ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CATAGCCGACTCTCCATCGCTGGAAACTGCCGCATGTGTCTCGTCGAGGTCGAGAAGTCGCCCAAGCCCGTCGCTTCCTGTGCCATGCCCGCGCTCCCAGgtcagctggctcctctgcattccgtcggcggcggttttcatgttcttgcgcgctgttctgatattgaaatgtggttaatgttggtctgctgcgcttcttt...

Basic information

species	Zea mays
transcript	GRMZM2G126038_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G126038_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g50540.1 (Oryza sativa), 5'ss of exon 1

CATAGCCGACTCTCCATCGCTGGAAACTGCCGCATGTGTCTCGTCGAGGTCGAGAAGTCGCCCAAGCCCGTCGCTTCCTGTGCCATGCCCGCGCTCCCAGgtcagctggctcctctgcattccgtcggcggcggttttcatgttc-ttgcgcgctgtt----ctgatattgaaatgtggttaatgttggtctgctgcgcttcttt-
|| ||||| ||||||||||| || |||||||||||||| ||||||||||||||||||||||||||||||||||| ||||| |||||||||||||| |||||| ||| |  | |  |||   |   ||||| ||   |||  |  | || | | |||||      | | |||||| |  |  ||||||||| || |  ||    |  
CACAGCCGTCTCTCCATCGCCGGCAACTGCCGCATGTGCCTCGTCGAGGTCGAGAAGTCGCCCAAGCCCGTCGCCTCCTGCGCCATGCCCGCGCTTCCAGgtgagcag--ttcgatgcggacg--cggcgtcgcgcttcgcggccattactctctgttgaattgggttttgaaacg--gacaatgttggtgtggtttgcaaaatgt

upper sequence: GRMZM2G126038_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA11G33480.1 (Glycine max), 5'ss of exon 1

CATAGCCGACTCTCCATCGCTGGAAACTGCCGCATGTGTCTCGTCGAGGTCGAGAAGTCGCCCAAGCCCGTCGCTTCCTGTGCCATGCCCGCGCTCCCAGgtcagctggctcctctgcattccgtcggcggcggttttcatgttcttgcgcgctgttctgatattgaaatgtggttaatgttggt-ctgctgcgcttcttt--
|| ||| ||||||||||||| ||||||||||||||||| ||||||||||||||||| |||||||| || ||||| || || ||||||||||| ||||| |||||||   ||| ||    | | |     || |  | |  |||  ||    | | |  |||   |  | |  | |  |  ||| |  || ||   |||     
CACAGCAGACTCTCCATCGCCGGAAACTGCCGCATGTGCCTCGTCGAGGTCGAGAAATCGCCCAAACCTGTCGCCTCTTGCGCCATGCCCGCTCTCCCTGgtcagc---ctcttcaatttcctgattttggtgtctgttttgtgattatctgatatgatgacgatttagttcgttagagtttgatgttgttggtgttcagagt

upper sequence: GRMZM2G126038_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA18G04730.1 (Glycine max), 5'ss of exon 1

CATAGCCGACTCTCCATCGCTGGAAACTGCCGCATGTGTCTCGTCGAGGTCGAGAAGTCGCCCAAGCCCGTCGCTTCCTGTGCCATGCCCGCGCTCCCAGgtcagctggctcctctgcattccgtcggcggcggttttcatgttcttgcgcgctgttctgatattgaaatgtggttaatgttggt-ctgctgcgcttcttt-
 | ||| ||||||||||||| || || ||||||||||| ||||||||||||||||| |||||||| |||||||| || || ||||||||||| || || ||| |||    |||  | | |    | || | | |||||  |||  ||    | |    || |  |  | |  | |  |  ||| |  || ||    | ||| 
-ACAGCAGACTCTCCATCGCCGGCAATTGCCGCATGTGCCTCGTCGAGGTCGAGAAATCGCCCAAACCCGTCGCCTCTTGCGCCATGCCCGCTCTTCCTGGttagcctcttccatttcctgattttggtgtctgttttt-tgtgattatctgataggttggtgatttagttcgttagagtttgatgttgttgttggtgttta

upper sequence: GRMZM2G126038_T01 (Zea mays), 5'ss of exon 1
lower sequence: AT5G37510.2 (Arabidopsis thaliana), 5'ss of exon 1

