ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

AAAGTGTGGATGTATAGTTGAAAGACATTTAGAAGATGGAGATGTTGTCCTCTTTAATAGACAGCCGAGCCTGCATAGAATGTCAATTATGTGTCACAGGgtatcaatgtctccttatttcataaaagtatacatcaagcatttcttcacctttgaatatttgcttttatacttgagcacag

Basic information

species	Zea mays
transcript	GRMZM2G080176_T01
intron #	10
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G080176_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os04g41490.1 (Oryza sativa), 5'ss of exon 10

AAAGTGTGGATGTATAGTTGAAAGACATTTAGAAGATGGAGATGTTGTCCTCTTTAATAGACAGCCGAGCCTGCATAGAATGTCAATTATGTGTCACAGGgtatcaatgtctccttatttcataaaagta--tacatcaag-catttcttcacctttgaatatttgcttttatacttgagcacag
 |||| ||| ||| |||| ||||| |||||||||||||||||  |||||||||| |||||||| |||||| ||||||||||||||||||||| ||||||||||| |||  ||| | ||| ||    |     ||||| ||    || | |||  || |    ||    ||| || || | |||||
GAAGTATGGCTGTGTAGTCGAAAGGCATTTAGAAGATGGAGACATTGTCCTCTTCAATAGACAACCGAGCTTGCATAGAATGTCAATTATGTCTCACAGGgtataaattgctcttcattacactgcacccgctacatgaaaatgttacctcatattggtcccttgctctttgtatttaatcacag

upper sequence: GRMZM2G080176_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA11G15530.1 (Glycine max), 5'ss of exon 8

AAAGTGTGGATGTATAGTTGAAAGACATTTAGAAGATGGAGATGTTGTCCTCTTTAATAGACAGCCGAGCCTGCATAGAATGTCAATTATGTGTCACAGGgtatcaatgtctccttatttcataaaagtatacatcaagcatttcttcacctttgaatatttgcttttatacttgagcacag
 | |  |||   ||| |||||  | ||||| |||||||||||  |||| || || ||||||||||| ||| ||||| | ||||| || |||||||||||||||   || |||    |  | | |     |    | |   ||||     |  ||| ||   |  ||   |  |     ||||
GAGGATTGGTGATATTGTTGATCGCCATTTGGAAGATGGAGACATTGTTCTTTTCAATAGACAGCCAAGCTTGCATCGGATGTCTATAATGTGTCACAGGgta---atttcttaaaaagtgaaatgtagaattgtgagagattttgatccaattgcattaatatttaatttttcacatacag

upper sequence: GRMZM2G080176_T01 (Zea mays), 5'ss of exon 10
lower sequence: AT5G60040.1 (Arabidopsis thaliana), 5'ss of exon 11

AAAGTGTGGATGTATAGTTGAAAGACATTTAGAAGATGGAGATGTTGTCCTCTTTAATAGACAGCCGAGCCTGCATAGAATGTCAATTATGTGTCACAGGgtatcaatgtctccttatttcataaaagtatacatcaagcatttcttcacctttgaatatttgcttt---tatacttgagcacag
      ||| || ||||||||  | |||||  |||| ||||||||||| || ||||| || || ||||| |||||| | ||||| || ||||||||||||||  || |      ||||       |   |||  |    | |  | |||      |||  |   |||   |||  |    || ||
GGCCATTGGCTGCATAGTTGACCGCCATTTGCAAGAAGGAGATGTTGTTCTTTTTAACAGGCAACCGAGTCTGCATCGGATGTCTATCATGTGTCACAGGgt--cagtactggtttataatgcttagtcataattttctcttgccctcatagc--aatcctaattttacatatgttgtcccatag

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|91877387|gb|EB407344.1|EB407344

EST:     TCTTTAATAGACAGCCGAGCCTGCATAGAATGTCAATTATGTGTCACAGG                         GCAAGGATAATGCCATGGAGAACACTCAGATTTAATGAGTCTGTTTGCAAC
genomic: TCTTTAATAGACAGCCGAGCCTGCATAGAATGTCAATTATGTGTCACAGGgtatcaatgt ... ttgagcacagGCAAGGATAATGCCATGGAGAACACTCAGATTTAATGAGTCTGTTTGCAAC

EST: gi|166464329|gb|EG129119.1|EG129119

EST:     TCTTTAATAGACAGCCGAGCCTGCATAGAATGTCAATTATGTGTCACAGG                         GCAAGGATAATGCCATGGAGAACAC
genomic: TCTTTAATAGACAGCCGAGCCTGCATAGAATGTCAATTATGTGTCACAGGgtatcaatgt ... ttgagcacagGCAAGGATAATGCCATGGAGAACAC

EST: gi|32848455|gb|CD988136.1|CD988136

EST:     TCTTTAATAGACAGCCGAGCCTGCATAGAATGTCAATTATGTGTCACAGG                         GCAAGGATAATGCCATGGAGAACACTCAGATTTAATGAGTCTGTTTGCAAC
genomic: TCTTTAATAGACAGCCGAGCCTGCATAGAATGTCAATTATGTGTCACAGGgtatcaatgt ... ttgagcacagGCAAGGATAATGCCATGGAGAACACTCAGATTTAATGAGTCTGTTTGCAAC

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: 62

AAAGTGTGGATGTATAGTTGAAAGACATTTAGAAGATGGAGATGTTGTCCTCTTTAATAGACAGCCGAGCCTGCATAGAATGTCAATTATGTGTCACAGGgtatcaatgt ... ttgagcacagGCAAGGATAATGCCATGGAGAACACTCAGATTTAATGAGTCTGTTTGCAACCCTTACAATGCTGATTTTGACGGAGATGAAATGAATTTGCATGTCCCTC

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

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 57