ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GTTCCTTATGAAGCTGAACAATGAGACGGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCGgtacgcttcgactctaacctctagcggggccgcgggaaaacctttaaattttctgcgatctgaagaggcttcaaattttaaggtgttttgtacgatgcgt...

Basic information

species	Zea mays
transcript	GRMZM2G027571_T02
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G027571_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os04g39444.1 (Oryza sativa), 5'ss of exon 2

GTTCCTTATGAAGCTGAACAATGAGACGGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCGgtacgcttcgactctaacctctagcggggccgcggg--aaaacctttaaattttctgcgatctgaagaggcttcaaattttaaggtgttttgtacgatgcgt---
||| || |||||||||||||| |||||||||||||||||||||||||||||||| || || ||||| ||||||||||||| ||||     ||  ||   ||    ||| | ||    ||      ||||||     |  | | | |   ||     |    |||||   || |||   |   
GTTTCTGATGAAGCTGAACAACGAGACGGTCACCATCGAGCTCAAGAACGGCACCGTCGTCCACGGAACCATCACCGgtaagcttttcacctcgcccacag----gccacaggtcgcaagtagggaatttttgaaaaatttaggggctctccctggtgcttgtgttcc-taggatttattat

upper sequence: GRMZM2G027571_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA03G30880.1 (Glycine max), 5'ss of exon 2

GTTCCTTATGAAGCTGAACAATGAGACGGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCGgtacgcttcgactctaacctctagcggggccgcgggaaaacctttaaattttctgcgatctgaagaggcttcaaattttaaggtgttttgtacgatgcgt----
||| || |||||||||||||| || || ||  | ||||||||||||||||| || ||||| || |||||||| || ||| | ||||  ||||  | ||   |   |   |        ||| |      || |  | ||  |  ||||    |        |||| ||     || |    
GTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAGgttctcttct-ctcttccgtccttctccgaatctttttgttcttca---ccgctccattttgttgctgcttttgttaaaccctagtttcgtttcgcgcttaaac

upper sequence: GRMZM2G027571_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA19G33700.1 (Glycine max), 5'ss of exon 2

GTTCCTTATGAAGCTGAACAATGAGACGGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCGgtacgcttcgactctaacctctagcggggccgcgggaaaacctttaaattttctgcgatctgaagaggct-tcaaattttaaggtgttttgtacgatgcgt
||| || |||||||||||||| || || ||  | |||||||||||||||||||| ||||| ||||||||||| || ||||| ||||  |  |   ||||      |   ||       |||      ||        ||  |    | | |||   ||   || |||   || |    
GTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAGgtactcttctcccttccgctcttttcccgtatcgttttgttcttcgccgcttgattttgttgctgcttttgttaaaccctagtttggttt-cgcgcttaaa

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|148944677|gb|EC889813.2|EC889813

EST:     GGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCG                         GTGTTGACATAAGCATGAACACTCATCTGAAGACAGTGAAGCTTACACTGA
genomic: GGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCGgtacgcttcg ... ttttgggtagGTGTTGACATAAGCATGAACACTCATCTGAAGACAGTGAAGCTTACACTGA

EST: gi|71762881|gb|DR960818.1|DR960818

EST:     GGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCG                         GTGTTGACATAAGCATGAACACTCATCTGAAGACAGTGAAGCTTACACTGA
genomic: GGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCGgtacgcttcg ... ttttgggtagGTGTTGACATAAGCATGAACACTCATCTGAAGACAGTGAAGCTTACACTGA

EST: gi|71445025|gb|DR826075.1|DR826075

EST:     GGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCG                         GTGTTGACATAAGCATGAACACTCATCTGAAGACAGTGAAGCTTACACTGA
genomic: GGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCGgtacgcttcg ... ttttgggtagGTGTTGACATAAGCATGAACACTCATCTGAAGACAGTGAAGCTTACACTGA

EST: gi|88749844|gb|DY533985.1|DY533985

EST:     GGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCG                         GTGTTGACATAAGCATGAACACTCATCTGAAGACAGTGAAGCTTACACTGA
genomic: GGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCGgtacgcttcg ... ttttgggtagGTGTTGACATAAGCATGAACACTCATCTGAAGACAGTGAAGCTTACACTGA

EST: gi|149094950|gb|EE180534.2|EE180534

EST:     GGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCG                         GTGTTGACATAAGCATGAACACTCATCTGAAGACAGTGAAGCTTACACTGA
genomic: GGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCGgtacgcttcg ... ttttgggtagGTGTTGACATAAGCATGAACACTCATCTGAAGACAGTGAAGCTTACACTGA

EST: gi|91057155|gb|EB167573.1|EB167573

EST:     GGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCG                         GTGTTGACATAAGCATGAACACTCATCTGAAGACAGTGAAGCTTACACTGA
genomic: GGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCGgtacgcttcg ... ttttgggtagGTGTTGACATAAGCATGAACACTCATCTGAAGACAGTGAAGCTTACACTGA

EST: gi|50330686|gb|CO525812.1|CO525812

EST:     GGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCG                         GTGTTGACATAAGCATGAACACTCATCTGAAGACAGTGAAGCTTACACTGA
genomic: GGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCGgtacgcttcg ... ttttgggtagGTGTTGACATAAGCATGAACACTCATCTGAAGACAGTGAAGCTTACACTGA

EST: gi|31558692|gb|CD527904.1|CD527904

EST:     GGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCG                         GTGTTGACATAAGCATGAACACTCATCTGAAGACAGTGAAGCTTACACTGA
genomic: GGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCGgtacgcttcg ... ttttgggtagGTGTTGACATAAGCATGAACACTCATCTGAAGACAGTGAAGCTTACACTGA

EST: gi|45847704|gb|CN071647.1|CN071647

EST:     GGCACCATCACCG                         GTGTTGACATAAGCATGAACACTCATCTGAAGACAGTGAAGCTTACCCTGA
genomic: GGCACCATCACCGgtacgcttcg ... ttttgggtagGTGTTGACATAAGCATGAACACTCATCTGAAGACAGTGAAGCTTACACTGA

EST: gi|15590053|gb|BI674669.1|BI674669

EST:     GTCACCATCGANGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCG                         GTGTTGACATAAGCATGAACACTCATCTGAAGACAGTGAAGCTTACACTGA
genomic: GTCACCATCGA-GCTCAAGAACGGCACGGTTGTACACGGCACCATCACCGgtacgcttcg ... ttttgggtagGTGTTGACATAAGCATGAACACTCATCTGAAGACAGTGAAGCTTACACTGA

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), 48 (downstream exon)
Score: 276

GTTCCTTATGAAGCTGAACAATGAGACGGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCGgtacgcttcg ... ttttgggtagGTGTTGACATAAGCATGAACACTCATCTGAAGACAGTGAAGCTTACACTGAAAGGGAAGAACCCTGTAACACTTGACCACCTCAGCGTGCGAGGAAACAA

Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 50

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 66

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 60

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCCTTATGAAGCTGAACAATGAGACGGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCGgtacgcttcgactctaacctctagcggggccgcgggaaaacctttaaattttctgcgatctgaagaggcttcaaattttaaggtgttttgtacgatgcgt

- - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - -  AAGAAC