ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

AAAAAGATTGGCTGTCACTAGTCGCGGTGCACAGTGATGCTTGGTTGCTGGCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttttgctgctgctctatttctaaggatttcttatgttctggaaacaaatcttgttgttaccatatgctgcttccattatgtttataccagtac...

Basic information

species	Zea mays
transcript	GRMZM2G008259_T02
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G008259_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os11g14010.2 (Oryza sativa), 5'ss of exon 2

AAAAAGATTGGCTGTCACTAGTCGCGGTGCACAGTGATGCTTGGTTGCTGGCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttttgctgctgc------tctatttctaaggatttcttatgttctggaaacaaatcttgttgttaccatatgctgcttccattatgtttataccagtac
| ||||||||||||||||| || ||||| || |||||| | ||| |||| || || ||||||||||| || |||||||| || |||||||||||||||||||| | | |||| || |        |  | || | |   |   ||   |   |      ||| | ||| |  |  |   ||  ||  | ||| ||  |        
AGAAAGATTGGCTGTCACTTGTTGCGGTTCATAGTGATACCTGGCTGCTAGCAGTAGCCTTTTACTTTGGAGCAAGATTCGGGTTTGACAAAGAATCCAGgtactatatttgttgttctggggcatacaattttgattgtcagttgcttgtggttgttcaatgtggtttt--ctgtcccctatttttaatatattgttcttg----

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|60341456|gb|DN208429.1|DN208429

EST:     GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAG                         GAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT

EST: gi|78544063|gb|DV621561.1|DV621561

EST:     CAAGATTTGGTTTTGACAAAGAATCCAG                         GAAGCGTCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: CAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT

EST: gi|101398089|gb|EB820919.1|EB820919

EST:     GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAG                         GAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT

EST: gi|149070148|gb|EE158549.2|EE158549

EST:     GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAG                         GAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT

EST: gi|76916780|gb|DV166549.1|DV166549

EST:     GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAG                         GAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT

EST: gi|76290977|gb|DV030545.1|DV030545

EST:     GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAG                         GAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT

EST: gi|76281879|gb|DV021447.1|DV021447

EST:     GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAG                         GAAGCGCCTTTTTGTCATGATTAATAACCTCTCTACAATATATGAAGTTGT
genomic: GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT

EST: gi|22819609|gb|BU499699.1|BU499699

EST:     GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAG                         GAAGCGTCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT

EST: gi|28910319|gb|CB331379.1|CB331379

EST:     GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAG                         GAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT

EST: gi|148930178|gb|EC872565.2|EC872565

EST:     GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAG                         GAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT

EST: gi|78544023|gb|DV621521.1|DV621521

EST:     GATTTGGTTTTGACAAAGAATCCAG                         GAAGCGTCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: GATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT

EST: gi|22819406|gb|BU499496.1|BU499496

EST:     GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAG                         GAAGCGTCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT

EST: gi|78114017|gb|DV532406.1|DV532406

EST:     GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAG                         GAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT

EST: gi|9794347|gb|BE552655.1|BE552655

EST:     GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAG                         GAAGCGTCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAA
genomic: GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAA

EST: gi|149075823|gb|EE164362.2|EE164362

EST:     GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAG                         GAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT

EST: gi|26455859|gb|CA827442.1|CA827442

EST:     GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAG                         GAAGCGTCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT

EST: gi|19822278|gb|BQ048302.1|BQ048302

EST:     GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAG                         GAAGCGTCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT

EST: gi|78118666|gb|DV537050.1|DV537050

EST:     GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAG                         GAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT

EST: gi|50337531|gb|CO532657.1|CO532657

EST:     TTTTGACAAAGAATCCAG                         GAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: TTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT

EST: gi|27522015|gb|CA989121.1|CA989121

EST:     GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAG                         GAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT

EST: gi|149106606|gb|EE188499.2|EE188499

EST:     GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAG                         GAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT

EST: gi|149106607|gb|EE188500.2|EE188500

EST:     GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAG                         GAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT

EST: gi|149008353|gb|EE040506.2|EE040506

EST:     GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAG                         GAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT

EST: gi|211244489|gb|FL128350.1|FL128350

EST:     GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAG                         GAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT

EST: gi|50338834|gb|CO533960.1|CO533960

EST:     GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAG                         GAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT

EST: gi|74236627|gb|DT644541.1|DT644541

EST:     GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAG                         GAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT

EST: gi|26559804|gb|CA832039.1|CA832039

EST:     GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAG                         GAAGCGTCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT

EST: gi|71766893|gb|DR964830.1|DR964830

EST:     GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAG                         GAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT

EST: gi|22546373|gb|BU098684.1|BU098684

EST:     GCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAG                         GAAGCGTCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: GCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT

EST: gi|78120146|gb|DV538530.1|DV538530

EST:     GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAG                         GAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT
genomic: GCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGT

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: 49 (upstream exon), 33 (downstream exon)
Score: 319

AAAAAGATTGGCTGTCACTAGTCGCGGTGCACAGTGATGCTTGGTTGCTGGCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttt ... attgctgcagGAAGCGCCTTTTTGTCATGATTAATAACCTCCCTACAATATATGAAGTTGTCACGGGAACTGCCAAGAAGCAAACCAAGGAGAAAACTCCGAAAAGCAGC

Block sizes: 49 (upstream exon), 33 (downstream exon)
Score: 97

Block sizes: 47 (upstream exon), 33 (downstream exon)
Score: 78

Block sizes: 48 (upstream exon), 33 (downstream exon)
Score: 72

Putative cis-regulatory sequences

atgc	intron	ATGC	exonic elements by Pertea et al.
ATGC	exon	atgc	putative intronic elements
		ATGC	putative exonic elements identified for retained introns

        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAAAGATTGGCTGTCACTAGTCGCGGTGCACAGTGATGCTTGGTTGCTGGCTGTGGCCTTTTACTTCGGTGCAAGATTTGGTTTTGACAAAGAATCCAGgtattgtttttgctgctgctctatttctaaggatttcttatgttctggaaacaaatcttgttgttaccatatgctgcttccattatgtttataccagtac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA