ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

gttctagttgcccctaatgccacccttgtgatttaacaatggtatttgcaaaaaactaattgtatatgtatttgcagCAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAGATTAAGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTG

Basic information

species	Zea mays
transcript	GRMZM2G083262_T02
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G083262_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g18510.1 (Oryza sativa), 3'ss of exon 2

gttctagttgcccctaatgccacccttgtgatttaacaatggtatttgcaaaaaactaattgtatatgtatttgcagCAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAGATTAAGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTG
||||| |||  ||||    |  |||||  | ||||   |   | ||| |  |   |||||| |   ||  |||||||||||| |||| ||| ||||||||||| || |||||||| ||||| |||||||||||||||||||| ||||||||||||||  |||||||||| || ||||
gttcttgttatccctgtgtcttcccttagggtttactgaaacttttt-cttatggctaattctggttggttttgcagCAAGCCATGAGGAAGGCTGAAGCTGCTGGTAATGATAATTGTCCAGTGAAGATTAAGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTG

upper sequence: GRMZM2G083262_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA11G35600.1 (Glycine max), 3'ss of exon 4

----------------------------------------------------------gttctagttgcccctaatgccacc-cttgtgatttaaca---atggtatttgcaaaaaactaattgtatatgtatttgcagCAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAGATTAAGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTG
                                                              | |||      | ||  |   | | |   ||| |    |  |||||  ||        | || || ||  | ||||| | || ||| | || ||||||||||| || |||||| |||| || || || ||||| || |||||||| |||||||||||| | ||||| ||||| || |
gtcttgattatttctattcctcctgtttcttattttggcttcttttcttttaagcatctaatttgttatgtgaagtgttatttcctatagcttatcttccaaagtattctcacgttttataatg-atttgattatgcagGAGGCAATGCATAAGGCTGAAGCTGCAGGAAATGATGACTGCCCCGTCAAAATTAAACTTGTTGCTCCCCCACTTTATGTTCTTACCACCCAGACACTGG

upper sequence: GRMZM2G083262_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA18G02820.1 (Glycine max), 3'ss of exon 4

-----------------------------------------------------------------gttctagttgcccctaatgccacccttgtgatttaacaatggtatttgcaaaaaactaattgtatatgtatttgcagCAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAGATTAAGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTG
                                                                 ||| ||        || ||||       |   ||  | |  |||||  ||        | || || ||  | ||||| | || |||   || |||||||||| ||| |||||| |||| ||||| || ||||| || |||||||| |||||||||||| | ||||| ||||| || |
gtatttgattatttgtattccttttgttttttactttggttccttttcttttaagcatctaatttgttatatgaatttttattgcctatagcttatctt--ccaaagtattctcaggttttataatg-atttgattatgcagGAGGCAATGCGTAAGGCTGAAGCTGTGGGAAATGATGACTGCCCTGTCAAAATTAAACTTGTTGCTCCCCCACTTTATGTTCTTACCACCCAGACACTGG

upper sequence: GRMZM2G083262_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv13s0067g01710.t01 (Vitis vinifera), 3'ss of exon 4

-------------------------------gttctagttgcc---cctaatgc----cacccttgtgatttaacaatggtatt-tgcaaaaaactaattgtatatgtatttg-----------------cagCAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAGATTAAGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTG
                                || || |||     ||||||      ||   ||| ||||| ||  | | |   |   ||  |||   ||  |   || |||                 ||| |||| |||  |||||| ||||| ||||||||| |  | ||||| ||||| ||||| || ||||||||||| ||||||||| | || || ||||| ||||
gttttattggtgtccttctttgccactttttattttatttgattggcctaatctgtttcataattgggattttactttagaaccgttttaagtactgtctgctttaatacttgttttatctttcactattcagGAAGCAATGCGGAAAGCAGAAGCGGCGGGCAATAAGGATTGTCCAGTGAAAATTAAACTGGTTGCTCCTCCGCTTTATGTTCTTACTACTCAGACGCTTG

upper sequence: GRMZM2G083262_T02 (Zea mays), 3'ss of exon 2
lower sequence: PP1S55_319V6.1 (Physcomitrella patens), 3'ss of exon 5

----------------------gttctagttgcccctaatgccaccctt-gtgatttaacaatggtatttgcaaaaaactaattgtatatgtat-ttgcagCAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAGATTAAGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTG
                      ||| | |        ||    || |   ||  |||  |  | || ||    | |   |  |  | | ||| | || ||| | || ||||  || || || ||||| || | |||  | |||||||||||||||||| |||| || || |||||||||||  | ||||||||||| ||||
caacggtctgttactaaaaggagttttggc-attaaaaacatgacgcacagttgtttgtcgttagttttattcacatcatgttcttctgtgtgtcttacagGATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAGATTAAGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTG

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|61117519|gb|DN558480.1|DN558480

EST:     CTGATATAGAGATGAAATGCTTCCAGTTTGATGGAGTGCTCCATATTAAG                         CAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAG
genomic: CTGATATAGAGATGAAATGCTTCCAGTTTGATGGAGTGCTCCATATTAAGgttctagttg ... gtatttgcagCAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAG

EST: gi|37390451|gb|CF632455.1|CF632455

EST:     TGATATAGAGATGAAATG-TTCCCAGTTTGATGGAGTGCTCCATATTAAG                         CAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAG
genomic: TGATATAGAGATGAAATGCTT-CCAGTTTGATGGAGTGCTCCATATTAAGgttctagttg ... gtatttgcagCAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAG

EST: gi|60400978|gb|DN233785.1|DN233785

EST:     CTGATATAGAGATGAAATGCTTCCAGTTTGATGGAGTGCTCCATATTAAG                         CAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAG
genomic: CTGATATAGAGATGAAATGCTTCCAGTTTGATGGAGTGCTCCATATTAAGgttctagttg ... gtatttgcagCAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAG

EST: gi|60337847|gb|DN204820.1|DN204820

EST:     TGAAATGCTTCCAGTTTGATGGAGTGCTCCATATTAAG                         CAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAG
genomic: TGAAATGCTTCCAGTTTGATGGAGTGCTCCATATTAAGgttctagttg ... gtatttgcagCAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAG

EST: gi|60351270|gb|DN218243.1|DN218243

EST:     CTGATATAGAGATGAAATGCTTCCAGTTTGATGGAGTGCTCCATATTAAG                         CAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAG
genomic: CTGATATAGAGATGAAATGCTTCCAGTTTGATGGAGTGCTCCATATTAAGgttctagttg ... gtatttgcagCAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAG

EST: gi|74235505|gb|DT643419.1|DT643419

EST:     CTGATATAGAGATGAAATGCTTCCAGTTTGATGGAGTGCTCCATATTAAG                         CAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAG
genomic: CTGATATAGAGATGAAATGCTTCCAGTTTGATGGAGTGCTCCATATTAAGgttctagttg ... gtatttgcagCAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAG

EST: gi|24763866|gb|CA399037.1|CA399037

EST:     TGAAATGCTTCCAGTTTGATGGAGTGCTCCATATTAAG                         CAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAG
genomic: TGAAATGCTTCCAGTTTGATGGAGTGCTCCATATTAAGgttctagttg ... gtatttgcagCAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAG

EST: gi|37381588|gb|CF627690.1|CF627690

EST:     CTGATATAGAGATGAAATGCTTCCAGTTTGATGGAGTGCTCCATATTAAG                         CAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAG
genomic: CTGATATAGAGATGAAATGCTTCCAGTTTGATGGAGTGCTCCATATTAAGgttctagttg ... gtatttgcagCAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAG

EST: gi|60353715|gb|DN220688.1|DN220688

EST:     CTGATATAGAGATGAAATGCTTCCAGTTTGATGGAGTGCTCCATATTAAG                         CAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAG
genomic: CTGATATAGAGATGAAATGCTTCCAGTTTGATGGAGTGCTCCATATTAAGgttctagttg ... gtatttgcagCAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAG

EST: gi|29577089|gb|CB617201.1|CB617201

EST:     CTGATATAGAGATGAAATGCTTCCAGTTTGATGGAGTGCTCCATATTAAG                         CAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAG
genomic: CTGATATAGAGATGAAATGCTTCCAGTTTGATGGAGTGCTCCATATTAAGgttctagttg ... gtatttgcagCAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAG

EST: gi|60352316|gb|DN219289.1|DN219289

EST:     CTGATATAGAGATGAAATGCTTCCAGTTTGATGGAGTGCTCCATATTAAG                         CAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAG
genomic: CTGATATAGAGATGAAATGCTTCCAGTTTGATGGAGTGCTCCATATTAAGgttctagttg ... gtatttgcagCAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAG

EST: gi|60400924|gb|DN233731.1|DN233731

EST:     CTGATATAGAGATGAAATGCTTCCAGTTTGATGGAGTGCTCCATATTAAG                         CAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAG
genomic: CTGATATAGAGATGAAATGCTTCCAGTTTGATGGAGTGCTCCATATTAAGgttctagttg ... gtatttgcagCAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAG

EST: gi|60351973|gb|DN218946.1|DN218946

EST:     CTGATATAGAGATGAAATGCTTCCAGTTTGATGGAGTGCTCCATATTAAG                         CAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAG
genomic: CTGATATAGAGATGAAATGCTTCCAGTTTGATGGAGTGCTCCATATTAAGgttctagttg ... gtatttgcagCAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAG

EST: gi|28982561|gb|BQ538174.2|BQ538174

EST:     CTGATATAGAGATGAAATGCTTCCAGTTTGATGGAGTGCTCCATATTAAG                         CAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAG
genomic: CTGATATAGAGATGAAATGCTTCCAGTTTGATGGAGTGCTCCATATTAAGgttctagttg ... gtatttgcagCAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAG

EST: gi|13149573|gb|BG319895.1|BG319895

EST:     CTGATATAGAGATGAAATGCTTCCAGTTTGATGGAGTGCTCCATATTAAG                         CAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAG
genomic: CTGATATAGAGATGAAATGCTTCCAGTTTGATGGAGTGCTCCATATTAAGgttctagttg ... gtatttgcagCAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAG

EST: gi|60354041|gb|DN221014.1|DN221014

EST:     CTGATATAGAGATGAAATGCTTCCAGTTTGATGGAGTGCTCCATATTAAG                         CAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAG
genomic: CTGATATAGAGATGAAATGCTTCCAGTTTGATGGAGTGCTCCATATTAAGgttctagttg ... gtatttgcagCAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAG

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: 380

GGTTAAGAACATAAGGAGGAGGATGACACCACAGCCTCTCAAGATCCGTGCTGATATAGAGATGAAATGCTTCCAGTTTGATGGAGTGCTCCATATTAAGgttctagttg ... gtatttgcagCAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAGATTAAGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 316

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 284

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 278

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

cccttgtgatttaacaatggtatttgcaaaaaactaattgtatatgtatttgcagCAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAGATTAAGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTG

                               aactaat  putative branch site (score: 278)
                           aaaaaactaattgtat  TA-rich tract

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttctagttgcccctaatgccacccttgtgatttaacaatggtatttgcaaaaaactaattgtatatgtatttgcagCAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAGATTAAGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC