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

gtacgttctacctgtttttacagaagatatatttttatttttccttggcaacattcattttttttgtttatatagGTTACTGTCGTCAAGAACGAAGATGGTGGAAATTCAGTGGCTACTGTTGTCCTGAGAGGCAGTACTGACAGTATACTAGATGATCTTGAAAGAGCTGTTG

Basic information

species	Zea mays
transcript	GRMZM2G381744_T01
intron #	8
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G381744_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g59020.1 (Oryza sativa), 3'ss of exon 8

gtacgttctac----ctgtt--tttacagaagatatatttttatttttccttggcaacattcattttttttgtttatatagGTTACTGTCGTCAAGAACGAAGATGGTGGAAATTCAGTGGCTACTGTTGTCCTGAGAGGCAGTACTGACAGTATACTAGATGATCTTGAAAGAGCTGTTG
||| |||  |     |||||  ||| ||  ||| ||   || ||| ||| |   | || || | || |||       |||||| ||||| |||||||| ||||| |||||||| ||||||||||| |||||| | |||||||| || || |||||| | ||||||||||||||||||||||
gtatgtttcatgcctctgttcctttccaatagacatgacttcattcttctt--accacgtttaattcttt-------atagGTAACTGTTGTCAAGAATGAAGAAGGTGGAAACTCAGTGGCTACGGTTGTCTTAAGAGGCAGCACCGATAGTATATTGGATGATCTTGAAAGAGCTGTTG

upper sequence: GRMZM2G381744_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA16G26920.1 (Glycine max), 3'ss of exon 8

-------------------------------------------------------------------------------gtacgttctacctgtttttacagaagatatat--ttttatttttccttggcaacattcattttttttgtttatatagGTTACTGTCGTCAAGAACGAAGATGGTGGAAATTCAGTGGCTACTGTTGTCCTGAGAGGCAGTACTGACAGTATACTAGATGATCTTGAAAGAGCTGTTG
                                                                                |  ||||| |   ||| ||   | |  ||    |||| |||||  ||    | | | || |  |      ||  |||| ||  | || || || ||||| ||||||||||| ||||||||||||||  |  |||| |||||||| |||||||||||||||||||||||||| || |
gtatgttaaagctggattattttggttctgcctttttatgggttccatgttcctttttttagcttattcccttacttctttttgttcttctcatttctaagtatggcatgcagttttcttttttttttttgataatgatatgat------atgcagGTGACCATTGTGAAAAATGAAGAGGGTGGAAATTCTGTGGCTACTGTTGTTTTACGAGGAAGTACTGATAGTATACTAGATGATCTTGAAAGAGCAGTGG

upper sequence: GRMZM2G381744_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA02G07910.1 (Glycine max), 3'ss of exon 8

-----------------------------------------------------------------gtacgttctacctgtttttacagaagatat-atttttatttttccttggcaacattcattttttttgttta-----------tatagGTTACTGTCGTCAAGAACGAAGATGGTGGAAATTCAGTGGCTACTGTTGTCCTGAGAGGCAGTACTGACAGTATACTAGATGATCTTGAAAGAGCTGTTG
                                                                 |    |||      || ||   |  | | | |||||||  | |     ||||  ||| | |||||||  ||           |  |||| ||  | || || || ||||| ||||||||||| || || ||||||||  |  |||| |||||||| |||||||||||||||||||||||||| || |
gtatgttaaagctggattctttcagttctgtcattttctgggttccatgtttcttttttattttagcttattcccttgcttctttttgttgttgtcatttttaagtattgcatgcaattttcttattttttggataatgatatgatatgcagGTGACCATTGTGAAAAATGAAGAGGGTGGAAATTCTGTAGCCACTGTTGTTTTACGAGGAAGTACTGATAGTATACTAGATGATCTTGAAAGAGCAGTGG

upper sequence: GRMZM2G381744_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv08s0007g07460.t01 (Vitis vinifera), 3'ss of exon 8

------------gtacgttc-tacctgtttttacagaagat--------atatttttatt---tttccttggcaacattcat---tttttttgtttatata----------gGTTACTGTCGTCAAGAACGAAGATGGTGGAAATTCAGTGGCTACTGTTGTCCTGAGAGGCAGTACTGACAGTATACTAGATGATCTTGAAAGAGCTGTTG
            || |   | || ||   |  | | |  ||        |||||||| ||   |||| ||  ||  || |||   ||||  | || | |||          ||| ||  | || || || ||||| |||||||| || ||    ||||| ||  |  |||| |||||||| |||||| ||||||| ||||||||||| ||||
gtacttccaaacgtccacccctatcttcctggatatagcattttggttcatatttttcttccctttcattaccatgatgcatgtgttttcctcttcaaataatatctattagGTCACCATTGTGAAAAATGAAGAAGGTGGAAACTCCGTATGCACTGTGGTTTTACGAGGAAGTACTGATAGTATATTAGATGACCTTGAAAGAGCAGTTG

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|28873655|gb|CB329613.1|CB329613

EST:     AACTAGGATACGCAGATTCTGTTTCTGTAGAAGAAATTGGTGGTACTCGG                         GTTACTGTCGTCAAGAACGAAGATGGTGGAAAT
genomic: AACTAGGATACGCAGATTCTGTTTCTGTAGAAGAAATTGGTGGTACTCGGgtacgttcta ... gtttatatagGTTACTGTCGTCAAGAACGAAGATGGTGGAAAT

EST: gi|9794809|gb|BE553117.1|BE553117

EST:     AACTAGGATACGCAGATTCTGTTTCTGTAGAAGAAATTGGTGGTACTCGG                         GTTATTGTCGTCAAGAACGAAGATGGTGGAAATTCAGTGGCTACTGTTGTC
genomic: AACTAGGATACGCAGATTCTGTTTCTGTAGAAGAAATTGGTGGTACTCGGgtacgttcta ... gtttatatagGTTACTGTCGTCAAGAACGAAGATGGTGGAAATTCAGTGGCTACTGTTGTC

EST: gi|32919903|gb|CF024715.1|CF024715

EST:     AACTAGGATACGCAGATTCTGTTTCTGTAGAAGAAATTGGTGGTACTCGG                         GTTACTGTCGTCAAGAACGAAGATGGTGGAAATTCAGTGGCTACTGTTGTC
genomic: AACTAGGATACGCAGATTCTGTTTCTGTAGAAGAAATTGGTGGTACTCGGgtacgttcta ... gtttatatagGTTACTGTCGTCAAGAACGAAGATGGTGGAAATTCAGTGGCTACTGTTGTC

EST: gi|60347495|gb|DN214468.1|DN214468

EST:     AACTAGGATACGCAGATTCTGTTTCTGTAGAAGAAATTGGTGGTACTCGG                         GTTACTGTCGTCAAGAACGAAGATGGTGGAAATTCAGTGGCTACTGTTGTC
genomic: AACTAGGATACGCAGATTCTGTTTCTGTAGAAGAAATTGGTGGTACTCGGgtacgttcta ... gtttatatagGTTACTGTCGTCAAGAACGAAGATGGTGGAAATTCAGTGGCTACTGTTGTC

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: 1028

TTGAAACTTAGCCAACCCAATGCGGACGAACTAGGATACGCAGATTCTGTTTCTGTAGAAGAAATTGGTGGTACTCGGgtacgttcta ... gtttatatagGTTACTGTCGTCAAGAACGAAGATGGTGGAAATTCAGTGGCTACTGTTGTCCTGAGAGGCAGTACTGACAGTATACTAGATGATCTTGAAAGAGCTGTTG

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 511

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 434

Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 552

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

cagaagatatatttttatttttccttggcaacattcattttttttgtttatatagGTTACTGTCGTCAAGAACGAAGATGGTGGAAATTCAGTGGCTACTGTTGTCCTGAGAGGCAGTACTGACAGTATACTAGATGATCTTGAAAGAGCTGTTG

                                 ttcattttttttgttt  CT-rich tract
                             aacattcatttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgttctacctgtttttacagaagatatatttttatttttccttggcaacattcattttttttgtttatatagGTTACTGTCGTCAAGAACGAAGATGGTGGAAATTCAGTGGCTACTGTTGTCCTGAGAGGCAGTACTGACAGTATACTAGATGATCTTGAAAGAGCTGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT