTCCCTTGACCTCTTCGACCAGCTTCGCGGCATAAGgtaaaggcgc ... cgttacatagGAGTTTTGGCACCTGGCCAGTCGCAATGCTGGGC

EST: gi|78084269|gb|DV512662.1|DV512662

EST:     GAGGACAACGTGTACTCCCTTGACCTCTTCGACCAGCTTCGCGGCATAAG                         GAGTTTTGGCACCTGGCCAGTCGCAATGCTGGGCGTGGGGAAGAGCAAGAC
genomic: GAGGACAACGTGTACTCCCTTGACCTCTTCGACCAGCTTCGCGGCATAAGgtaaaggcgc ... cgttacatagGAGTTTTGGCACCTGGCCAGTCGCAATGCTGGGCGTGGGGAAGAGCAAGAC

EST: gi|76928245|gb|DV171538.1|DV171538

EST:     GAGGACAACGTGTACTCCCTTGACCTCTTCGACCAGCTTCGCGGCATAAG                         GAGTTTTGGCACCTGGCCAGTCGCAATGCTGGGCGTGGGGAAGAGCAAGAC
genomic: GAGGACAACGTGTACTCCCTTGACCTCTTCGACCAGCTTCGCGGCATAAGgtaaaggcgc ... cgttacatagGAGTTTTGGCACCTGGCCAGTCGCAATGCTGGGCGTGGGGAAGAGCAAGAC

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: 43 (upstream exon), 44 (downstream exon)
Score: 24

TCGACCACATCGAGCACCACCGCATCCACGGCCTCGTCTACTTCGCCGACGAGGACAACGTGTACTCCCTTGACCTCTTCGACCAGCTTCGCGGCATAAGgtaaaggcgc ... cgttacatagGAGTTTTGGCACCTGGCCAGTCGCAATGCTGGGCGTGGGGAAGAGCAAGACACTTGTGGAAGGGCCGGTTTGTGACAACAGCCAGGTAGTGGGATGGCAC

Block sizes: 47 (upstream exon), 39 (downstream exon)
Score: 100

Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 122