ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

AACATGTAATTAGGGAACAGAACTTTATGGCAGCCAACGAGATCATTGAGCTCTTCTGCGAGCTGATTGTTACACGCCTTCCTATCATCGCAAAACAGAAgtttgtctttaactaccatcaccttcctaaacttatttgttctcataagtatggaaaataaggtcctaatcttgtgccaactttttattcag

Basic information

species	Zea mays
transcript	GRMZM2G012413_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G012413_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os09g37510.1 (Oryza sativa), 5'ss of exon 3

AACATGTAATTAGGGAACAGAACTTTATGGCAGCCAACGAGATCATTGAGCTCTTCTGCGAGCTGATTGTTACACGCCTTCCTATCATCGCAAAACAGAAgtttgtctttaactacc--atcaccttcctaaacttatttgttctcataagta--tggaaaataaggtcctaatcttgtgccaactttttattcag
| ||||| ||||| ||||||||| |||||||||| || ||||||||||| || ||||| ||||||||||||||||||||||| ||||| ||||| |||||||||||  ||    ||    |    ||   ||  ||   |||||| | || |   | | || |  |  |   |||     | ||| |||| || ||
AGCATGTCATTAGAGAACAGAACATTATGGCAGCGAATGAGATCATTGATCTTTTCTGTGAGCTGATTGTTACACGCCTTCCCATCATTGCAAAGCAGAAgtttgtactttggaacttgcttgtgttatcaattttgcatgttctgaaaactgggttgtaattgtgtgctgtatcgctgtcaaaccttttctttag

upper sequence: GRMZM2G012413_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT4G35730.1 (Arabidopsis thaliana), 5'ss of exon 3

AACATGTAATTAGGGAACAGAACTTTATGGCAGCCAACGAGATCATTGAGCTCTTCTGCGAGCTGATTGTTACACGCCTTCCTATCATCGCAAAACAGAAgtttgtctttaactaccatcaccttcc-taaacttatttgttct-cataagtatggaaaataaggtcctaatcttgtgccaactttttattcag
| ||||| || |||||||||||| ||  |||||| ||||| ||||||||||| ||||| || || |||||| | || ||  |||||||| | || || |||| |||   || |||| ||||  || | |     | |||| | | | | ||| |||    | |  |    ||   |||      |||  || ||
AGCATGTGATAAGGGAACAGAACATTCAGGCAGCAAACGAAATCATTGAGCTTTTCTGTGAACTTATTGTTTCTCGTCTCACTATCATCACTAAGCAAAAgtatgttcatatctactatcagttttcatttgtctctttgctttgcttcagtttggcttcttatatgtgtat---gtgtttggctttcttttag

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|74241634|gb|DT649548.1|DT649548

EST:     CTCTTCTGCGAGCTGATTGTTACACGCCTTCCTATCATCGCAAAACAGAA                         GGAATGTCCAGCAGACTTGAAAGAAGGTATCTGCAGTTTGATATTTGCAGC
genomic: CTCTTCTGCGAGCTGATTGTTACACGCCTTCCTATCATCGCAAAACAGAAgtttgtcttt ... ttttattcagGGAATGTCCAGCAGACTTGAAAGAAGGTATCTGCAGTTTGATATTTGCAGC

EST: gi|148999901|gb|EE036946.2|EE036946

EST:     CTCTTCTGCGAGCTGATTGTTACACGCCTTCCTATCATCGCAAAACAGAA                         GGAATGTCCAGCAGACTTGAAAGAAGGTATCTGCAGTTTGATATTTGCAGC
genomic: CTCTTCTGCGAGCTGATTGTTACACGCCTTCCTATCATCGCAAAACAGAAgtttgtcttt ... ttttattcagGGAATGTCCAGCAGACTTGAAAGAAGGTATCTGCAGTTTGATATTTGCAGC

EST: gi|149076185|gb|EE164779.2|EE164779

EST:     CTCTTCTGCGAGCTGATTGTTACACGCCTTCCTATCATCGCAAAACAGAA                         GGAATGTCCAGCAGACTTGAAAGAAGGTATCTGCAGTTTGATATTTGCAGC
genomic: CTCTTCTGCGAGCTGATTGTTACACGCCTTCCTATCATCGCAAAACAGAAgtttgtcttt ... ttttattcagGGAATGTCCAGCAGACTTGAAAGAAGGTATCTGCAGTTTGATATTTGCAGC

EST: gi|211369839|gb|FL433659.1|FL433659

EST:     ATCGCAAAACAGAA                         GGAATGTCCAGCAGACTTGAAAGAAGGTATCTGCAGTTTGATATTTGCAGC
genomic: ATCGCAAAACAGAAgtttgtcttt ... ttttattcagGGAATGTCCAGCAGACTTGAAAGAAGGTATCTGCAGTTTGATATTTGCAGC

EST: gi|211434274|gb|FL405875.1|FL405875

EST:     CTCTTCTGCGAGCTGATTGTTACACGCCTTCCTATCATCGCAAAACAGAA                         GGAATGTCCAGCAGACTTGAAAGAAGGTATCTGCAGTTTGATATTTGCAGC
genomic: CTCTTCTGCGAGCTGATTGTTACACGCCTTCCTATCATCGCAAAACAGAAgtttgtcttt ... ttttattcagGGAATGTCCAGCAGACTTGAAAGAAGGTATCTGCAGTTTGATATTTGCAGC

EST: gi|148945139|gb|EC890337.2|EC890337

EST:     CTCTTCTGCGAGCTGATTGTTACACGCCTTCCTATCATCGCAAAACAGAA                         GGAATGTCCAGCAGACTTGAAAGAAGGTATCTGCAGTTTGATATTTGCAGC
genomic: CTCTTCTGCGAGCTGATTGTTACACGCCTTCCTATCATCGCAAAACAGAAgtttgtcttt ... ttttattcagGGAATGTCCAGCAGACTTGAAAGAAGGTATCTGCAGTTTGATATTTGCAGC

EST: gi|20802742|gb|BQ293792.1|BQ293792

EST:     CTCTTCTGCGAGCTGATTGTTACACGCCTTCCTATCATCGCAAAACAGAA                         GGAATGTCCAGCAGACTTGAAAGAAGGTATCTGCAGTTTGATATTTGCAGC
genomic: CTCTTCTGCGAGCTGATTGTTACACGCCTTCCTATCATCGCAAAACAGAAgtttgtcttt ... ttttattcagGGAATGTCCAGCAGACTTGAAAGAAGGTATCTGCAGTTTGATATTTGCAGC

EST: gi|78111386|gb|DV529783.1|DV529783

EST:     TCTTCTGCGAGCTGATTGTTACACGCCCTTCCTATCATCGCAAAACAGAA                         GGAATGTCCAGCAGACTTGAAAGAAGGTATCTGCAGTTTGATATTTGCAGC
genomic: TCTTCTGCGAGCTGATTGTTACACGCC-TTCCTATCATCGCAAAACAGAAgtttgtcttt ... ttttattcagGGAATGTCCAGCAGACTTGAAAGAAGGTATCTGCAGTTTGATATTTGCAGC

EST: gi|71322908|gb|DR798137.1|DR798137

EST:     CTCTTCTGCGAGCTGATTGTTACACGCCTTCCTATCATCGCAAAACAGAA                         GGAATGTCCAGCAGACTTGAAAGAAGGTATCTGCAGTTTGATATTTGCAGC
genomic: CTCTTCTGCGAGCTGATTGTTACACGCCTTCCTATCATCGCAAAACAGAAgtttgtcttt ... ttttattcagGGAATGTCCAGCAGACTTGAAAGAAGGTATCTGCAGTTTGATATTTGCAGC

EST: gi|71767968|gb|DR965905.1|DR965905

EST:     CTCTTCTGCGAGCTGATTGTTACACGCCTTCCTATCATCGCAAAACAGAA                         GGAATGTCCAGCAGACTTGAAAGAAGGTATCTGCAGTTTGATATTTGCAGC
genomic: CTCTTCTGCGAGCTGATTGTTACACGCCTTCCTATCATCGCAAAACAGAAgtttgtcttt ... ttttattcagGGAATGTCCAGCAGACTTGAAAGAAGGTATCTGCAGTTTGATATTTGCAGC

EST: gi|86466457|gb|DY232827.1|DY232827

EST:     CTCTTCTGCGAGCTGATTGTTACACGCCTTCCTATCATCGCAAAACAGAA                         GGAGTGTCCAGCAGACTTGAAAGAAGGTATCTGCAGTTTGATATTTGCAGC
genomic: CTCTTCTGCGAGCTGATTGTTACACGCCTTCCTATCATCGCAAAACAGAAgtttgtcttt ... ttttattcagGGAATGTCCAGCAGACTTGAAAGAAGGTATCTGCAGTTTGATATTTGCAGC

EST: gi|28910124|gb|CB331273.1|CB331273

EST:     CTCTTCTGCGAGCTGATTGTTACACGCCTTCCTATCATCGCAAAACAGAA                         GGAATGTCCAGCAGACTTGAAAGAAGGTATCTGCA
genomic: CTCTTCTGCGAGCTGATTGTTACACGCCTTCCTATCATCGCAAAACAGAAgtttgtcttt ... ttttattcagGGAATGTCCAGCAGACTTGAAAGAAGGTATCTGCA

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: 108

AACATGTAATTAGGGAACAGAACTTTATGGCAGCCAACGAGATCATTGAGCTCTTCTGCGAGCTGATTGTTACACGCCTTCCTATCATCGCAAAACAGAAgtttgtcttt ... ttttattcagGGAATGTCCAGCAGACTTGAAAGAAGGTATCTGCAGTTTGATATTTGCAGCTCCAAGGTGCTCTGAGCTCCCTGAACTTGGTCGCATACGTGACATTTTT

Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 20

Block sizes: 44 (upstream exon), 39 (downstream exon)
Score: 11

Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 43

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACATGTAATTAGGGAACAGAACTTTATGGCAGCCAACGAGATCATTGAGCTCTTCTGCGAGCTGATTGTTACACGCCTTCCTATCATCGCAAAACAGAAgtttgtctttaactaccatcaccttcctaaacttatttgttctcataagtatggaaaataaggtcctaatcttgtgccaactttttattcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT