ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CACAGATAGAGGATTTACAGCAATTGGCACTGGAGGTGATGATTTTGTCCAGTCAATGGTAGTTGCTGTTGAATCTGTTCTTCAAGAATCAATTCCCAAGgttagtttttatcattcttataattatttgtaaaccatgtagttatcaacaagaagatgtgattagactgctagtgctttgcgcggagccaatacttccg...

Basic information

species	Zea mays
transcript	GRMZM2G025042_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G025042_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os04g31690.2 (Oryza sativa), 5'ss of exon 3

CACAGATAGAGGATTTACAGCAATTGGCACTGGAGGTGATGATTTTGTCCAGTCAATGGTAGTTGCTGTTGAATCTGTTCTTCAAGAATCAATTCCCAAGgttagtttttatcattcttataatta--tttgtaaaccatgtagttatcaacaagaagatgtg-attagactgctagtgctttgcgcggagccaatacttccg
|||| |||||||||||||||||||||| |||||||||||||||||||||||||||||||| ||||| ||||||||||||||||||||| | |||||||||||||   |||     | ||  ||  |  ||| |  |       ||| |  || | ||||  || | ||      |||   ||| |     || |    ||   
CACAAATAGAGGATTTACAGCAATTGGTACTGGAGGTGATGATTTTGTCCAGTCAATGGTTGTTGCGGTTGAATCTGTTCTTCAAGAACCCATTCCCAAGgttaaaatttccagctgttgaaaacacttttattgatgtccatgttttgtactaaaagaaatgcactaattccatagaaattt-cagattgctagcctttt--

upper sequence: GRMZM2G025042_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA08G10990.1 (Glycine max), 5'ss of exon 3

CACAGATAGAGGATTTACAGCAATTGGCACTGGAGGTGATGATTTTGTCCAGTCAATGGTAGTTGCTGTTGAATCTGTTCTTCAAGAATCAATTCCCAAGgttagtttttatcattcttataattatttgtaaaccatgtagttatcaacaagaagatgtgattagactgctagtgctttgcgcggagccaatacttccg---
 || ||| |||||||||| || ||||| ||||||||||| |||||||| ||  | ||||| |||||||| ||||||||  | ||| || |||||||  ||||   | | |||||      | ||      | |||  | | ||||||    |     |   |||| | || ||   ||      |    | ||  |   |   
AACCGATCGAGGATTTACCGCCATTGGAACTGGAGGTGAGGATTTTGTGCAAGCCATGGTTGTTGCTGTCGAATCTGTAATCCAACAACCAATTCCTCAGgtatatctatatcaagtcatttatggaaattgaac--tttcgttatcggataagttttactattata-tgataaaactccaaatgacatccattttgatgtca

upper sequence: GRMZM2G025042_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT1G27385.1 (Arabidopsis thaliana), 5'ss of exon 3

CACAGATAGAGGATTTACAGCAATTGGCACTGGAGGTGATGATTTTGTCCAGTCAATGGTAGTTGCTGTTGAATCTGTTCTTCAAGAATCAATTCCCAAGgttagtttttatcattcttataattatttgtaaaccatgt-agttatcaacaagaagatgtgattagac---tgctagtgctttgcgcggagccaatacttccg-
 ||||| ||||| ||||| |||||||| ||||| ||  |||| ||||| ||  | ||||| |||||||||||||||||| || |   |  ||||||  |||| |  |||  ||  ||||| || ||| |  |     |    | |   |  |      | ||||  ||    ||||||||  ||         ||||| ||  | 
AACAGAAAGAGGGTTTACTGCAATTGGGACTGGTGGCAATGACTTTGTGCATGCTATGGTTGTTGCTGTTGAATCTGTTATTGACCGACAAATTCCAGAGgtaatatttcgtc-ctcttaaaagtatctagatgatttaccggcttatactatctttttttgatacgatatttgctagtgtcttctata----caatattttggc

upper sequence: GRMZM2G025042_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv01s0010g03660.t01 (Vitis vinifera), 5'ss of exon 3

CACAGATAGAGGATTTACAGCAATTGGCACTGGAGGTGATGATTTTGTCCAGTCAATGGTAGTTGCTGTTGAATCTGTTCTTCAAGAATCAATTCCCAAGgttagtttttatcattcttataat-tatttgtaaaccatgtagttatcaacaagaagatgtgattagactgctagtgctttgcgcggagccaatacttccg
 |||| |||||| ||||| |||||||| ||||||||||| |||||||| ||  | ||||| ||||||||||||||||| |||||| |  |||| ||  ||||   |   |  | |  |   ||| | |||||  || | |  ||| || |    | |   |||| | |      |   |   |    ||   |   ||   
AACAGTTAGAGGGTTTACTGCAATTGGAACTGGAGGTGACGATTTTGTGCAAGCTATGGTTGTTGCTGTTGAATCTGTACTTCAACATCCAATACCTGAGgtacatagatcacttgttgcaaatgtttttgttgactaagatgttttctagtttatgcattgat-acatccaaggaaataaactttaaggtgaccatttaa

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|211402882|gb|FL375613.1|FL375613

EST:     AGTCAATGGTAGTTGCTGTTGAATCTGTTCTTCAAGAATCAATTCCCAAG                         GGCCGGGTATCTCAGAAATTATCTTCAAGAGGGAAATATGTTTCTGTAAAC
genomic: AGTCAATGGTAGTTGCTGTTGAATCTGTTCTTCAAGAATCAATTCCCAAGgttagttttt ... tcttgaacagGGCCGGGTATCTCAGAAATTATCTTCAAGAGGGAAATATGTTTCTGTAAAC

EST: gi|211443951|gb|FL410271.1|FL410271

EST:     AGTCAATGGTAGTTGCTGTTGAATCTGTTCTTCAAGAATCAATTCCCAAG                         GGCCGGGTATCTCAGAAATTATCTTCAAGAGGGAAATATGTTTCTGTAAAC
genomic: AGTCAATGGTAGTTGCTGTTGAATCTGTTCTTCAAGAATCAATTCCCAAGgttagttttt ... tcttgaacagGGCCGGGTATCTCAGAAATTATCTTCAAGAGGGAAATATGTTTCTGTAAAC

EST: gi|148953492|gb|EE152999.2|EE152999

EST:     AGTCAATGGTAGTTGCTGTTGAATCTGTTCTTCAAGAATCAATTCCCAAG                         GGCCGGGTATCTCAGAAATTATCTTCAAGAGGGAAATATGTTTCTGTAAAC
genomic: AGTCAATGGTAGTTGCTGTTGAATCTGTTCTTCAAGAATCAATTCCCAAGgttagttttt ... tcttgaacagGGCCGGGTATCTCAGAAATTATCTTCAAGAGGGAAATATGTTTCTGTAAAC

EST: gi|28910260|gb|CB331350.1|CB331350

EST:     AGTCAATGGTAGTTGCTGTTGAATCTGTTCTTCAAGAATCAATTCCCAAG                         GGCCGGGTATCTCAGAAATTATCTTCAAGAGGGAAATATGTTTCTGTAAAC
genomic: AGTCAATGGTAGTTGCTGTTGAATCTGTTCTTCAAGAATCAATTCCCAAGgttagttttt ... tcttgaacagGGCCGGGTATCTCAGAAATTATCTTCAAGAGGGAAATATGTTTCTGTAAAC

EST: gi|88748691|gb|DY532832.1|DY532832

EST:     AGTCAATGGTAGTTGCTGTTGAATCTG-TCTTCAAGAATCAATTCCCAAG                         GGCCGGGTATCTCAGAAATTATCTTCAAGAGGGAAATATGTTTCTGTAAAC
genomic: AGTCAATGGTAGTTGCTGTTGAATCTGTTCTTCAAGAATCAATTCCCAAGgttagttttt ... tcttgaacagGGCCGGGTATCTCAGAAATTATCTTCAAGAGGGAAATATGTTTCTGTAAAC

EST: gi|76014839|gb|DT942009.1|DT942009

EST:     AGTCAATGGTAGTTGCTGTTGAATCTGTTCTTCAAGAATCAATTCCCAAG                         GGCCGGGTATCTCAGAAATTATCTTCAAGAGGGAAATATGTTTCTGTAAAC
genomic: AGTCAATGGTAGTTGCTGTTGAATCTGTTCTTCAAGAATCAATTCCCAAGgttagttttt ... tcttgaacagGGCCGGGTATCTCAGAAATTATCTTCAAGAGGGAAATATGTTTCTGTAAAC

EST: gi|211444194|gb|FL421114.1|FL421114

EST:     AGTCAATGGTAGTTGCTGTTGAATCTGTTCTTCAAGAATCAATTCCCAAG                         GGCCGGGTATCTCAGAAATTATCTTCAAGAGGGAAATATGTTTCTGTAAAC
genomic: AGTCAATGGTAGTTGCTGTTGAATCTGTTCTTCAAGAATCAATTCCCAAGgttagttttt ... tcttgaacagGGCCGGGTATCTCAGAAATTATCTTCAAGAGGGAAATATGTTTCTGTAAAC

EST: gi|211220755|gb|FL455708.1|FL455708

EST:     AGTCAATGGTAGTTGCTGTTGAATCTGTTCTTCAAGAATCAATTCCCAAG                         GGCCGGGTATCTCAGAAATTATCTTCAAGAGGGAAATATGTTTCTGTAAAC
genomic: AGTCAATGGTAGTTGCTGTTGAATCTGTTCTTCAAGAATCAATTCCCAAGgttagttttt ... tcttgaacagGGCCGGGTATCTCAGAAATTATCTTCAAGAGGGAAATATGTTTCTGTAAAC

EST: gi|148995059|gb|EE034374.2|EE034374

EST:     AGTCAATGGTAGTTGCTGTTGAATCTGTTCTTCAAGAATCAATTCCCAAG                         GGCCGGGTATCTCAGAAATTATCTTCAAGAGGGAAATATGTTTCTGTAAAC
genomic: AGTCAATGGTAGTTGCTGTTGAATCTGTTCTTCAAGAATCAATTCCCAAGgttagttttt ... tcttgaacagGGCCGGGTATCTCAGAAATTATCTTCAAGAGGGAAATATGTTTCTGTAAAC

EST: gi|76013875|gb|DT941045.1|DT941045

EST:     AGTCAATGGTAGTTGCTGTTGAATCTGTTCTTCAAGAATCAATTCCCAAG                         GGCCGGGTATCTCAGAAATTATCTTCAAGAGGGAAATATGTTTCTGTAAAC
genomic: AGTCAATGGTAGTTGCTGTTGAATCTGTTCTTCAAGAATCAATTCCCAAGgttagttttt ... tcttgaacagGGCCGGGTATCTCAGAAATTATCTTCAAGAGGGAAATATGTTTCTGTAAAC

EST: gi|211385110|gb|FL405372.1|FL405372

EST:     AGTCAATGGTAGTTGCTGTTGAATCTGTTCTTCAAGAATCAATTCCCAAG                         GGCCGGGTATCTCAGAAATTATCTTCAAGAGGGAAATATGTTTCTGTAAAC
genomic: AGTCAATGGTAGTTGCTGTTGAATCTGTTCTTCAAGAATCAATTCCCAAGgttagttttt ... tcttgaacagGGCCGGGTATCTCAGAAATTATCTTCAAGAGGGAAATATGTTTCTGTAAAC

EST: gi|211149178|gb|FL419649.1|FL419649

EST:     AGTCAATGGTAGTTGCTGTTGAATCTGTTCTTCAAGAATCAATTCCCAAG                         GGCCGGGTATCTCAGAAATTATCTTCAAGAGGGAAATATGTTTCTGTAAAC
genomic: AGTCAATGGTAGTTGCTGTTGAATCTGTTCTTCAAGAATCAATTCCCAAGgttagttttt ... tcttgaacagGGCCGGGTATCTCAGAAATTATCTTCAAGAGGGAAATATGTTTCTGTAAAC

EST: gi|78117325|gb|DV535712.1|DV535712

EST:     AGTCAATGGTAGTTGCTGTTGAATCTGTTCTTCAAGAATCAATTCCCAAG                         GGCCGGGTATCTCAGAAATTATCTTCAAGAGGGAAATATGTTTCTGTAAAC
genomic: AGTCAATGGTAGTTGCTGTTGAATCTGTTCTTCAAGAATCAATTCCCAAGgttagttttt ... tcttgaacagGGCCGGGTATCTCAGAAATTATCTTCAAGAGGGAAATATGTTTCTGTAAAC

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: 36 (upstream exon), 47 (downstream exon)
Score: 30

CACAGATAGAGGATTTACAGCAATTGGCACTGGAGGTGATGATTTTGTCCAGTCAATGGTAGTTGCTGTTGAATCTGTTCTTCAAGAATCAATTCCCAAGgttagttttt ... tcttgaacagGGCCGGGTATCTCAGAAATTATCTTCAAGAGGGAAATATGTTTCTGTAAACATTGGGCCAATTCGTGTTGTTTCTAGTGAGCAG

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 110

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 44

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 77

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACAGATAGAGGATTTACAGCAATTGGCACTGGAGGTGATGATTTTGTCCAGTCAATGGTAGTTGCTGTTGAATCTGTTCTTCAAGAATCAATTCCCAAGgttagtttttatcattcttataattatttgtaaaccatgtagttatcaacaagaagatgtgattagactgctagtgctttgcgcggagccaatacttccg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacaagaa