ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gttaatttgcatcaaaatctttatatttcttgttttgttgccaccatcaggagtatttagttgaccttttcttttattatcacaaagGTAACAAAGTCACTGCTTGAGACATCAAGGAGAGGATACCTTGCTGCAATTTCAGCATCTAGTTATTCTTATGTTTCTTTACTTCAACACTTCCTTCCCA

Basic information

species	Zea mays
transcript	GRMZM2G079256_T01
intron #	7
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G079256_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os09g10600.1 (Oryza sativa), 3'ss of exon 7

----gttaatttgcatcaaaatctttatat--ttcttgttttgttgccaccatcaggagtattta-gttgaccttttcttttattat-cacaaagGTAACAAAGTCACTGCTTGAGACATCAAGGAGAGGATACCTTGCTGCAATTTCAGCATCTAGTTATTCTTATGTTTCTTTACTTCAACACTTCCTTCCCA
    |  | | |   ||    ||||||| |  || | ||  | |    | | ||   |  | | |  |  |  |||| || | || | | ||||||||| ||| ||  |||| ||||||||||| | ||| || ||||||||| |||||||||||||||| ||||   | |||||||| |||||||||||||| |
gtatgccactatctttctctttctttatctcattgtcgtcatctgattatcctcgtcatcactaacatctatttttttttattttctgctcaaagGTAAAAAACTCTTTGCTGGAGACATCAAGAAAAGGGTATCTTGCTGCAGTTTCAGCATCTAGTTACTCTTTCATCTCTTTACTCCAACACTTCCTTCCTA

upper sequence: GRMZM2G079256_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA11G10770.1 (Glycine max), 3'ss of exon 7

gttaatttgcatcaaaatcttta-tatttcttgttttgttgccacca-tcaggagtatttagttgaccttttcttttattatcacaaagGTAACAAAGTCACTGCTTGAGACATCAAGGAGAGGATACCTTGCTGCAATTTCAGCATCTAGTTATTCTTATGTTTCTTTACTTCAACACTTCCTTCCCA
       | ||  ||| || ||| ||    |||   |  |   |  | |  ||  |||  | || |        |  | | | | | |||| || ||  || || | ||||||||  ||| |||||| ||||||||||| || ||||||||||| || ||||||||||||||  | || || ||||| |
------gtacaataaattcattaataagcattgaagttcttttatgaatttggtatatg-actttaataaaaagtaaactctgatatagGTGACCAAACCATTGTTGGAGACATCTCGGAAAGGATATCTTGCTGCAATATCTGCATCTAGTTACTCCTATGTTTCTTTACTCAAGCATTTTCTTCCAA

upper sequence: GRMZM2G079256_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA12G03060.1 (Glycine max), 3'ss of exon 8

gttaatttgcatcaaaatctttatatttcttgttttgttgccaccatcagg--agtatttagttg-accttttcttttattatcacaaagGTAACAAAGTCACTGCTTGAGACATCAAGGAGAGGATACCTTGCTGCAATTTCAGCATCTAGTTATTCTTATGTTTCTTTACTTCAACACTTCCTTCCCA
     |  | || || |  || ||| |     ||    | ||   ||       |||| | |||  |       ||| | | | |   |||| || ||  || || | ||||||||  |||  || || ||||||||||| || ||||||||||| || ||||||||||||||  | || || ||||| |
----gtacg-ataaatacattaataataagcattgaagttcctttatgcatttggtatctggttttaataagaatttaactctgatgtagGTGACCAAACCATTGTTGGAGACATCTCGGAATGGGTATCTTGCTGCAATATCTGCATCTAGTTACTCATATGTTTCTTTACTCAAGCATTTTCTTCCAA

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|60345537|gb|DN212510.1|DN212510

EST:     ACTTTGGTAGCATTGATATCCTTGTACACTCTCTCGCCAACGGTCCTGAG                         GTAACAAAGTCACTGCTTGAGACATCAAGGAGAGGATACCTTGCTGCAATT
genomic: ACTTTGGTAGCATTGATATCCTTGTACACTCTCTCGCCAACGGTCCTGAGgttaatttgc ... tatcacaaagGTAACAAAGTCACTGCTTGAGACATCAAGGAGAGGATACCTTGCTGCAATT

EST: gi|78076466|gb|DV504900.1|DV504900

EST:     ACTTTGGTAGCATTGATATCTTTGTACACTCTCTCGCCAACGGTCCTGAG                         GTAACAAAGTCACTG
genomic: ACTTTGGTAGCATTGATATCCTTGTACACTCTCTCGCCAACGGTCCTGAGgttaatttgc ... tatcacaaagGTAACAAAGTCACTG

EST: gi|67011703|gb|CO440452.1|CO440452

EST:     CTTTGGTAGCATTGATATCCTTGTACACTCTCTCCGC-AACGGTCCTGAA                         GTAACANAGTCACTGCTTGAGACATCAAGGAGAGGATACCCTTGCTGCAAT
genomic: CTTTGGTAGCATTGATATCCTTGTACACTCTCTC-GCCAACGGTCCTGAGgttaatttgc ... tatcacaaagGTAACAAAGTCACTGCTTGAGACATCAAGGAGAGGATACC-TTGCTGCAAT

EST: gi|71332949|gb|DR803501.1|DR803501

EST:     ACTTTGGTAGCATTGATATCCTTGTACACTCTCTCGCCAACGGTCCTGAG                         GTAACAAAGTCACTGCTTG
genomic: ACTTTGGTAGCATTGATATCCTTGTACACTCTCTCGCCAACGGTCCTGAGgttaatttgc ... tatcacaaagGTAACAAAGTCACTGCTTG

EST: gi|31356068|gb|CD440425.1|CD440425

EST:     ACTTTGGTAGCATTGATATCCTTGTACACTCTCTCGCCAACGGTCCTGAG                         GTAACAAAGTCACTGCTTGAGACATCAAGGAGAGGATACCTTGCTGCAATT
genomic: ACTTTGGTAGCATTGATATCCTTGTACACTCTCTCGCCAACGGTCCTGAGgttaatttgc ... tatcacaaagGTAACAAAGTCACTGCTTGAGACATCAAGGAGAGGATACCTTGCTGCAATT

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), 47 (downstream exon)
Score: 245

GAAGTTGTTGAGACTGTAAAGAATGACTTTGGTAGCATTGATATCCTTGTACACTCTCTCGCCAACGGTCCTGAGgttaatttgc ... tatcacaaagGTAACAAAGTCACTGCTTGAGACATCAAGGAGAGGATACCTTGCTGCAATTTCAGCATCTAGTTATTCTTATGTTTCTTTACTTCAACACTTCCTTCCCA

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 184

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 54

Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 125

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttttgttgccaccatcaggagtatttagttgaccttttcttttattatcacaaagGTAACAAAGTCACTGCTTGAGACATCAAGGAGAGGATACCTTGCTGCAATTTCAGCATCTAGTTATTCTTATGTTTCTTTACTTCAACACTTCCTTCCCA