ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtgagtgcgccgccgccctttctccctatcctccttctctctgggctaatatgtgctgacgtggtgtcctatggatgctttgcagGTGCTGTACTGGCTCTCGGGTCTCACCTGCACCGACGAGAATTTCATCATAAAGTCCGGCGCCCAGCGCGCCGCCGCTGCCCACGGCATCGCCCTCGTGG

Basic information

species	Zea mays
transcript	GRMZM2G046558_T01
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G046558_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g71300.1 (Oryza sativa), 3'ss of exon 1

gtgagtgcgccgccgccctttctccctatcctccttctctctgggctaatatgtg--ctgacgtggtgtcctatggatgctttgcagGTGCTGTACTGGCTCTCGGGTCTCACCTGCACCGACGAGAATTTCATCATAAAGTCCGGCGCCCAGCGCGCCGCCGCTGCCCACGGCATCGCCCTCGTGG
|| ||||| || |||||   |||||   ||||||  |||   |  || ||  | |   |  | || |  |   ||| || |  ||||||||||||||||||||| || ||||| |||| ||||||||| ||| |||  ||| ||||||| |||||||||||||| |||||||||||||||||||| |
gtaagtgctcctccgcctcgtctcc---tcctccgcctcga-gatctgatgaggggtttcgcatgctaccgcgtggttg-tgcgcagGTGCTGTACTGGCTCTCCGGCCTCACGTGCAACGACGAGAACTTCGTCACCAAGGCCGGCGCGCAGCGCGCCGCCGCCGCCCACGGCATCGCCCTCGTCG

upper sequence: GRMZM2G046558_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA02G33350.1 (Glycine max), 3'ss of exon 1

gtgagtgcgccgccgccctttctccctatcctccttctctctgggctaat--------------atgtgctgacgtgg----tgtcctatggatgctttgcagGTGCTGTACTGGCTCTCGGGTCTCACCTGCACCGACGAGAATTTCATCATAAAGTCCGGCGCCCAGCGCGCCGCCGCTGCCCACGGCATCGCCCTCGTGG
|||||| |  | |  |  |||| || | ||    | |  | |   |||||              ||    ||||  ||    ||| || || |||  |   ||||||||||||  ||||| || ||||| |||||||||||||| |||||  | ||||| || || ||||| |||||  | ||| | ||  | ||| | || |
gtgagtccctctct-caatttccccatttctcattccaatttaacctaattttgcacttcctcgattgattgacccggctattgtgctttgaatgaataatagGTGCTGTACTTTCTCTCTGGCCTCACTTGCACCGACGAGAACTTCATATTCAAGTCGGGTGCTCAGCGTGCCGCTTCCGCCGAGGGTGTTGCCTTGGTTG

upper sequence: GRMZM2G046558_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT2G41530.1 (Arabidopsis thaliana), 3'ss of exon 1

----------gtgagtgcgccgccgccct---ttctccctatcctccttctctctgggctaatatgtgctgacgtggtgtcctatg--gatgctttgcagGTGCTGTACTGGCTCTCGGGTCTCACCTGCACCGACGAGAATTTCATCATAAAGTCCGGCGCCCAGCGCGCCGCCGCTGCCCACGGCATCGCCCTCGTGG
           ||  |        ||| |   |||    |     |       |||     || | ||      || |   | |||  | || ||  |||||||| |||||||| || || ||||||||||| |||||||| ||||| || || || || || || || || ||  || | |||||||| || || || |
atgattgtttttggattttttattgccttgatttcgttgtgatgccaaaacaactgattggatttttggatgaatgattctccatgttgttgattgacagGTGCTTTACTGGCTTTCTGGCCTCACCTGCACGGACGAGAACTTCATTATCAAATCAGGAGCTCAACGTGCTGCTTCTACTCACGGCATTGCTCTTGTTG

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|50324809|gb|CO519935.1|CO519935

EST:     CCATGACTTTCTCCATCTACCTGCCCCCGTCCCCGGCGTCCAACCTTCCC                         GTGCTGAACTGGCTCTCGGGTCTCACCTGCACCGAC
genomic: CCATGACTTTCTCCATCTACCTGCCCCCGTCCCCGGCGTCCAACCTTCCCgtgagtgcgc ... tgctttgcagGTGCTGTACTGGCTCTCGGGTCTCACCTGCACCGAC

EST: gi|30591380|gb|CD052344.1|CD052344

EST:     CCATGACTTTCTCAATCTACCTGCCCCCGTCCCCGGCGTCCAACCTTCCC                         GTGCTGTACTGGCTCTCGGGTCTCACCTGCACCGACGAGAATTTCATCATA
genomic: CCATGACTTTCTCCATCTACCTGCCCCCGTCCCCGGCGTCCAACCTTCCCgtgagtgcgc ... tgctttgcagGTGCTGTACTGGCTCTCGGGTCTCACCTGCACCGACGAGAATTTCATCATA

EST: gi|21760089|gb|BQ635630.1|BQ635630

EST:     CCATGACTTTCTCAATCTACCTGCCCCCGTCCCCGGCGTCCAACCTTCCC                         GTGCTGTACTGGCTCTCGGGTCTCACCTGCACCGACGAGAATTTCATCATA
genomic: CCATGACTTTCTCCATCTACCTGCCCCCGTCCCCGGCGTCCAACCTTCCCgtgagtgcgc ... tgctttgcagGTGCTGTACTGGCTCTCGGGTCTCACCTGCACCGACGAGAATTTCATCATA

EST: gi|211475445|gb|FL342188.1|FL342188

EST:     -CATGACTTTCTCCATCTACCTGCCCCCGTCCCCGGCGTCCAACCTTCCC                         GTGCTGTACTGGCTCTCGGGTCTCACCTGCACCGACGAGAATTTCATCATA
genomic: CCATGACTTTCTCCATCTACCTGCCCCCGTCCCCGGCGTCCAACCTTCCCgtgagtgcgc ... tgctttgcagGTGCTGTACTGGCTCTCGGGTCTCACCTGCACCGACGAGAATTTCATCATA

EST: gi|24462576|gb|BM660107.1|BM660107

EST:     CCATGACTTTCTCAATCTACCTGCCCCCGTCCCCGGCGTCCAACCTTCCC                         GTGCTGTACTGGCTCTCGGGTCTCACCTGCACCGACGAGAATTTCATCATA
genomic: CCATGACTTTCTCCATCTACCTGCCCCCGTCCCCGGCGTCCAACCTTCCCgtgagtgcgc ... tgctttgcagGTGCTGTACTGGCTCTCGGGTCTCACCTGCACCGACGAGAATTTCATCATA

EST: gi|211376339|gb|FL031212.1|FL031212

EST:     ATGACTTTCTCCATCTACCTGCCCCCGTCCCCGGCGTCCAACCTTCCC                         GTGCTGTACTGGCTCTCGGGTCTCACCTGCACCGACGAGAATTTCATCATA
genomic: ATGACTTTCTCCATCTACCTGCCCCCGTCCCCGGCGTCCAACCTTCCCgtgagtgcgc ... tgctttgcagGTGCTGTACTGGCTCTCGGGTCTCACCTGCACCGACGAGAATTTCATCATA

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 3 RNA-Seq libraries.

Block sizes: 49 (upstream exon), 37 (downstream exon)
Score: 9

CGACGGCTTCAATCTCCGCTTCCGCCACCAGAGCGCCACCCTTGGCTGCGCCATGACTTTCTCCATCTACCTGCCCCCGTCCCCGGCGTCCAACCTTCCCgtgagtgcgc ... tgctttgcagGTGCTGTACTGGCTCTCGGGTCTCACCTGCACCGACGAGAATTTCATCATAAAGTCCGGCGCCCAGCGCGCCGCCGCTGCCCACGGCATCGCCCTCGTGG

Block sizes: 48 (upstream exon), 41 (downstream exon)
Score: 8

Block sizes: 49 (upstream exon), 12 (downstream exon)
Score: 9

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ctccttctctctgggctaatatgtgctgacgtggtgtcctatggatgctttgcagGTGCTGTACTGGCTCTCGGGTCTCACCTGCACCGACGAGAATTTCATCATAAAGTCCGGCGCCCAGCGCGCCGCCGCTGCCCACGGCATCGCCCTCGTGG