ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CGGCAGCGTCGCGCCGCGGACCAACGTCGTGGGCCGGGTGTTCACCGCCAACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAGgtaatcgactgttgaaccatctccccctgcagtctgcagtctggtggcactggcacttggtctttgaaacattgcctttggtctttgaccgtatgtacct...

Basic information

species	Zea mays
transcript	GRMZM2G165769_T02
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G165769_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g09430.1 (Oryza sativa), 5'ss of exon 1

CGGCAGCGTCGCGCCGCGGACCAACGTCGTGGGCCGGGTGTTCACCGCCAACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAGgt--aatcgactgttgaaccatctccccctgcagtctgcagtctggtgg-cactggcacttggtctttgaaacattgcct----ttggtctttgaccgtatgtacct-----------
|||| ||| ||| ||||||| |||||| ||||| || || |||||||||||||| ||||||||||| ||||||||||||||||||||||||||||| |||||  |    ||  |   | ||  ||      || |  |   ||  |      ||  | ||      ||  |  | ||  |    ||   ||  ||    || ||  |           
CGGCGGCGCCGCCCCGCGGAGCAACGTGGTGGGGCGTGTCTTCACCGCCAACGAGTCGCCGCCCGACCAGAAGATCCCCTTCCACCACGAGATGGCGCAGgtccaccatacaatcacagcaaatcgaatc-caattcgagttcaagaaaatgctttcgctacaagcttatactaatgtttaaaattaagctgagatttcatatatgtttttggttcag

upper sequence: GRMZM2G165769_T01 (Zea mays), 5'ss of exon 1
lower sequence: AT3G21360.1 (Arabidopsis thaliana), 5'ss of exon 1

CGGCAGCGTCGCGCCGCGGACCAACGTCGTGGGCCGGGTGTTCACCGCCAACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAGgtaatcgactgttgaaccatctccccctgcagtctgcagtctggtggcactggcacttggtctttgaaacattgcctttggtctttgaccgtatgtacct-
|||  |||  || || || || | |||||| || || || ||||| || || || || || || ||||||||||| || || ||||||||||||||||||||| | ||      || ||  |     |  | | || | | || |     |  ||  |    |||  | | ||        |  ||||  || | |     
CGGAGGCGCTGCTCCTCGCACTAGCGTCGTCGGTCGTGTCTTCACTGCTAATGAATCTCCTCCTGATCAGAAGATTCCTTTTCACCACGAGATGGCTCAGgta-ttgatca--aaatcagatttgggttta-tgtg-aatttgat--tttttacatctaaagttttgagctttattgaatttgattgatggtgtttgttag

upper sequence: GRMZM2G165769_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv09s0002g03450.t01 (Vitis vinifera), 5'ss of exon 1

CGGCAGCGTCGCGCCGCGGACCAACGTCGTGGGCCGGGTGTTCACCGCCAACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAGgtaatcgactgttgaaccatctccccctgcagtctgcagtctggtggcactggcacttggtctttgaaacattgcctttggtctttgaccgtatgtacct--------------------------------------------
|||| |||  || ||  ||||||| || ||||| ||||| |||||  |||| || || ||||| ||||||||||||||||| |||||||| |||||||||||       | ||  | ||  ||    || ||       | |  |     |     |     ||| |    || ||  |  | ||||    | || |                                               
CGGCGGCGCGGCTCCCAGGACCAAAGTGGTGGGTCGGGTTTTCACGTCCAATGAGTCACCGCCGGATCAGAAGATCCCCTTTCACCACGAAATGGCTCAGgtgcgtt-ttattttaacaggtcatgatgaaggggatttttttttttttttaattatcttattttaatttttttcccgtaatttttggatatttggaatcccagatttggtcgattttgttgaagactctgggcttttctgcag

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|21330931|gb|BQ486312.1|BQ486312

EST:     ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAG                         GTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG
genomic: ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAGgtaatcgact ... gtttttttagGTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG

EST: gi|71331686|gb|DR802695.1|DR802695

EST:     ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAG                         GTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG
genomic: ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAGgtaatcgact ... gtttttttagGTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG

EST: gi|76927000|gb|DV171101.1|DV171101

EST:     ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAG                         GTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG
genomic: ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAGgtaatcgact ... gtttttttagGTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG

