ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GTCTATGGCGGCTGCACTGGGCGCCGTGCTCCGGCGGCTGCATACGGCGGCGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTCgtgagtctccgcttcccagacgaccagcgcttcctcctcccccacatccgtagatcctgcctacctcaggtcttacctgattcatgcggctctctactgc...

Basic information

species	Zea mays
transcript	GRMZM2G006277_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G006277_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g67730.1 (Oryza sativa), 5'ss of exon 1

---GTCTATGGCGGCTGCACTGGGCGCCGTGCTCCGGCGGCTGCATACGGCGGCGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTCgtgagtctccgcttcccagacgaccagcgcttcctcctcccccacatccgtagatcctgcctacctcaggtcttacctgattcatgcggctctctactgc-
   |     |||||   |   ||  ||   ||  | ||||| ||   ||||||||||||||||||| |||||||||||  | |||||||||||||||| ||  ||||||  |  || | | | |   | |||  |  |     ||| | |   |       || |  |      ||| | |  ||| | | | |   |  ||  
GATGGGCGCGGCGGTC-CGGCGGATGC-ACGCCGCAGCGGCGGCG-GCGGCGGCGGCGCAGCCCCCGCGCCTGACGAAGCTTGCGCTGCACCCGCCCAGATCGgtgagttcctcctcctccg-ctctcggcggctaatttcttcccgcttagatcccgtgcgctttgcctgttccttgcttccttcctactgttggttggtggt

upper sequence: GRMZM2G006277_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g10430.1 (Oryza sativa), 5'ss of exon 1

GTCTATGGCGGCTGCACTGGGCGCCGTGCTCCGGCGGCTGCATACGGCG-----GC-GGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTCgtgagtctccgcttcccagacgaccagc-gc-ttcctcctcccccacatccgtagatcctgcctacctcaggtcttacctgattcatgcggctctctactgc
   |   |||  ||  |  ||||  ||| |||||||||| ||  |||||     || |||||||||||| || ||||||||  ||||||| | | |||||||||||||||||  |  |  | |  |  | |||  ||  |  |||   |||   | |  |  ||  | | || |   |    ||  |||| | | || | | |     
---TGCAGCGA-TGGGCGCGGCG--GTGGTCCGGCGGCTCCACGCGGCGCAGGCGCAGGCGCAGCCCCCGCGGCTGACGAAGCTCGCGCTTCGCGCGCCCAAATTCgtgagttccttcccctcccaaaagcagttgcactgttccaatcccttgttca-acgtcgcggcgacttgctggtgaacgagatt-acgagggtatatgacaa

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|211392362|gb|FL377415.1|FL377415

EST:     CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTC                         GTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT
genomic: CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTCgtgagtctcc ... ctcatcctagGTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT

EST: gi|18172861|gb|BM348249.1|BM348249

EST:     CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTC                         GTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT
genomic: CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTCgtgagtctcc ... ctcatcctagGTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT

EST: gi|211443955|gb|FL410275.1|FL410275

EST:     CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTC                         GTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT
genomic: CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTCgtgagtctcc ... ctcatcctagGTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT

EST: gi|211108340|gb|FL388580.1|FL388580

EST:     CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTC                         GTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT
genomic: CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTCgtgagtctcc ... ctcatcctagGTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT

EST: gi|18167915|gb|BM337755.1|BM337755

EST:     CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTC                         GTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT
genomic: CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTCgtgagtctcc ... ctcatcctagGTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT

EST: gi|211301554|gb|FL430309.1|FL430309

EST:     CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTC                         GTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT
genomic: CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTCgtgagtctcc ... ctcatcctagGTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT

EST: gi|211321452|gb|FL399586.1|FL399586

EST:     CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTC                         GTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT
genomic: CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTCgtgagtctcc ... ctcatcctagGTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT

EST: gi|18176507|gb|BM351440.1|BM351440

EST:     CACCCGCCCAAATTC                         GTTGAAATCGAATTCCCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT
genomic: CACCCGCCCAAATTCgtgagtctcc ... ctcatcctagGTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT

EST: gi|67021891|gb|CO450640.1|CO450640

EST:     CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTC                         GTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT
genomic: CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTCgtgagtctcc ... ctcatcctagGTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT

EST: gi|211057895|gb|FL423513.1|FL423513

EST:     CGGCGCA--NCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTC                         GTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT
genomic: CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTCgtgagtctcc ... ctcatcctagGTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT

EST: gi|211220783|gb|FL456545.1|FL456545

EST:     CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTC                         GTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT
genomic: CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTCgtgagtctcc ... ctcatcctagGTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT

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: 48 (upstream exon), 49 (downstream exon)
Score: 18

GTCTATGGCGGCTGCACTGGGCGCCGTGCTCCGGCGGCTGCATACGGCGGCGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTCgtgagtctcc ... ctcatcctagGTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTTCTCAGAGTATACAGCCCAGCAGCTGATAGCAAAATCCGATCAGTGGGCG

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

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 23