CATAGCCGACTCTCCATCGCTGGAAACTGCCGCATGTGTCTCGTCGAGGTCGAGAAGTCGCCCAAGCCCGTCGCTTCCTGTGCCATGCCCGCGCTCCCAGgtcagctggctcctctgca--ttccgtcggcggcggttttcatgttcttgcgcgctgttctgatattgaaatgtggttaatgttggtctgctgcgcttcttt-----
|||   ||  | || || |||||||| ||| | |||||||| || ||||| ||||| || || ||||| || ||||| ||||||||||| ||||| || ||| || | | | |   | |  || |   |  |  || ||   | |  | |     || |   ||||  |  ||   ||  || |  |     | | || | |     
CATTCTCGTTTATCTATTGCTGGAAATTGCAGGATGTGTCTTGTTGAGGTTGAGAAATCTCCTAAGCCTGTAGCTTCATGTGCCATGCCTGCGCTTCCTGgttagttcgattccaggaaaatttctatgctgatggattgattttgatcgttgattggtggaatat--atttggatttggtgctattgctaagagtttttgtaacag

upper sequence: GRMZM2G126038_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv14s0006g02020.t01 (Vitis vinifera), 5'ss of exon 1

CATAGCCGACTCTCCATCGCTGGAAACTGCCGCATGTGTCTCGTCGAGGTCGAGAAGTCGCCCAAGCCCGTCGCTTCCTGTGCCATGCCCGCGCTCCCAGgtcagctggctcctctgcattccgtcggcggcggttttcatgttcttgcgcgctgttctgatattgaaatgtggttaatgttggtctgctgcgcttcttt---
|| ||||| ||||||||||| || |||||||| |||||| | |||||||| ||||||||||| ||||||||||||||||| ||||||||||| || || ||| ||  || |       |||   |    |    |||   || |  |  | ||| || |  |         |      | |         | | || |||   
CACAGCCGCCTCTCCATCGCCGGGAACTGCCGTATGTGTTTGGTCGAGGTAGAGAAGTCGCCTAAGCCCGTCGCTTCCTGCGCCATGCCCGCTCTTCCTGgttag--ggttttcagaaattttttatttgttcatttgtttggtagtttg-gcttttgtactgcgtggccttacactgtttcatcaattcgtgtttttttgtc

upper sequence: GRMZM2G126038_T01 (Zea mays), 5'ss of exon 1
lower sequence: PP1S170_67V6.1 (Physcomitrella patens), 5'ss of exon 1

CATAGCCGACTCTCCATCGCTGGAAACTGCCGCATGTGTCTCGTCGAGGTCGAGAAGTCGCCCAAGCCCGTCGCTTCCTGTGCCATGCCCGCGCTCCCAGgtc----------agctggc--tcctctgcattccgtcggcggcggtttt-catgttcttgcgcgctgttctgata--ttgaaatgtggttaatgttggtctgctgcgcttcttt-------------------
|| || || |||||||| || || || |||||||||||||| || |||||||||||| | |||||||| || || || ||||||||||| ||  | |||||||          || | |    |||||    || || |   || ||||  |||    || || || ||||| |||  |||   ||||  |||    ||  | ||  |                          
CACAGTCGTCTCTCCATAGCAGGGAATTGCCGCATGTGTCTGGTTGAGGTCGAGAAGACTCCCAAGCCTGTGGCCTCATGTGCCATGCCTGCTTTGCCAGgtctgattccattagttagtaaccctcttttctcagttgcaagctgtttgacatacaatt-cgtgcggttcttataacttggggtgtgtctaaaagcgggatactaagaggtcgaatggctgaattgcgtatag

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|32802898|gb|CD955134.1|CD955134

EST:     CGAGAAGTCGCCCAAGCCCGTCGCTTCCTGTGCCATGCCCGCGCTCCCAG                         GGATGAAGATTA
genomic: CGAGAAGTCGCCCAAGCCCGTCGCTTCCTGTGCCATGCCCGCGCTCCCAGgtcagctggc ... gctggattagGGATGAAGATTA

EST: gi|148961644|gb|EE012413.2|EE012413

EST:     CGAGAAGTCGCCCAAGCCCGTCGCTTCCTGTGCCATGCCCGCGCTCCCAG                         GGATGAAGATTAAGAACAA-CACCCCAGTGGCCAAGAAGG
genomic: CGAGAAGTCGCCCAAGCCCGTCGCTTCCTGTGCCATGCCCGCGCTCCCAGgtcagctggc ... gctggattagGGATGAAGATTAAGA-CAAACACCCCAGTGGCAAAGAAGG

EST: gi|149088448|gb|EE177551.2|EE177551

EST:     CGAGAAGTCGCCCAAGCCCGTCGCTTCCTGTGCCATGCCCGCGCTCCCAG                         GGATGAAGATTAAGACAAACACCCCAGTGGCAAAGAAGGCAAGGGAGGGTG
genomic: CGAGAAGTCGCCCAAGCCCGTCGCTTCCTGTGCCATGCCCGCGCTCCCAGgtcagctggc ... gctggattagGGATGAAGATTAAGACAAACACCCCAGTGGCAAAGAAGGCAAGGGAGGGTG

EST: gi|148995495|gb|EE034685.2|EE034685

EST:     CGAGAAGTCGCCCAAGCCCGTCGCTTCCTGTGCCATGCCCGCGCTCCCAG                         GGATGAAGATTAAGACAAACACCCCAGTGGCAAAGAAGGCAAGGGAGGGTG
genomic: CGAGAAGTCGCCCAAGCCCGTCGCTTCCTGTGCCATGCCCGCGCTCCCAGgtcagctggc ... gctggattagGGATGAAGATTAAGACAAACACCCCAGTGGCAAAGAAGGCAAGGGAGGGTG

EST: gi|148999521|gb|EE036489.2|EE036489

EST:     CGAGAAGTCGCCCAAGCCCGTCGCTTCCTGTGCCATGCCCGCGCTCCCAG                         GGATGAAGATTAAGACAAACACCCCAGTGGCAAAGAAGGCAAGGGAGGGTG
genomic: CGAGAAGTCGCCCAAGCCCGTCGCTTCCTGTGCCATGCCCGCGCTCCCAGgtcagctggc ... gctggattagGGATGAAGATTAAGACAAACACCCCAGTGGCAAAGAAGGCAAGGGAGGGTG

EST: gi|78085646|gb|DV514039.1|DV514039

EST:     CGAGAAGTCGCCCAAGCCCGTCGCTTCCTGTGCCATGCCCGCGCTCCCAG                         GGATGAAGATTAAGACAAACACCCCAGTGGCAAAGAAGGCAAGGGAGGGTG
genomic: CGAGAAGTCGCCCAAGCCCGTCGCTTCCTGTGCCATGCCCGCGCTCCCAGgtcagctggc ... gctggattagGGATGAAGATTAAGACAAACACCCCAGTGGCAAAGAAGGCAAGGGAGGGTG

EST: gi|148972320|gb|EE023227.2|EE023227

EST:     CGAGAAGTCGCCCAAGCCCGTCGCTTCCTGTGCCATGCCCGCGCTCCCAG                         GGATGAAGATTAAGACAAACACCCCAGTGGCAAAGAAGGCAAGGGAGGGTG
genomic: CGAGAAGTCGCCCAAGCCCGTCGCTTCCTGTGCCATGCCCGCGCTCCCAGgtcagctggc ... gctggattagGGATGAAGATTAAGACAAACACCCCAGTGGCAAAGAAGGCAAGGGAGGGTG

EST: gi|211379124|gb|FL373844.1|FL373844

EST:     CGAGAAGTCGCCCAAGCCCGTCGCTTCCTGTGCCATGCCCGCGCTCCCAG                         GGATGAAGATTAAGACAAACACCCCAGTGGCAAAGAAGGCAAGGGAGGGTG
genomic: CGAGAAGTCGCCCAAGCCCGTCGCTTCCTGTGCCATGCCCGCGCTCCCAGgtcagctggc ... gctggattagGGATGAAGATTAAGACAAACACCCCAGTGGCAAAGAAGGCAAGGGAGGGTG

EST: gi|211281181|gb|FL428442.1|FL428442

EST:     CGAGAAGTCGCCCAAGCCCGTCGCTTCCTGTGCCATGCCCGCGCTCCCAG                         GGATGAAGATTAAGACAAACACCCCAGTGGCAAAGAAGGCAAGGGAGGGTG
genomic: CGAGAAGTCGCCCAAGCCCGTCGCTTCCTGTGCCATGCCCGCGCTCCCAGgtcagctggc ... gctggattagGGATGAAGATTAAGACAAACACCCCAGTGGCAAAGAAGGCAAGGGAGGGTG

EST: gi|91052333|gb|EB162751.1|EB162751

EST:     CGAGAAGTCGCCCAAGCCCGTCGCTTCCTGTGCCATGCCCGCGCTCCCAG                         GGATGAAGATTAAGACAAACACCCCAGTGGCAAAGAAGGCAAGGGAGGGTG
genomic: CGAGAAGTCGCCCAAGCCCGTCGCTTCCTGTGCCATGCCCGCGCTCCCAGgtcagctggc ... gctggattagGGATGAAGATTAAGACAAACACCCCAGTGGCAAAGAAGGCAAGGGAGGGTG

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: 318

CATAGCCGACTCTCCATCGCTGGAAACTGCCGCATGTGTCTCGTCGAGGTCGAGAAGTCGCCCAAGCCCGTCGCTTCCTGTGCCATGCCCGCGCTCCCAGgtcagctggc ... gctggattagGGATGAAGATTAAGACAAACACCCCAGTGGCAAAGAAGGCAAGGGAGGGTGTCATGGAGTTCTTGCTGATGAACCATCCACTCGACTGCCCAATCTGTGA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 415

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 347

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 336

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATAGCCGACTCTCCATCGCTGGAAACTGCCGCATGTGTCTCGTCGAGGTCGAGAAGTCGCCCAAGCCCGTCGCTTCCTGTGCCATGCCCGCGCTCCCAGgtcagctggctcctctgcattccgtcggcggcggttttcatgttcttgcgcgctgttctgatattgaaatgtggttaatgttggtctgctgcgcttcttt

- - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT