ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TACTATAGGACAATGCTGGCGATATGAGCGCATGACCAGAGGAAGAAGGCGGGAACATTACCAATGGAATATGGATATATTTGGTGTGCCTAAAGTTCGGgtaccacccttctcatttattgattctggatgctgctttgcttgtatacctttgaactgatttggcattgccatcttgttgttcgaattag

Basic information

species	Zea mays
transcript	GRMZM2G158228_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G158228_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g51830.1 (Oryza sativa), 5'ss of exon 4

TACTATAGGACAATGCTGGCGATATGAGCGCATGACCAGAGGAAGAAGGCGGGAACATTACCAATGGAATATGGATATATTTGGTGTGCCTAAAGTTCGGgta----------ccaccct----------tctcatttatt----gattctggatgctgctttgct----tgta-tacctt--------tgaactgatttggcattgccatcttgttgttcgaa-ttag
|||||||||||||||||||||||||||||| ||||| ||||||||| |||| |||||||| |||||||| |||||||| |||||  ||||||||||||| |||           |   ||          ||  |||| |     |||||  |||||  || ||||    ||||  |||||        | || |||||| | |||| | | |||||  |  || | ||
TACTATAGGACAATGCTGGCGATATGAGCGTATGACAAGAGGAAGACGGCGTGAACATTATCAATGGAACATGGATATTTTTGGCATGCCTAAAGTTCGAgtaagtagtaaattcgttctagtgtgagattcatatttgtccttggattcaagatgccactctgctacattgtagcaccttgtttgattttaattgatttagaattgacttattgttaataaaaatcag

upper sequence: GRMZM2G158228_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT3G46100.1 (Arabidopsis thaliana), 5'ss of exon 4

TACTATAGGACAATGCTGGCGATATGAGCGCATGACCAGAGGAAGAAGGCGGGAACATTACCAATGGAATATGGATATATTTGGTGTGCCTAAAGTTCGGgtac-cacccttctcatttattgattctggatgctgct---ttgcttg-tatacc--tttgaactgatttggcattgccatcttgttgttcgaattag-----------
| | || || || || |||||||||||| | ||||| ||||||||  | || || |||||||||||||||||||||||  ||||||||||| ||||    |||   |||   |   || | | | | |  | ||   |   || |||| ||||      | | |||  ||    ||   |  | ||    | |||| |           
TGCAATTGGGCAGTGTTGGCGATATGAGAGAATGACAAGAGGAAGGCGACGTGAGCATTACCAATGGAATATGGATATTATTGGTGTGCCTCAAGTAACTgtatgtacctcacaacttcaatcacttttaaggcctttgagtttcttgctatattaacctcacctgtgtttatttttttaagtcgtgccgctaatttggtttcttttag

upper sequence: GRMZM2G158228_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT5G03406.1 (Arabidopsis thaliana), 5'ss of exon 4

TACTATAGGACAATGCTGGCGATATGAGCGCATGACCAGAGGAAGAAGGCGGGAACATTACCAATGGAATATGGATATATTTGGTGTGCCTAAAGTTCGGgtac-cacccttctcatttattgattctggatgctgctttgcttgtatacctttgaac-tgatttggcattgccatcttgttgttcgaattag--------------------------
| || | || || || ||| |||||||| | |||||  |||||||  | || || |||||||| ||||||||||||||  ||||||||||| |||||   |||   | |  ||  |  | |     ||  | ||    | | || |     | ||||| |||| ||   ||    |||   |   |    ||                           
TGCTGTTGGGCAGTGTTGGAGATATGAGAGAATGACACGAGGAAGGCGACGTGAGCATTACCAGTGGAATATGGATATTATTGGTGTGCCTGAAGTTACAgtatgtatctctcatacctttaatcactttaggccttctagttttttgttatatgaacctgatctgtgtttaaagtctctataagccggctaatttggttcacaaaccttttcttttag

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|91049651|gb|EB160069.1|EB160069

EST:     GGGAACATTACCAATGGAATATGGATATATTTGGTGTGCCTAAAGTTCGG                         GCTGAGGCTGAGCTTCTTCATGCTATTGTTCTCTTATTTCAACGTCTTGGA
genomic: GGGAACATTACCAATGGAATATGGATATATTTGGTGTGCCTAAAGTTCGGgtaccaccct ... ttcgaattagGCTGAGGCTGAGCTTCTTCATGCTATTGTTCTCTTATTTCAACGTCTTGGA

EST: gi|76918728|gb|DV167428.1|DV167428

EST:     GGGAACATTACCAATGGAATATGGATATATTTGGTGTGCCTAAAGTTCGG                         GTTGAGGCTGAGCTTCTTCATGCTATTGTTCTCTTATTTNCA-CGTCTT
genomic: GGGAACATTACCAATGGAATATGGATATATTTGGTGTGCCTAAAGTTCGGgtaccaccct ... ttcgaattagGCTGAGGCTGAGCTTCTTCATGCTATTGTTCTCTTATTT-CAACGTCTT

EST: gi|76927459|gb|DV171253.1|DV171253

EST:     GGGAACATTACCAATGGAATATGGATATATTTGGTGTGCCTAAAGTTCGG                         GCTGAGGCTGAGCTTCTTCATGCTATTGTTCTCTTATTTCAACGTCTTGGA
genomic: GGGAACATTACCAATGGAATATGGATATATTTGGTGTGCCTAAAGTTCGGgtaccaccct ... ttcgaattagGCTGAGGCTGAGCTTCTTCATGCTATTGTTCTCTTATTTCAACGTCTTGGA

EST: gi|148985468|gb|EE029669.2|EE029669

EST:     GGGAACATTACCAATGGAATATGGATATATTTGGTGTGCCTAAAGTTCGG                         GCTGAGGCTGACCTTCTTCATGCTATTGTTCTCTTATTTCAACGTCTTGGA
genomic: GGGAACATTACCAATGGAATATGGATATATTTGGTGTGCCTAAAGTTCGGgtaccaccct ... ttcgaattagGCTGAGGCTGAGCTTCTTCATGCTATTGTTCTCTTATTTCAACGTCTTGGA

EST: gi|76910390|gb|DV163842.1|DV163842

EST:     GGGAACATTACCAATGGAATATGGATATATTTGGTGTGCCTAAAGTTCGG                         GCTGAGGCTGAGCTTCTTCATGCTATTGTTCTCTTATTTCAACGTCTTGGA
genomic: GGGAACATTACCAATGGAATATGGATATATTTGGTGTGCCTAAAGTTCGGgtaccaccct ... ttcgaattagGCTGAGGCTGAGCTTCTTCATGCTATTGTTCTCTTATTTCAACGTCTTGGA

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), 47 (downstream exon)
Score: 36

TACTATAGGACAATGCTGGCGATATGAGCGCATGACCAGAGGAAGAAGGCGGGAACATTACCAATGGAATATGGATATATTTGGTGTGCCTAAAGTTCGGgtaccaccct ... ttcgaattagGCTGAGGCTGAGCTTCTTCATGCTATTGTTCTCTTATTTCAACGTCTTGGAATTACATCTTCAGATGTGGGGATCAGGGTGTCCAGTCGGAAG

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 98

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 60