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

gtacacatggaacatacatatatcccataatctgagttctgttagctcttaacctaaaaggctacgacacatcttttacgctcttgttaagGAGAAGCTGCCACCGACGGATTCAAGGCTGAGACCAGATCAACGGCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGCCTCGAGA

Basic information

species	Zea mays
transcript	GRMZM2G061099_T01
intron #	8
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G061099_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os10g40590.1 (Oryza sativa), 3'ss of exon 8

gtacacatggaacatacatatatcccataatctgagttctgttagctcttaacctaaaaggctacgacacatcttttacgctcttgttaagGAGAAGCTGCCACCGACGGATTCAAGGCTGAGACCAGATCAACGGCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGCCTCGAGA
             || |  | | |  |||||  |  |  |||||| | ||        |       ||  |   |||      |||||||||||||||| ||||| ||||||||||| || || |||||||| ||||| || ||||||||||||||||| ||||| ||  |||||||| ||||||| ||||
-----------gtatgcgcaaagcatataattcgcctattgttagttttttgtagtgcaaagcctaacgtactatttgatgatttgttaagGAGAAGCTTCCACCAACGGATTCAAGACTCAGGCCAGATCAGCGGCATCTAGAGAATGGGGAGTACGAAAAGGCTAACTCTGAAAAATTGCGCCTGGAGA

upper sequence: GRMZM2G061099_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA05G04340.2 (Glycine max), 3'ss of exon 9

gtacacatggaacatacatatatcccataatctgagttctgttagctctta------acctaaaaggctacgacaca-tcttttacgctcttg------------------ttaagGAGAAGCTGCCACCGACGGATTCAAGGCTGAGACCAGATCAACGGCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGCCTCGAGA
||| | |||    ||  |   ||      || || ||| | ||   ||||       | ||  ||  ||  |  | |  |||||  | ||  |                  | ||||||||||| ||||| |||||||| ||||||||||||||||| ||||| || ||||||||||| ||||||||||| |||   |||||||   |  | || |
gtata-atgatgtattaaatcattattcgatgtgcgttttcttttttcttcttatgcatctctaattctttgttatagccttttctgatcccgggtaatttgatcacggattaaagGAGAAGCTTCCACCCACGGATTCCAGGCTGAGACCAGATCAGCGGCATCTAGAGAATGGGGAATACGAGAAGGCTAATATGGAAAAACAAAGGTTGGAAA

upper sequence: GRMZM2G061099_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA01G41940.1 (Glycine max), 3'ss of exon 8

-------------------gtacacatggaacatacatatatcccataatctgagttctgttagctcttaacctaaaaggctacgacacatct----tttacgctcttg---ttaagGAGAAGCTGCCACCGACGGATTCAAGGCTGAGACCAGATCAACGGCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGCCTCGAGA
                    |    ||   | |  |||    |   | || |  |    ||      ||    |  |  |||    |  |||     | |  | ||  |   | |||||||| || || || |||||||| ||||| ||||||||||||||||| || ||||||||||| |||||||||||||||   || ||||   |  | || |
gtatataatgatgtattagatcattatttgatacgcattccacttcttatatatgcgtcgtctctaattgttgtttatagctttttctgatcccgggtatttgatcacggattaaagGAGAAACTCCCGCCCACGGATTCCAGGCTCAGACCAGATCAACGGCATCTAGAGAATGGGGAATACGAGAAGGCCAATTTGGAGAAACAAAGGTTGGAAA

upper sequence: GRMZM2G061099_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA11G03420.1 (Glycine max), 3'ss of exon 10

---------------------gtacacatgg-aacatacatatatcccataatctgagttctgttagctcttaacc-taaaaggctacgacacatcttttacgctcttg---ttaagGAGAAGCTGCCACCGACGGATTCAAGGCTGAGACCAGATCAACGGCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGCCTCGAGA
                         |  ||  |  |  |||    |   | || |  |      ||  | ||     ||      |  ||  |    | |  | ||  |   | ||||||||||| || || |||||||| ||||| ||||||||||||||| | || |||||||||||                                      
gtatataatgatgtattagatcattatttgatagtacgcattccacttcttatatatgcgtctctaattgttgtttatagCTTTTTCTGATCCCGGGTATTTGATCACGGATTAAAGGAGAAGCTCCCGCCCACGGATTCCAGGCTCAGACCAGATCAACGGGATCTAGAGAATGGGGAA-------------------------------------

upper sequence: GRMZM2G061099_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA17G14820.1 (Glycine max), 3'ss of exon 9

--gtacacatggaacatacatatatcccataatctgagttctgttagctctta---acctaaaaggctacgacaca-tcttttacgctcttg------------------ttaagGAGAAGCTGCCACCGACGGATTCAAGGCTGAGACCAGATCAACGGCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGCCTCGAGA
   ||   ||| |  | |    ||| | ||   |    | || ||   |||||   | ||  ||  ||  |  | |  |||||  | ||  |                  | ||||||||||| ||||| |||||||| |||||||||||||| || || || || ||||||||||| ||||||||||| |||   || ||||   |  | || |
gtataatgatgtattaaatcattattcgatgtgcgttttcctttttcttcttatgcatctctaattctttgttatagccttttctgatcccgggtaatttgatcacggattaaagGAGAAGCTTCCACCCACGGATTCCAGGCTGAGACCAGACCAGCGACATCTAGAGAATGGGGAATACGAGAAGGCTAATATGGAGAAACAAAGGTTGGAAA

upper sequence: GRMZM2G061099_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT4G12460.2 (Arabidopsis thaliana), 3'ss of exon 8

----------------------------------gtacacatggaacatacatatatcccataatctgagttctgttagctcttaacctaaaaggctacgacacatcttttacgctcttgttaagGAGAAGCTGCCACCGACGGATTCAAGGCTGAGACCAGATCAACGGCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGCCTCGAGA------
                                  ||| ||||| |   |   | | | |  || |   | |  ||||   |   |||        ||       || || | | ||    ||||||| |||||||| || || ||||| |||||  ||||||||||||| ||| ||||||| || || || |||||||| ||||  || ||||   |  | ||||      
gtatattagtatttttttaattttggatttgtttgtaaacatgaattttgggtttctgctgtacttgaaatcttgtt--ttagcaactgtgtgatcttttcgtaattttgttcccttggtttaaggaaaagCTGCCTCCAACAGATTCTAGGCTCCGACCAGATCAACGACACTTGGAGAACGGTGAATATGAGAAGGCAAATGAAGAGAAACAAAGATTAGAGAGAAGAC

upper sequence: GRMZM2G061099_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT4G12460.1 (Arabidopsis thaliana), 3'ss of exon 8

----------------------------------gtacacatggaacatacatatatcccataatctgagttctgttagctcttaacctaaaaggctacgacacatcttttacgctcttgttaagGAGAAGCTGCCACCGACGGATTCAAGGCTGAGACCAGATCAACGGCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGCCTCGAGA
                                  ||| ||||| |   |   | | | |  || |   | |  ||||   |   |||        ||       || || | | ||    ||||||| |||||||| || || ||||| |||||  ||||||||||||| ||| ||||||| || || || |||||||| ||||  || ||||   |  | ||||
gtatattagtatttttttaattttggatttgtttgtaaacatgaattttgggtttctgctgtacttgaaatcttgtt--ttagcaactgtgtgatcttttcgtaattttgttcccttggtttaagGAAAAGCTGCCTCCAACAGATTCTAGGCTCCGACCAGATCAACGACACTTGGAGAACGGTGAATATGAGAAGGCAAATGAAGAGAAACAAAGATTAGAGA

upper sequence: GRMZM2G061099_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT4G22540.3 (Arabidopsis thaliana), 3'ss of exon 8

----gtacacatgg----aacatacatatatcccataatctgagttctgt--tagctcttaacctaaaaggctacgacacatcttttacgctcttgtta-----agGAGAAGCTGCCACCGACGGATTCAAGGCTGAGACCAGATCAACGGCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGCCTCGAGA
    || || ||||    | | |   | ||| |  |     || | || |  || || || |  || |    |  ||  | | | |||   |  || |      ||||||  || || || || || || ||||| ||||||||||||||||| || |||||||| || || |||||||| ||    || ||||  ||  | || |
gtatgttcagatggtttaatcttgtttttattctgtttatggattgctatactatcttttcatatagacttgtctgat-cttgtgttaacttgatgatggatgtagGAGATACTTCCTCCCACAGACTCTAGGCTCAGACCAGATCAACGGCATCTTGAGAATGGTGAATATGAGAAGGCGAACTTAGAGAAACAACGGTTAGAAA

upper sequence: GRMZM2G061099_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv02s0154g00250.t01 (Vitis vinifera), 3'ss of exon 7

------------------------gtacacatg-gaacatacatatatcccataatctgagttctgttagctcttaacctaaaaggctacgacacatcttttacgctcttgttaagGAGAAGCTGCCACCGACGGATTCAAGGCTGAGACCAGATCAACGGCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGCCTCGAGA
                         |    ||| | | || ||| | |||  | ||     |    ||  || |||            |   |   | ||| |  | |   ||||||||||||| ||||| ||||||||||| || |||||||||||||| || || |||||||| || || || ||||| ||||| |||||||| ||  | ||||
gtagagataatgtattgaatcaatttttttatgtgcatattcat-tttcctcttatgcatatctaattgtcttttatagctctgtctgatcccgggtatttgat-cacggattaagGAGAAGCTCCCACCCACGGATTCAAGACTTAGACCAGATCAACGACATCTAGAGAATGGAGAATATGAAAAGGCAAATGCAGAAAAACTACGGTTAGAGA

upper sequence: GRMZM2G061099_T01 (Zea mays), 3'ss of exon 8
lower sequence: PP1S67_260V6.1 (Physcomitrella patens), 3'ss of exon 8

---------------------------------------------------gtacacatggaacatacatatatcccataatctgag---ttctgttagctcttaacctaaaaggcta-------cgaca--catct---------tttacgctcttgttaagGAGAAGCTGCCACCGACGGATTCAAGGCTGAGACCAGATCAACGGCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGCCTCGAGA
                                                    || | ||||    |   | | |    |  | |      ||| ||||      ||  | ||  | ||       | |||  |||||         ||||   | || |  |||| ||| ||||||| || ||||||||| ||||||| |||||| | || ||||||||||| || || ||    |||||| | ||||||||||| || ||  
gtgagtatctgcaattttcttagacttaaatgcttatactagagatttgacttatatatggctgttttttttctttttttcttttttcctttcagttaataagaaatatgaatcggtagacgagtcaacattcatctacttataaatttaatttattttgtagGAAAAGTTGCCACCTACAGATTCAAGGTTGAGACCTGATCAAAGACATCTGGAGAATGGTGAATATGATGCTGCCAATTCAGAAAAACTGCGACTTGAAC

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|60336647|gb|DN203620.1|DN203620

EST:     ACTTGTCCGCATTTGCAATAACACTAAATGAGTTAACACCAGAGCTCGAG                         GAGAAGCTGCCACCGACGGATTCAAGGCTGAGACCAGATCAACGGCACCTG
genomic: ACTTGTCCGCATTTGCAATAACACTAAATGAGTTAACACCAGAGCTCGAGgtacacatgg ... tcttgttaagGAGAAGCTGCCACCGACGGATTCAAGGCTGAGACCAGATCAACGGCACCTG

EST: gi|211218427|gb|FL445373.1|FL445373

EST:     ACTTGTCCGCATTTGCAATAACACTAAATGAGTTAACACCAGAGCTCGAG                         GAGAAGCTGCCACCGACGGATTCAAGGCTGAGACCAGATCAACGGCACCTG
genomic: ACTTGTCCGCATTTGCAATAACACTAAATGAGTTAACACCAGAGCTCGAGgtacacatgg ... tcttgttaagGAGAAGCTGCCACCGACGGATTCAAGGCTGAGACCAGATCAACGGCACCTG

EST: gi|211038131|gb|FL097458.1|FL097458

EST:     GTTAACACCAGAGCTCGAG                         GAGAAGCTGCCACCGACGGATTCAAGGCTGAGACCAGATCAACGGCACCTG
genomic: GTTAACACCAGAGCTCGAGgtacacatgg ... tcttgttaagGAGAAGCTGCCACCGACGGATTCAAGGCTGAGACCAGATCAACGGCACCTG

EST: gi|211038130|gb|FL097457.1|FL097457

EST:     ACTTGTCCGCATTTGCAATAACACTAAATGAGTTAACACCAGAGCTCGAG                         GAGAAGCTGCCACCGACGGATTCAAGGCTGAGACCAGATCAACGGCACCTG
genomic: ACTTGTCCGCATTTGCAATAACACTAAATGAGTTAACACCAGAGCTCGAGgtacacatgg ... tcttgttaagGAGAAGCTGCCACCGACGGATTCAAGGCTGAGACCAGATCAACGGCACCTG

EST: gi|32910642|gb|CF015454.1|CF015454

EST:     ACTTGTCCGCATTTGCAATAACACTAAATGAGTTAACACCAGAGCTCGAG                         GAGAAGCTGCCACCGACGGATTCAAGGCTGAGACCAGATCAACGGCACCTG
genomic: ACTTGTCCGCATTTGCAATAACACTAAATGAGTTAACACCAGAGCTCGAGgtacacatgg ... tcttgttaagGAGAAGCTGCCACCGACGGATTCAAGGCTGAGACCAGATCAACGGCACCTG

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: 170

CACTTTGCTATGGGAGAAAAATGAGCCTCCAGTCAATCCTACCCGCTACAACTTGTCCGCATTTGCAATAACACTAAATGAGTTAACACCAGAGCTCGAGgtacacatgg ... tcttgttaagGAGAAGCTGCCACCGACGGATTCAAGGCTGAGACCAGATCAACGGCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGCCTCGAGA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 119

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 228

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 197

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttctgttagctcttaacctaaaaggctacgacacatcttttacgctcttgttaagGAGAAGCTGCCACCGACGGATTCAAGGCTGAGACCAGATCAACGGCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGCCTCGAGA

                                   tcttttacgctctt  CT-rich tract
                                  atctttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacacatggaacatacatatatcccataatctgagttctgttagctcttaacctaaaaggctacgacacatcttttacgctcttgttaagGAGAAGCTGCCACCGACGGATTCAAGGCTGAGACCAGATCAACGGCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGCCTCGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG