ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaagttctgttcgactcctatgtctctatcaatcacacttgactccattcagtacgtatctttcccacgcatcctctcattcctacaacacctgctttttgccgccgcagTCTGGACCAGACGAAAGATGCATTCCTGGAAACACCATCGCCGTCCAAGCTGACATGCCATACAGTGGCCTGTCATCGTTCGGAACAGCATTTTTGTCCA

Basic information

species	Zea mays
transcript	GRMZM2G065012_T02
intron #	10
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G065012_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os04g57350.1 (Oryza sativa), 3'ss of exon 10

gtaagttctgttcgactcctatgtctctatcaatcacacttgactccattcag---tacgtatct--ttcccacgcatcctctcattcctacaacacctgctttttgccgccgcagTCTGGACCAGACGAAAGATGCATTCCTGGAAACACCATCGCCGTCCAAGCTGACATGCCATACAGTGGCCTGTCATCGTTCGGAACAGCATTTTTGTCCA
||| ||||| |  |      |||| || ||        | | |||    |  |   ||| || |   |  ||||  ||| || | | || |  | || | | | |  |  | |||||||||||| || ||||||||||| ||||||||||| || ||||| ||||| ||||||||||| |||||| ||||||| || || ||||||||| | || |
gtaggttctatatggag---atgtgtcaatttgctttgcctaacttttgtttgttctacctaacatatctccactgatcttcacttcccaatgatacat-cctctcactactgcagTCTGGACCTGATGAAAGATGCATCCCTGGAAACACAATTGCCGTGCAAGCAGACATGCCATATAGTGGCTTGTCATCTTTTGGGACAGCATTTCTATCAA

upper sequence: GRMZM2G065012_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA18G10150.1 (Glycine max), 3'ss of exon 10

gtaagttctgt-tcgactcctatgtctctatcaatcacacttgactccattcagtacgtatctttcccacgcatcctctcattcctacaacacctgctttttgccgccgcagTCTGGACCAGACGAAAGATGCATTCCTGGAAACACCATCGCCGTCCAAGCTGACATGCCATACAGTGGCCTGTCATCGTTCGGAACAGCATTTTTGTCCA
 ||   |  || |  | |   || | |  |  ||| | | ||       |   | |  ||  | |    |   |  |      |  |  | |      |||||    |  |||||||||| || |||||| |||||||||| || || || || |||||||| ||||||||||  ||||| ||  || | || || ||| ||||||||||||
-tagcattagtattaagtttaatatgttga--aatgatagtta----tgtagggaaattaattgttgtgctagtttttaagagctaattatag-----ttttgtttacatagTCTGGACCTGATGAAAGAAGCATTCCTGGCAATACTATTGCTGTCCAAGCAGACATGCCATTTAGTGGTCTTACAACTTTTGGTACATCATTTTTGTCCA

upper sequence: GRMZM2G065012_T02 (Zea mays), 3'ss of exon 10
lower sequence: Vv19s0090g01130.t01 (Vitis vinifera), 3'ss of exon 10

gtaagttctgttcgactcctatgtctctatcaatcacacttgactccattcagtacgtatctttcccacgcatcctctcattcctacaacacctgctttttgccgccgcagTCTGGACCAGACGAAAGATGCATTCCTGGAAACACCATCGCCGTCCAAGCTGACATGCCATACAGTGGCCTGTCATCGTTCGGAACAGCATTTTTGTCCA
       || ||  |||  |  || |      ||     |  | |   |||  |    ||||||||||    |  | ||||    ||  |||      |         ||||||||||| || |||||| | |||||||||||||| || || || ||||| |||||||| |||||||| ||| || | || ||||| |||||||||||||
-----ggcttttttactttttagttt-----gatttttttaaatttttttctctgtccatctttcccaatatttttttcatcttcact-cactaatcctgcttttatacagTCTGGACCTGATGAAAGAAGTATTCCTGGAAACACAATTGCTGTTCAAGCAGACATGCCTTACAGTGGTCTGACAACTTTTGGAACGGCATTTTTGTCCA

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|50323441|gb|CO518567.1|CO518567

EST:     GCGCTCATATTGGGCCAGAGCCTACAACGGACAGGTTTGTTGTCATCACT                         TCTGGACCAGACGAAAGATGCATTCCTGGAAACACCATCGCCGTCCAAGCT
genomic: GCGCTCATATTGGGCCAGAGCCTACAACGGACAGGTTTGTTGTCATCACTgtaagttctg ... gccgccgcagTCTGGACCAGACGAAAGATGCATTCCTGGAAACACCATCGCCGTCCAAGCT

EST: gi|78124010|gb|DV542394.1|DV542394

EST:     GCGCTCATATTGGGCCAGAGCCTACAACGGACAGGTTTGTTGTCATCACT                         TCTGGACCAGACAAAAGATGCATTCCTGGAAACACCATCGCCGTCCAAGCT
genomic: GCGCTCATATTGGGCCAGAGCCTACAACGGACAGGTTTGTTGTCATCACTgtaagttctg ... gccgccgcagTCTGGACCAGACGAAAGATGCATTCCTGGAAACACCATCGCCGTCCAAGCT

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 2 RNA-Seq libraries.

Block sizes: 44 (upstream exon), 32 (downstream exon)
Score: 3

GCGCTCATATTGGGCCAGAGCCTACAACGGACAGGTTTGTTGTCATCACTgtaagttctg ... gccgccgcagTCTGGACCAGACGAAAGATGCATTCCTGGAAACACCATCGCCGTCCAAGCTGACATGCCATACAGTGGCCTGTCATCGTTCGGAACAGCATTTTTGTCCA

Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 188