ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TGCCCAGAGAAGTTGCCAAATTACGAGGCTAAGATAAAGAATTTCTTTGAAGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCGgtaggtgcctttgttttgcatctggaggcgttttttttgaagacagaaaatctaatagtcagcaggttttctttctagttactgtcgatgtttaatcgtttttacacttatgttctcaag

Basic information

species	Zea mays
transcript	GRMZM2G165998_T03
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G165998_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g06620.1 (Oryza sativa), 5'ss of exon 4

TGCCCAGAGAAGTTGCCAAATTACGAGGCTAAGATAAAGAATTTCTTTGAAGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCGgtaggtgcctttgttttgcatctggaggcgttttttttgaagacagaaaatctaatagtcagca--ggttttctttctagttactgtcgatgtttaatcgtttttacacttatgttc-tcaag
|| ||||| ||| ||||||| || ||||||||| | || ||||||||||||||||||||||||||||||||||||||||| ||||| |||||||| || |||| |   |||| || | |   | |  | |   ||  | |  |   | ||  |  |   |||||    |  |  |   |  |  ||| | |||   ||  || ||   || ||| || || ||
TGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTGAAAAATTTCTTTGAAGAACACTTGCATACTGATGAAGAGATACGCTATTGTCTTGAGGGAAGTGgtatgcatctttattatac---tagttgagcacttgataactagtaataacttgctt-ccagcaataatcatggtggcatgttttgtggttgtcacatacttctttttctcatgctcctctag

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|32915127|gb|CF019939.1|CF019939

EST:     AGAACACTTGCATACTGATGAAGAGATACGCTATTGCCTTGAGGGCAGCG                         GCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA
genomic: AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCGgtaggtgcct ... tgttctcaagGCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA

EST: gi|32910309|gb|CF015121.1|CF015121

EST:     AGAACACTTGCATACTGATGAAGAGATACGCTATTGCCTTGAGGGCAGCG                         GCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA
genomic: AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCGgtaggtgcct ... tgttctcaagGCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA

EST: gi|211136266|gb|FL235028.1|FL235028

EST:     AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCG                         GCTACTTTGATGTGAGGGACCAATATGATCAGTGGATCCGTGTAGCGGTAA
genomic: AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCGgtaggtgcct ... tgttctcaagGCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA

EST: gi|42491995|gb|CK701041.1|CK701041

EST:     AGAACACTTGCATACTGATGAAGAGATACGCTATTGCCTTGAGGGCAGCG                         GCTACTTTGATGTGAGGGACCCAGATGATCAGTGGATCCGTGTAGCGGTAA
genomic: AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCGgtaggtgcct ... tgttctcaagGCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA

EST: gi|32918894|gb|CF023706.1|CF023706

EST:     AGAACACTTGCATACTGATGAAGAGATACGCTATTGCCTTGAGGGCAGCG                         GCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA
genomic: AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCGgtaggtgcct ... tgttctcaagGCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA

EST: gi|211136272|gb|FL235034.1|FL235034

EST:     AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCG                         GCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTA-CGGTAA
genomic: AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCGgtaggtgcct ... tgttctcaagGCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA

EST: gi|32858130|gb|CD997811.1|CD997811

EST:     AGAACACTTGCATACTGATGAAGAGATACGCTATTGCCTTGAGGGCAGCG                         GCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA
genomic: AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCGgtaggtgcct ... tgttctcaagGCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA

EST: gi|5895571|gb|AW036817.1|AW036817

EST:     AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCG                         GCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA
genomic: AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCGgtaggtgcct ... tgttctcaagGCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA

EST: gi|26557489|gb|CA829724.1|CA829724

EST:     AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCG                         GCTACTTTGATGTGAGGG
genomic: AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCGgtaggtgcct ... tgttctcaagGCTACTTTGATGTGAGGG

EST: gi|211136265|gb|FL235027.1|FL235027

EST:     AAACACTTGCATACTGATGAAGAGATACGATTATTGCCTTGAGGGTAGCG                         GCTACTTTGATGTGAGGGACCAATATGATCAGTGGATCCGTGTAGC
genomic: AA-CACTTGCATACTGATGAAGAGATACGAT-ATTGCCTTGAGGGTAGCGgtaggtgcct ... tgttctcaagGCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGC

EST: gi|32851451|gb|CD991132.1|CD991132

EST:     AGAACACTTGCATACTGATGAAGAGATACGCTATTGCCTTGAGGGCAGCG                         GCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAN
genomic: AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCGgtaggtgcct ... tgttctcaagGCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA

EST: gi|32915396|gb|CF020208.1|CF020208

EST:     AGAACACTTGCATACTGATGAAGAGATACGCTATTGCCTTGAGGGCAGCG                         GCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA
genomic: AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCGgtaggtgcct ... tgttctcaagGCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA

EST: gi|32910482|gb|CF015294.1|CF015294

EST:     AGAACACTTGCATACTGATGAAGAGATACGCTATTGCCTTGAGGGCAGCG                         GCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA
genomic: AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCGgtaggtgcct ... tgttctcaagGCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA

EST: gi|31611894|gb|CD568516.1|CD568516

EST:     AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCG                         GCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA
genomic: AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCGgtaggtgcct ... tgttctcaagGCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA

EST: gi|211137218|gb|FL235045.1|FL235045

EST:     AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCG                         GCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA
genomic: AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCGgtaggtgcct ... tgttctcaagGCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA

EST: gi|9731247|gb|BE509999.1|BE509999

EST:     AGAACACTTGCATACTGATGAAGAGATACGCTATTGCCTTGAGGGCAGCG                         GCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA
genomic: AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCGgtaggtgcct ... tgttctcaagGCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA

EST: gi|32916506|gb|CF021318.1|CF021318

EST:     AGAACACTTGCATACTGATGAAGAGATACGCTATTGCCTTGAGGGCAGCG                         GCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA
genomic: AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCGgtaggtgcct ... tgttctcaagGCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA

EST: gi|32916207|gb|CF021019.1|CF021019

EST:     AGAACACTTGCATACTGATGAAGAGATACGCTATTGCCTTGAGGGCAGCG                         GCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA
genomic: AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCGgtaggtgcct ... tgttctcaagGCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA

EST: gi|111990462|gb|EE331881.1|EE331881

EST:     AGAACACTTGCATACTGATGAAGAGATACGCTATTGCCTTGAGGGCAGCG                         GCTACTTTGATGTGAGGGACCAAGATGATCAAGTGGATCCGTGTAGCGGTA
genomic: AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCGgtaggtgcct ... tgttctcaagGCTACTTTGATGTGAGGGACCAAGATGATCA-GTGGATCCGTGTAGCGGTA

EST: gi|74034874|gb|DT535365.1|DT535365

EST:     AGAACACTTGCATACTGATGAAGAGATACGCTATTGCCTTGAGGGCACCG                         GCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA
genomic: AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCGgtaggtgcct ... tgttctcaagGCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA

EST: gi|211135335|gb|FL235023.1|FL235023

EST:     AGAACACTTGCATACTGATGAAGAGATACGCTATTGCCTTGAGGGCAGCG                         GCTACTTTGATGTGAGGGACCA
genomic: AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCGgtaggtgcct ... tgttctcaagGCTACTTTGATGTGAGGGACCA

EST: gi|211137219|gb|FL235046.1|FL235046

EST:     AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCG                         GCTACTTTGATGTGAGGAACCAAGATGATCAGTGGATCCGGGTAGCGGGAA
genomic: AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCGgtaggtgcct ... tgttctcaagGCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA

EST: gi|193502968|gb|AM938541.1|AM938541

EST:     AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCG                         GCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCATGTAGCGGTGA
genomic: AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCGgtaggtgcct ... tgttctcaagGCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA

EST: gi|40287017|gb|CK327409.1|CK327409

EST:     AGAACACTTGCATACTGATGAAGAGATACGCTATTGCCTTGAGGGCAGCG                         GCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA
genomic: AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCGgtaggtgcct ... tgttctcaagGCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA

EST: gi|32868008|gb|CF007690.1|CF007690

EST:     AGAACACTTGCATACTGATGAAGAGATACGCTATTGCCTTGAGGGCAGCG                         GCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGGAA
genomic: AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCGgtaggtgcct ... tgttctcaagGCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA

EST: gi|71770494|gb|DR968431.1|DR968431

EST:     AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCG                         GCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA
genomic: AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCGgtaggtgcct ... tgttctcaagGCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA

EST: gi|211137225|gb|FL235052.1|FL235052

EST:     AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCG                         GCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA
genomic: AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCGgtaggtgcct ... tgttctcaagGCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA

EST: gi|108824274|gb|EC278282.1|EC278282

EST:     AGAACACTTGCATACTGATGAAGAGATACGCTATTGCCTTGAGGGCAGCG                         GCTACTTTGATGTGAGGG
genomic: AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCGgtaggtgcct ... tgttctcaagGCTACTTTGATGTGAGGG

EST: gi|21626225|gb|BQ621146.1|BQ621146

EST:     AGAACACTAGCATACTGATGAAGAGATACGCTATTGCCTTGAGGGCAGCG                         GCTACTTTGATGTGAGGGACCAAGATGATC
genomic: AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCGgtaggtgcct ... tgttctcaagGCTACTTTGATGTGAGGGACCAAGATGATC

EST: gi|32933164|gb|CF037976.1|CF037976

EST:     AGAACACTTGCATACTGATGAAGAGATACGCTATTGCCTTGAGGGCAGCG                         GCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA
genomic: AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCGgtaggtgcct ... tgttctcaagGCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA

EST: gi|32858765|gb|CD998446.1|CD998446

EST:     AGAACACTTGCATACTGATGAAGAGATACGCTATTGCCTTGAGGGCAGCG                         GCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA
genomic: AGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCGgtaggtgcct ... tgttctcaagGCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAA

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), 49 (downstream exon)
Score: 423

TGCCCAGAGAAGTTGCCAAATTACGAGGCTAAGATAAAGAATTTCTTTGAAGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCGgtaggtgcct ... tgttctcaagGCTACTTTGATGTGAGGGACCAAGATGATCAGTGGATCCGTGTAGCGGTAAAGAAAGGGGGCATGATCGTTTTGCCTGCAGGAATGTATCATCGCTTTAC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1186

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1874

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 903

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCCCAGAGAAGTTGCCAAATTACGAGGCTAAGATAAAGAATTTCTTTGAAGAACACTTGCATACTGATGAAGAGATACGATATTGCCTTGAGGGTAGCGgtaggtgcctttgttttgcatctggaggcgttttttttgaagacagaaaatctaatagtcagcaggttttctttctagttactgtcgatgtttaatcgtttttacacttatgttctcaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA