ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GCCGAGGCATTCAGCATCCCCTTCGTGGCCTTTTTCTGAGAAGTTATCTTTCTCAAATAAGCAGAGACAAGTTGCCTGATATTGGTTCCGAGTATGAAGGgtactgtacctttacttcatgtcatgatattacttaaccaagcctttttagagtttcaatagtatcaagctaatttttggccaagagttagtttgttctt...

Basic information

species	Zea mays
transcript	GRMZM5G825524_T02
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G825524_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g58700.1 (Oryza sativa), 5'ss of exon 4

GCCGAGGCATTCAGCATCCCCTTCGTGGCCTTTTTCTGAGAAGTTATCTTTCTCAAATAAGCAGAGACAAGTTGCCTGATATTGGTTCCGAGTATGAAGGgtactgtacctttacttcatgtcat---gatattacttaacc-aagcctttttagagtttcaatagtat-caagctaat-ttttggccaaga--gttagtttgttctt
| |||||||| || ||||| |||||||| ||||| || ||||| || || ||||| |||||| |||||||  |||| |||||||||||||||||||||||||| || || |  |   ||||   |    || ||   ||||  |||      ||  ||||||   ||||  ||  |  | | ||   | | |   ||| ||       
GTCGAGGCATCCAACATCCTCTTCGTGGGCTTTTCCTAAGAAGCTACCTATCTCAGATAAGCCGAGACAAACTGCCAGATATTGGTTCCGAGTATGAAGGgtaatgcac-tccatgccatgctgtttaaatgttcagtaactgaagataaactaatgtttcatatgtatgtaaaatgttgtcttattctacaacattaatt-------

upper sequence: GRMZM5G825524_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA01G36870.1 (Glycine max), 5'ss of exon 4

GCCGAGGCATTCAGCATCCCCTTCGTGGCCTTTTTCTGAGAAGTTATCTTTCTCAAATAAGCAGAGACAAGTTGCCTGATATTGGTTCCGAGTATGAAGGgtactgtacctttacttcatgtcatgatattacttaaccaagcctttttagagtt-tcaatagtatcaagctaatttttggccaagagttagtttgttctt
| |||||||||||||| ||  ||||||| || ||||| |||||||| ||||||||| | || || || || ||||| ||||||||||| ||||| |||||||     | |   | ||  || | |  |  | |||    | ||    |||    | |     || ||    |    || |      ||||    ||  || 
GTCGAGGCATTCAGCACCCTGTTCGTGGACTCTTTCTCAGAAGTTACCTTTCTCAAGTTAGTAGGGATAAATTGCCAGATATTGGTTCAGAGTACGAAGGgtgagtaagcaagattttttgccctc-tgctcctttcataggcaggattattcctctttgaggtttcttagttgagttggatttgaagttttaatgaactg

upper sequence: GRMZM5G825524_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA11G08390.1 (Glycine max), 5'ss of exon 4

GCCGAGGCATTCAGCATCCCCTTCGTGGCCTTTTTCTGAGAAGTTATCTTTCTCAAATAAGCAGAGACAAGTTGCCTGATATTGGTTCCGAGTATGAAGGgt-actgtacctttacttcatg-tcatgatattacttaaccaagcctttttagagtttcaatagtatcaagctaatttttggccaagagttagtttgttctt
|||| ||||||||||| ||  |||| || || ||||| |||||||| ||||||||| | ||||| ||||| ||||| ||||||||||| ||||| ||||||| | |     ||| |    || || |   ||     |    |  | | || ||| ||   |||| | |  || ||||  ||     | | |  |    |  
GCCGTGGCATTCAGCACCCTGTTCGCGGACTCTTTCTCAGAAGTTACCTTTCTCAAGTTAGCAGGGACAAATTGCCAGATATTGGTTCAGAGTACGAAGGgtgagtaattttttgccctctgctcctttcataggcaagattattcctctttgaggtttcttagt-tgagtctgatttgaggtttc-aatgaactgagccag

upper sequence: GRMZM5G825524_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA14G40270.1 (Glycine max), 5'ss of exon 4

GCCGAGGCATTCAGCATCCCCTTCGTGGCCTTTTTCTGAGAAGTTATCTTTCTCAAATAAGCAGAGACAAGTTGCCTGATATTGGTTCCGAGTATGAAGGgtactgtacctttacttcatgtcatgatattacttaaccaagcctttttagagtttca---atagtatcaagctaatttttggccaagagttagtttgttctt--------
   | |   |||| |||||| ||||||| || ||| |||| ||||| ||||||||| | || | ||| ||||||||||||||||| |  || ||||||| |    |||   ||  |   ||    | | ||  | ||   |   |||| |  || |     ||  | |||   ||||||   |   |  ||   | | ||||         
---GTGCTGTTCAACATCCCATTCGTGGTCTATTTTTGAGGAGTTACCTTTCTCAAGTCAGTAAAGATAAGTTGCCTGATATTGGCTATGAATATGAAGAGGG-

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|19351762|gb|BM896294.1|BM896294

EST:     TCTCAAATAAGCAGAGACAAGTTGCCTGATATTGGTTCCGAGTATGAAGG                         GGATGCTGAAACTATTAACGACGC
genomic: TCTCAAATAAGCAGAGACAAGTTGCCTGATATTGGTTCCGAGTATGAAGGgtactgtacc ... aatcatgcagGGATGCTGAAACTATTAACGACGC

EST: gi|22491272|gb|BU051195.1|BU051195

EST:     TCTCAAATAAGCAGAGACAAGTTGCCTGATATTGGTTCCGAGTATGAAGG                         GGATGCTGAAACTATTAACGACGC
genomic: TCTCAAATAAGCAGAGACAAGTTGCCTGATATTGGTTCCGAGTATGAAGGgtactgtacc ... aatcatgcagGGATGCTGAAACTATTAACGACGC

EST: gi|18964924|gb|BM661289.1|BM661289

EST:     TCTCAAATAAGCAGAGACAAGTTGCCTGATATTGGTTCCGAGTATGAAGG                         GGATGCTGAAACTATTAACGACGC
genomic: TCTCAAATAAGCAGAGACAAGTTGCCTGATATTGGTTCCGAGTATGAAGGgtactgtacc ... aatcatgcagGGATGCTGAAACTATTAACGACGC

EST: gi|32824252|gb|CD963974.1|CD963974

EST:     TCTCAAATAAGCAGAGACAAATCGCCTGATATTGGTTCCGAGTATGAAGG                         GGATGCTGAAACTATTA
genomic: TCTCAAATAAGCAGAGACAAGTTGCCTGATATTGGTTCCGAGTATGAAGGgtactgtacc ... aatcatgcagGGATGCTGAAACTATTA

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: 76

GCCGAGGCATTCAGCATCCCCTTCGTGGCCTTTTTCTGAGAAGTTATCTTTCTCAAATAAGCAGAGACAAGTTGCCTGATATTGGTTCCGAGTATGAAGGgtactgtacc ... aatcatgcagGGATGCTGAAACTATTAACGACGCAGTTGAATTTGTTCTTCAGAATTTCATAGAAATGAACAAACTCTGGGTTCGGATGCAACATCTG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 106

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 81