EST: gi|50336088|gb|CO531214.1|CO531214

EST:     ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAG                         GTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG
genomic: ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAGgtaatcgact ... gtttttttagGTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG

EST: gi|91876722|gb|EB406679.1|EB406679

EST:     ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAG                         GTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG
genomic: ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAGgtaatcgact ... gtttttttagGTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG

EST: gi|78075351|gb|DV503785.1|DV503785

EST:     ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAG                         GTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG
genomic: ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAGgtaatcgact ... gtttttttagGTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG

EST: gi|91056666|gb|EB167084.1|EB167084

EST:     ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAG                         GTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG
genomic: ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAGgtaatcgact ... gtttttttagGTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG

EST: gi|21331168|gb|BQ486535.1|BQ486535

EST:     ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAG                         GGTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG
genomic: ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAGgtaatcgact ... gtttttttagGTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG

EST: gi|76015381|gb|DT942551.1|DT942551

EST:     ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAG                         GTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG
genomic: ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAGgtaatcgact ... gtttttttagGTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG

EST: gi|21481080|gb|BQ577763.1|BQ577763

EST:     ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAG                         GTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG
genomic: ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAGgtaatcgact ... gtttttttagGTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG

EST: gi|76293479|gb|DV033047.1|DV033047

EST:     ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAG                         GTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG
genomic: ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAGgtaatcgact ... gtttttttagGTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG

EST: gi|21481473|gb|BQ578156.1|BQ578156

EST:     ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAG                         GTTCCAACATTTCCGTCCAAATGGTTCTTCTTCTGCGAAGTGGAGCCAAAG
genomic: ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAGgtaatcgact ... gtttttttagGTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG

EST: gi|50339768|gb|CO534894.1|CO534894

EST:     ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAG                         GTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG
genomic: ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAGgtaatcgact ... gtttttttagGTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG

EST: gi|21330419|gb|BQ485800.1|BQ485800

EST:     ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAG                         GTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG
genomic: ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAGgtaatcgact ... gtttttttagGTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG

EST: gi|78081709|gb|DV510121.1|DV510121

EST:     ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAG                         GTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG
genomic: ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAGgtaatcgact ... gtttttttagGTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG

EST: gi|21481228|gb|BQ577911.1|BQ577911

EST:     ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAG                         GTTCCAACATTTCCGTCCAAATGGNTCTTCTTCTGCGAAGTGGAGCCAAAG
genomic: ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAGgtaatcgact ... gtttttttagGTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG

EST: gi|71433562|gb|DR814612.1|DR814612

EST:     ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAG                         GTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG
genomic: ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAGgtaatcgact ... gtttttttagGTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG

EST: gi|78113584|gb|DV531975.1|DV531975

EST:     ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAG                         GTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG
genomic: ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAGgtaatcgact ... gtttttttagGTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG

EST: gi|21390495|gb|BQ528544.1|BQ528544

EST:     ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAG                         GTTCCAACATTTGCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG
genomic: ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAGgtaatcgact ... gtttttttagGTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG

EST: gi|78111022|gb|DV529419.1|DV529419

EST:     ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAG                         GTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG
genomic: ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAGgtaatcgact ... gtttttttagGTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG

EST: gi|78086225|gb|DV514618.1|DV514618

EST:     ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAG                         GTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG
genomic: ACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAGgtaatcgact ... gtttttttagGTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAG

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 3 RNA-Seq libraries.

Block sizes: 22 (upstream exon), 28 (downstream exon)
Score: 1

CGGCAGCGTCGCGCCGCGGACCAACGTCGTGGGCCGGGTGTTCACCGCCAACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAGgtaatcgact ... gtttttttagGTTCCAACATTTCCGTCCAAATTGTTCTTCTTCTGCGAAGTGGAGCCAAAGAGTGGCGGAGAGACGCCGGTTGTACCGAGCCATTATGTCTACAAGAGGA

Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 6

Block sizes: 44 (upstream exon), 34 (downstream exon)
Score: 6

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGCAGCGTCGCGCCGCGGACCAACGTCGTGGGCCGGGTGTTCACCGCCAACGACTCGCCGCCCGATCAGAAGATCCCCTTCCACCACGAGATGGCTCAGgtaatcgactgttgaaccatctccccctgcagtctgcagtctggtggcactggcacttggtctttgaaacattgcctttggtctttgaccgtatgtacct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccccc