ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TAATGTGCACTTCCTGTCTAAGCCGGTCAAAGATGGAACAACTGGAACTGTCATTGTTCTAACAACGCCGGATGCACAGCGTACTATGCTTGCGTATCAGgtcaattccttttacttcctttgctgacaactcttctatatctgaacttgtcagatattatttcagttacacttgcttactgcgctttcccagccctctt...

Basic information

species	Zea mays
transcript	GRMZM2G121128_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G121128_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os10g42240.1 (Oryza sativa), 5'ss of exon 3

TAATGTGCACTTCCTGTCTAAGCCGGTCAAAGATGGAACAACTGGAACTGTCATTGTTCTAACAACGCCGGATGCACAGCGTACTATGCTTGCGTATCAGgtcaattcct---tttacttcctttgctgacaactcttctatatctgaacttgtcagatattatttcagttacacttgcttactgcgctttcccagccctctt
|||| |||| ||| |||||||||||||||||||||| || ||||||||||| |||||||||||||| || |||||||| || ||||||||||| |||||||||| ||  |   |||         | |    | ||  |  | |  | |||| |     | |||   | | |   ||  ||  ||    |    ||       
TAATTTGCATTTCTTGTCTAAGCCGGTCAAAGATGGGACTACTGGAACTGTGATTGTTCTAACAACTCCAGATGCACAACGAACTATGCTTGCATATCAGgtcagttgatatgtttgtacttcagggttgttattcccccttctagggacttctgttgcaatatcagactaaattttaatttttgaagatgagtagttta---

upper sequence: GRMZM2G121128_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT4G27600.1 (Arabidopsis thaliana), 5'ss of exon 3

TAATGTGCACTTCCTGTCTAAGCCGGTCAAAGATGGAACAACTGGAACTGTCATTGTTCTAACAACGCCGGATGCACAGCGTACTATGCTTGCGTATCAGgtcaattccttttacttcctttgctgacaactctt-ctatatctgaacttgtcagatattatttcagttacacttgcttactgcgcttt--cccagccctctt----
 |||||  | || || |||   ||  |||| || |||||||| ||||| || || ||||| ||||| || |||||||| |||||||||||||| ||||||||    |  || |  |  ||  ||  |   ||||| | || | | |   |   | || | |     ||| | ||| |||  | | |      | |||    ||    
AAATGTAAATTTTCTTTCTGCTCCAATCAAGGACGGAACAACAGGAACAGTGATAGTTCTCACAACTCCTGATGCACAACGTACTATGCTTGCATATCAGgtaggat--ttctgat--ctcagcaaattgctcttgcaatgtattactattcaaaatgtaag---ggtttccctttcttcttccacaagagtcgagcaaagtttaac

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|4730505|gb|AI649671.1|AI649671

EST:     TCATTGGTCTAACAACGCCGGATGCACAGCGTACTATGCTTGCGTATCAG                         GGTACTTCGTCAACTCTGAGTTACGATTCAGACTTGGCCAGTTTAGTGTCT
genomic: TCATTGTTCTAACAACGCCGGATGCACAGCGTACTATGCTTGCGTATCAGgtcaattcct ... gtctttgcagGGTACTTCGTCAACTCTGAGTTACGATTCAGACTTGGCCAGTTTAGTGTCT

EST: gi|67023167|gb|CO451916.1|CO451916

EST:     TCATTGTTCTAACAACGCCGGATGCACAGCGTACTATGCTTGCGTATCAG                         GGTACTTCGTCAACTCTGAGTTACGATTCAGACTTGGCCAGTTTAGTGTCT
genomic: TCATTGTTCTAACAACGCCGGATGCACAGCGTACTATGCTTGCGTATCAGgtcaattcct ... gtctttgcagGGTACTTCGTCAACTCTGAGTTACGATTCAGACTTGGCCAGTTTAGTGTCT

EST: gi|78117019|gb|DV535406.1|DV535406

EST:     TCATTGTTCTAACAACGCCGGATGCACAGCGTACTATGCTTGCGTATCAG                         GGTACTTCGTCAACTCTGAGTTACGATTCAGACTTGGCCAGTTTAGTGTCT
genomic: TCATTGTTCTAACAACGCCGGATGCACAGCGTACTATGCTTGCGTATCAGgtcaattcct ... gtctttgcagGGTACTTCGTCAACTCTGAGTTACGATTCAGACTTGGCCAGTTTAGTGTCT

EST: gi|149086701|gb|EE176240.2|EE176240

EST:     TCATTGTTCTAACAACGCCGGATGCACAGCGTACTATGCTTGCGTATCAG                         GGTACTTCGTCAACTCTGAGTTACGATTCAGACTTGGGCAGTTTAGTGTCT
genomic: TCATTGTTCTAACAACGCCGGATGCACAGCGTACTATGCTTGCGTATCAGgtcaattcct ... gtctttgcagGGTACTTCGTCAACTCTGAGTTACGATTCAGACTTGGCCAGTTTAGTGTCT

EST: gi|76915890|gb|DV166152.1|DV166152

EST:     TCATTGTTCTAACAACGCCGGATGCACAGCGTACTATGCTTGCGTATCAG                         GGTACTTCGTCAACTCTGAGGTACGATTCAGACTTGGCCAGTTTAGTGTCT
genomic: TCATTGTTCTAACAACGCCGGATGCACAGCGTACTATGCTTGCGTATCAGgtcaattcct ... gtctttgcagGGTACTTCGTCAACTCTGAGTTACGATTCAGACTTGGCCAGTTTAGTGTCT

EST: gi|149090339|gb|EE179645.2|EE179645

EST:     TCATTGTTCTAACAACGCCGGATGCACAGCGTACTATGCTTGCGTATCAG                         GGTACTTCGTCAACTCTGAGTTACGATTC
genomic: TCATTGTTCTAACAACGCCGGATGCACAGCGTACTATGCTTGCGTATCAGgtcaattcct ... gtctttgcagGGTACTTCGTCAACTCTGAGTTACGATTC

EST: gi|74244263|gb|DT652177.1|DT652177

EST:     TCATTGTTCTAACAACGCCGGATGCACAGCGTACTATGCTTGCGTATCAG                         GGTACTTCGTCAACTCTGAGTTACGATTCAGACTTGGCCAGTTTAGTGTCT
genomic: TCATTGTTCTAACAACGCCGGATGCACAGCGTACTATGCTTGCGTATCAGgtcaattcct ... gtctttgcagGGTACTTCGTCAACTCTGAGTTACGATTCAGACTTGGCCAGTTTAGTGTCT

EST: gi|148963253|gb|EE014242.2|EE014242

EST:     CATTGTTCTAAACA-CGCCGGATGCACAGCGTACTATGCTTGCGTATCAG                         GGTACTTCGTCAACTCTGAGTTACGATTCAGACTTGGCCAGTTTAGTGTCT
genomic: CATTGTTCTAA-CAACGCCGGATGCACAGCGTACTATGCTTGCGTATCAGgtcaattcct ... gtctttgcagGGTACTTCGTCAACTCTGAGTTACGATTCAGACTTGGCCAGTTTAGTGTCT

EST: gi|71448967|gb|DR830017.1|DR830017

EST:     TCATTGTTCTAACAACGCCGGATGCACAGCGTACTATGCTTGCGTATCAG                         GGTACTTCGTCAACTCTGAGTTACGATTCAGACTTGGCCAGTTTAGTGTCT
genomic: TCATTGTTCTAACAACGCCGGATGCACAGCGTACTATGCTTGCGTATCAGgtcaattcct ... gtctttgcagGGTACTTCGTCAACTCTGAGTTACGATTCAGACTTGGCCAGTTTAGTGTCT

EST: gi|78091988|gb|DV520362.1|DV520362

EST:     TCATTGTTCTAACANCGCCGGATGCACAGCGTACTATGCTTGCGTATCAG                         GGTACTTCGTCAACTCTGAGTTACGATTCAGACTTGGCCAGTTTAG
genomic: TCATTGTTCTAACAACGCCGGATGCACAGCGTACTATGCTTGCGTATCAGgtcaattcct ... gtctttgcagGGTACTTCGTCAACTCTGAGTTACGATTCAGACTTGGCCAGTTTAG

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: 44 (upstream exon), 47 (downstream exon)
Score: 46

TAATGTGCACTTCCTGTCTAAGCCGGTCAAAGATGGAACAACTGGAACTGTCATTGTTCTAACAACGCCGGATGCACAGCGTACTATGCTTGCGTATCAGgtcaattcct ... gtctttgcagGGTACTTCGTCAACTCTGAGTTACGATTCAGACTTGGCCAGTTTAGTGTCTAAATCAAATGTACTAATTGTGGAAGGTTATCTATTTGAGCTGCCTCACA

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 133

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 16

Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 57

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAATGTGCACTTCCTGTCTAAGCCGGTCAAAGATGGAACAACTGGAACTGTCATTGTTCTAACAACGCCGGATGCACAGCGTACTATGCTTGCGTATCAGgtcaattccttttacttcctttgctgacaactcttctatatctgaacttgtcagatattatttcagttacacttgcttactgcgctttcccagccctctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccagcc