ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TCTGTCACCAGAGAAACTGGCTGTGAAATTAGAATTTACTCTACCAGCATCATCTTATGCTACAATGGCCATAAGGGAGTTGACGAAAACTTCAACTTCGgtgacttcctgttcaattcttttttttggttttgtaaatacttaaattatctttgctactcttttttttcatcttttggtcattgaaccgaaccatttga...

Basic information

species	Zea mays
transcript	GRMZM2G459702_T02
intron #	18
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G459702_T01 (Zea mays), 5'ss of exon 17
lower sequence: LOC_Os01g56620.1 (Oryza sativa), 5'ss of exon 18

-TCTGTCACCAGAGAAACTGGCTGTGAAATTAGAATTTACTCTACCAGCATCATCTTATGCTACAATGGCCATAAGGGAGTTGACGAAAACTTCAACTTCGgtgacttcc---tgttcaattcttttttttggttttgtaaatacttaaattatctttgctactcttttttttcatcttttg-gtcattgaa-----ccgaaccatttga----------
   | |     |||||||||||  | ||||||| |||||||||||||||||||||||||||||||||||| || |||||||||| ||| ||||||||||||||   |  |   |  ||   || ||| |||| ||||   || ||| ||| |   ||     |   |||  |   | || || ||| || |         | |  ||||           
GGATAT-GTTGGAGAAACTGGCCATAAAATTAGCATTTACTCTACCAGCATCATCTTATGCTACAATGGCTATTAGGGAGTTGATGAAGACTTCAACTTCGgtatttctccaattctctgatcatttctttgatttttccaa-actaaaacttagttatgagcaaatttcatctgttttctgtgtcgttaatatatttttatctttttggctgcacacag

upper sequence: GRMZM2G459702_T01 (Zea mays), 5'ss of exon 17
lower sequence: GLYMA03G40600.1 (Glycine max), 5'ss of exon 21

TCTGTCACCAGAGA-AACTGGCTGTGAAATTAGAATTTACTCTACCAGCATCATCTTATGCTACAATGGCCATAAGGGAGTTGACGAAAACTTCAACTTCGgtga---cttcctgttc---aattcttttttttggttttgtaaatacttaaatta-tctttgctactcttttttttcatcttttggtcattgaaccgaaccatttga
 || |||  |     || | ||| | |||||    |||||||| || || |||| |||||| |||||||||||||||||| ||  ||| |||||||| || || |   |  ||  ||    || |||| | | || |  |  |  | ||  ||||| || |   |         ||| | | || ||    || ||  ||        
-CTCTCAAGATTCCCAAATCGCTCTAAAATTGAGCTTTACTCTTCCTGCTTCATGTTATGCAACAATGGCCATAAGGGAGCTGCTGAAGACTTCAACATCTgtaagcacccccaatttgaaaagtcttgtgtctgttactacaggtgctctaattaatcatgattgggaaaaacttttagcattgggaatatgcacataaa-------

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|93016989|gb|EB642509.1|EB642509

EST:     CATCTTATGCTACAATGGCCATAAGGGAGTTGAGGAAAACTTCAACTTCG                         GTTGCTTGCCAGAAAACATTAAACGGCTGACCAAGCCTTGCAGTGTAAAAT
genomic: CATCTTATGCTACAATGGCCATAAGGGAGTTGACGAAAACTTCAACTTCGgtgacttcct ... taatgtacagGTTGCTTGCCAGAAAACATTAAACGGCTGACCAAGCCTTGCAGTGTAAAAT

EST: gi|32942225|gb|CF047044.1|CF047044

EST:     CATCTTATGCTACAATGGCCATAAGGGAGTTGACGAAAACTTCAACTTCG                         GTTGCTTGCCAGAAAACATTAAACGGCTGACCAAGCCTTGCAGTGTAAAAT
genomic: CATCTTATGCTACAATGGCCATAAGGGAGTTGACGAAAACTTCAACTTCGgtgacttcct ... taatgtacagGTTGCTTGCCAGAAAACATTAAACGGCTGACCAAGCCTTGCAGTGTAAAAT

EST: gi|37391053|gb|CF632766.1|CF632766

EST:     CATCTTATGCTACAATGGCCATAAGGGAGTTGACGAAAACTTCAACTTCG                         GTTGCTTGCCAGAAAACATTAAACGGCTGACCAAGCCTTGCAGTGTAAAAT
genomic: CATCTTATGCTACAATGGCCATAAGGGAGTTGACGAAAACTTCAACTTCGgtgacttcct ... taatgtacagGTTGCTTGCCAGAAAACATTAAACGGCTGACCAAGCCTTGCAGTGTAAAAT

EST: gi|60352700|gb|DN219673.1|DN219673

EST:     CATCTTATGCTACAATGGCCATAAGGGAGTTGACGAAAACTTCAACTTCG                         GTTGCTTGCCAGAAAACATTAAACGGCTGACCAACCCTTGCAGTGTAAAAT
genomic: CATCTTATGCTACAATGGCCATAAGGGAGTTGACGAAAACTTCAACTTCGgtgacttcct ... taatgtacagGTTGCTTGCCAGAAAACATTAAACGGCTGACCAAGCCTTGCAGTGTAAAAT

EST: gi|40303670|gb|CK348057.1|CK348057

EST:     CATCTTATGCTACAATGGCCATAAGGGAGTTGACGAAAACTTCAACTTCG                         GTTGCTTGCCAGAAAACATTAAACGGCTGACCAAGCCTTGCAGTGTAAAAT
genomic: CATCTTATGCTACAATGGCCATAAGGGAGTTGACGAAAACTTCAACTTCGgtgacttcct ... taatgtacagGTTGCTTGCCAGAAAACATTAAACGGCTGACCAAGCCTTGCAGTGTAAAAT

EST: gi|78089966|gb|DV518340.1|DV518340

EST:     CATCTTATGCTACAATGGCCATAAGGGAGTTGACGAAAACTTCAACTTCG                         GTTGCTTGCCAGAAAACATTAAACGGCTGACCAAGCCTTGCAGTGTAAAAT
genomic: CATCTTATGCTACAATGGCCATAAGGGAGTTGACGAAAACTTCAACTTCGgtgacttcct ... taatgtacagGTTGCTTGCCAGAAAACATTAAACGGCTGACCAAGCCTTGCAGTGTAAAAT

EST: gi|67031718|gb|CO460467.1|CO460467

EST:     CATCTTATGCTACAATGGCCATGAGGGAGTTGACGAAAACTTCAACTTCG                         GTTGCTTGCCAGAAAACATTAAACGGCTGACCAAGCCTTGCAGTGTAAAAT
genomic: CATCTTATGCTACAATGGCCATAAGGGAGTTGACGAAAACTTCAACTTCGgtgacttcct ... taatgtacagGTTGCTTGCCAGAAAACATTAAACGGCTGACCAAGCCTTGCAGTGTAAAAT

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), 49 (downstream exon)
Score: 79

TCTGTCACCAGAGAAACTGGCTGTGAAATTAGAATTTACTCTACCAGCATCATCTTATGCTACAATGGCCATAAGGGAGTTGACGAAAACTTCAACTTCGgtgacttcct ... taatgtacagGTTGCTTGCCAGAAAACATTAAACGGCTGACCAAGCCTTGCAGTGTAAAATGCTTTCTTCGCAAGCTGGTATCCATTGTGACAAAACACACCATGTGGGT

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 27

Block sizes: 48 (upstream exon), 38 (downstream exon)
Score: 7