ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

AGATGAAAATGTGCTGGCATTTAGAGATATTAATCCACAAGCCCCTGTGCACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAGgcatgtatctcgttcacattacgtgccggtgcacaaactgagtcgagcctggaaaacattttaccatgacttctgtgacattgctgcatgttcttag

Basic information

species	Zea mays
transcript	GRMZM2G143767_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G143767_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os06g45660.1 (Oryza sativa), 5'ss of exon 4

AGATGAAAATGTGCTGGCATTTAGAGATATTAATCCACAAGCCCCTGTGCACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAGgcatgta-tctcgttcacattacgtgccggtgcacaaactgagtcgagcctggaaaacattttaccatgact---tctgtg-acattgctgcatgtt---cttag
 ||||| || ||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||    ||||||||| | || ||| ||||||||| ||| | | | ||||||  || |||   | |     | |      |  ||  |||||  | || |||| |    ||  || || | | |   || |   |||||
GGATGAGAAAGTGCTGGCATTTAGAGATATTAATCCACAAGCCCCTGTGCATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatgttgttcac--ta-gtgtttgcgagaggaatt--ctcaatctctaaaactgtgtagcatggcagtatccatgtacttcgttatgtgcttatcttag

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|6536550|gb|AW224863.1|AW224863

EST:     ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAG                         GCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTCCTTTACGCAGCGAAA
genomic: ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAGgcatgtatct ... atgttcttagGCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTCCTTTACGCAGCGAAA

EST: gi|60340294|gb|DN207267.1|DN207267

EST:     ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAG                         GCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTCCTTTACGCAGCGAAA
genomic: ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAGgcatgtatct ... atgttcttagGCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTCCTTTACGCAGCGAAA

EST: gi|211478458|gb|FL136947.1|FL136947

EST:     ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAG                         GCTGANCCAAGGCATACAGAAATCCTGGGCCGGCTTCTTTACGCAGCGAA
genomic: ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAGgcatgtatct ... atgttcttagGCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTCCTTTACGCAGCGAA

EST: gi|211478445|gb|FL136934.1|FL136934

EST:     ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAG                         GCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTCCTTTACGCAGCGAAA
genomic: ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAGgcatgtatct ... atgttcttagGCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTCCTTTACGCAGCGAAA

EST: gi|211478451|gb|FL136940.1|FL136940

EST:     ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAG                         GCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTCCTTTACGCAGCGAAA
genomic: ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAGgcatgtatct ... atgttcttagGCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTCCTTTACGCAGCGAAA

EST: gi|211478456|gb|FL136945.1|FL136945

EST:     ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAG                         GCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTTCTTTACGCAGCGAAA
genomic: ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAGgcatgtatct ... atgttcttagGCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTCCTTTACGCAGCGAAA

EST: gi|211478447|gb|FL136936.1|FL136936

EST:     ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAG                         GCTGAGCCCAAG-CATACAGAAATCCCTGG-CCGGCTCCTTTACGCAGCGA
genomic: ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAGgcatgtatct ... atgttcttagGCTGAGCC-AAGGCATACAGAAATCC-TGGGCCGGCTCCTTTACGCAGCGA

EST: gi|211478453|gb|FL136942.1|FL136942

EST:     ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAG                         GCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTCCTTTACGCAGCGAAA
genomic: ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAGgcatgtatct ... atgttcttagGCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTCCTTTACGCAGCGAAA

EST: gi|211376140|gb|FL136932.1|FL136932

EST:     ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAG                         GCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTCCTTTACGCAGCGAAA
genomic: ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAGgcatgtatct ... atgttcttagGCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTCCTTTACGCAGCGAAA

EST: gi|211478444|gb|FL136933.1|FL136933

EST:     ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAG                         GCTGAGCCAAGGCATACANGAAATCCTGGGCCGGCTTCTTTACGCAGC
genomic: ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAGgcatgtatct ... atgttcttagGCTGAGCCAAGGCATACA-GAAATCCTGGGCCGGCTCCTTTACGCAGC

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: 46 (upstream exon), 45 (downstream exon)
Score: 61

AGATGAAAATGTGCTGGCATTTAGAGATATTAATCCACAAGCCCCTGTGCACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAGgcatgtatct ... atgttcttagGCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTCCTTTACGCAGCGAAAGTAGTGGCAGAAAAGGAAGGTGTAGCGAGTGGGTACCGTGTTGTCATCA

Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 79

Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 30

Block sizes: 45 (upstream exon), 43 (downstream exon)
Score: 47

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATGAAAATGTGCTGGCATTTAGAGATATTAATCCACAAGCCCCTGTGCACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAGgcatgtatctcgttcacattacgtgccggtgcacaaactgagtcgagcctggaaaacattttaccatgacttctgtgacattgctgcatgttcttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG