ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gtgaatatttcaaatgctatcttttgtgttgatgccgtcggtaatacaaattttatttctaagattgttggcttcatatgatctgttgaatttatgttcattttgggtttcatatgatctgttgaatttatgtgatgcagTATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTATGGCCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGAAAACA

Basic information

species	Zea mays
transcript	GRMZM2G070273_T01
intron #	17
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os04g57140.2 (Oryza sativa), 3'ss of exon 18

gtgaatatttcaaatgctatcttttgtgttgatgccgtcggtaatacaaattttatttctaagattgttggcttcatatgatctgttgaatttatgttcattttgggtttcatatgatc-tgttgaatttatgtgatgcagTATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTATGGCCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGAAAACA
                                        || |      |||||   ||    || ||  | | | |||  ||  | |  |||| | || || ||  | ||| || |  |  ||||||| ||||||||||||||| || ||||| || ||||||||||||||||| ||||||||||| ||||| ||||||||||||||||| ||||| || |||||||| || |||||||
----------------------------------------gtgaccttttttttaacacttc--tttttaacat-acatgtgctcattagattatttgcaatt-ggactccatgtgtttatcatgaattt-tgtgatgcagTATCTAGTTCAATCGGCCGTTGATGGATATAATGTTTGTATATTTGCTTATGGGCAAACTGGTTCTGGAAAAACTTTTACAATTTATGGATCTGAAAACA

upper sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA01G35950.1 (Glycine max), 3'ss of exon 19

--gtgaatatttcaaatgctatcttttgtgttgatgccgtcggtaatacaaattttatttctaagattgttggcttcatatgatctgttgaatttatgttcattttgggtttcatatgatctgttgaatttatgtgatgcagTATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTATGGCCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGAAAACA-------
   | | |||  |||||  ||  |  |   ||  |||  | | ||  | | |  ||       | || |        || | || | |    |||||  |||||     | |  |    ||| ||| |  | ||  ||||||||  | || ||||| ||||| ||||| |||||||| || |||||||| ||||| ||||||||||||||||||||||| || || |||||    |||||||       
gtcttagtataacaaattatagatcatagttttttgctttagatagcatatacatt------gaaatgg--------atttaatattt----tttatactcattaccaatgtttt----tcttttggaaatttgcaatgcagtacttagTGCAATCTGCTGTGGATGGTTATAATGTTTGCATATTTGCTTATGGTCAAACTGGTTCTGGAAAGACTTTTACAATCTATGGAGTTGAAAACAATCCTGG

upper sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA11G09480.1 (Glycine max), 3'ss of exon 19

gtgaatatttcaaatgctatcttttgtgttgatgccgtcggtaatacaaattttatttctaagattgttggcttcatatgatctgttgaatttatgttcattttgggt-ttcatatgat-ctgttgaatttatgtgatgcagTATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTATGGCCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGAAAACA
               || |   || || |        |     || | | |||| |   | ||||  |  |     |   ||   || ||| | | |  ||  |   |  | || |  | || ||| |  | ||  ||||||||  | || ||||| ||||| ||||| |||||||| || |||||||| || || |||||||||||||| |||||||| || || |||||  | |||||||
---------------gcaagtcttagtataacaa--attaaagatcctagttttttgctttagataatatgtacattgaaatagatttaatatttttctatactcattactaatgtttttcttttggacatttgcaatgcagTACTTAGTGCAATCTGCTGTAGATGGTTATAATGTTTGCATATTTGCTTACGGTCAAACTGGTTCTGGGAAGACTTTTACAATCTATGGAGCTGAAAACA

upper sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 19

gtgaatatttcaaatgctatcttttgtgttgatgccgtcggtaatacaaattttatttctaagattgttggcttcatatgatctgttgaatttatgttcattttgggtttcatatgatctgttgaatttatgtgatgcagTATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTATGGCCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGAAAACA
                      | | ||  ||| |    || ||  ||  | | || | |   |||  | | ||      |  | |  || |||   ||||| |   ||||   ||   |          ||  ||||||||| |||| || || ||||| ||||| |||||||| || |||||||| ||||| |||||||| ||||||||||| || || || ||||| || || ||||
---------------------gtatttgaggatacaaa-ggcaagtcatttatcatattt---atttcttgtttatgggaacatatataacttacactcattatcaatttctcgtggatt----------tgcaatgcagTATTTGGTGCAGTCTGCTGTAGATGGTTATAATGTTTGCATATTTGCCTATGGTCAAACTGGCTCTGGAAAGACATTTACAATCTATGGATCTGACAACA

upper sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 22

gtgaatatttcaaatgctatcttttgtgttgatgccgtcggtaatacaaattttatttctaagattgttggcttcatatgatctgttgaatttatgttcattttgggtttcatatgatctgttgaatttatgtgatgcagTATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTATGGCCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGAAAACA
                                    |   || |||  |||| |||||     |||  | ||||      |  | |  || |||   |||||     ||||   ||          | | ||  ||||||||| |||| ||||| ||||| ||||| |||||||| || |||||||| ||||| |||||||| ||||||||||| || || || ||||| || || | ||
------------------------------------gcaagtcata--aattgtattt-----atttcttgcttatggaaacatatataacttacactcattaccaatttctcgtg----------tatttgcaatgcagTATTTGGTGCAATCTGCTGTAGATGGTTATAATGTTTGCATATTTGCTTATGGTCAAACTGGATCTGGAAAGACATTTACAATCTATGGATCGGACATCA

upper sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 17
lower sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 16

gtgaatatttcaaatgctatcttttgtgttgatgccgtcggtaatacaaattttatttctaagattgttggcttcatatgatctgttgaatttatgttcattttgggtttcatatgatctgttgaatttatgtgatgcagTATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTATGGCCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGAAAACA
                                                  | |||||  || | |   ||  ||||| |    |      ||| |  |  | ||| | ||  ||  ||| |||    || |      |||||| ||||||| || ||||| ||||| ||||| || || || ||||| ||||| ||||||||||||||||| ||||||||||| |||||    || | ||
-------------------------------------------------gtattattgatatg-taactgtgttcatttacctttcatcctttgttattttcttgtggttactaacatc-gttttcctttta----acagTATTTGGTACAGTCGGCTGTAGATGGGTATAACGTTTGCATCTTTGCATATGGTCAAACTGGTTCTGGAAAAACTTTCACTATATATGGGCATGAGAGCA

upper sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 17
lower sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 18

gtgaatatttcaaatgctatcttttgtgttgatgccgtcggtaatacaaattttatttctaagattgttggcttcatatgatctgttgaatttatgttcattttgggtttcatatgatctgttgaatttatgtgatgcagTATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTATGGCCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGAAAACA
                                        | ||  |||  |     |  | | ||||| ||   |  || |   ||  ||| ||    | ||   |||   |   || |  |   ||||||   |||||||| |||| ||||| ||||| |||||||||||||| || |||||||| ||||| || ||||||||||||||||| ||||| ||||||||||| ||    |
----------------------------------------gcaagtcaacatc---atgaatgtttgttagca--acttgtttgattacattaattagtagttcaagttgtgtgatattttctatgtttatg-attgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATATGGTCAGACTGGTTCTGGAAAGACATTCACAATTTATGGTTCTGATGGTA

upper sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 17
lower sequence: PP1S199_47V6.1 (Physcomitrella patens), 3'ss of exon 20

-------------------------------gtg-aatatttcaa--atgctatcttttgtgttgatgccgtcggt---aatacaaattttattt-ctaagattgttggcttcatatgatctgttgaatttatgtt------cattttgggtttcatatgatctgttgaatttatgtg-atgcagTATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTATGGCCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGAAAACA
                               ||| ||| |||  |  |||  ||   ||  ||||   |    | |    ||   |||   |    |||| |    | | ||     ||  |||| | ||  | |        | ||||  ||      | |||   |   ||   ||  |||||||| |||| ||||||||  |||| ||||| ||||||||||||||||| || || |||||||| || || || || || || ||||| ||||| || ||||
gtatagttggtcagagtaattgagtcaatccgtgcaatctttttatcatggaatggctttggttgtaactactgatcccgatgagaataaaaccaactaaaagaccttgattagatcgacttgtttatttggtatcattgaatactttgtcttctgcgcg-tctaacgtgctttaatgtgtgcagTATTTGGTCCAATCAGCAATTGACGGATACAATGTCTGTATATTTGCATACGGGCAAACTGGGTCAGGCAAAACGTTTACGATTTACGGTTCTGACAACA

upper sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 17
lower sequence: PP1S83_25V6.1 (Physcomitrella patens), 3'ss of exon 19

gtgaatatttcaaatgctatcttttgtgttgatgccgtcggtaatacaaattttatttctaagattgttggcttcatatgatctgttg--aatttatgttcattttgggtttcatatgatctgt-tgaatttatgtgatgcagTATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTATGGCCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGAAAACA
                                           | ||  | ||    |      ||   |  |||| |   |   |||  | |  ||  | ||| ||  ||              ||||| ||     |||||||| |||| ||||||||  ||||||| || ||||||||||| ||||| || || |||||||| || || || ||||| |||||||||||||| ||||| |
-------------------------------------------acacctagttgtcctgctgttttagggtattcaaaaacttcattgttattcaataatgattctgtattctgcgcagctaacatgaatgtaacgtgtgcagTATTTGGTCCAATCAGCGATTGATGGGTACAATGTCTGTATTTTTGCATACGGACAAACTGGATCAGGGAAAACTTTTACTATTTATGGTTCTGAAAATA

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|211116600|gb|FL350312.1|FL350312

EST:     GTGTTTTTGATGCAAACACAAGTCAAGAAGAAGTCTTTGAGGATACTAAG                         TATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTAT
genomic: GTGTTTTTGATGCAAACACAAGTCAAGAAGAAGTCTTTGAGGATACTAAGgtgaatattt ... tgtgatgcagTATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTAT

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: 48 (upstream exon), 48 (downstream exon)
Score: 84

AATTTCACATCCATGGAAAGATGAAAAGTCAAAGCAACATATATATGATCGTGTTTTTGATGCAAACACAAGTCAAGAAGAAGTCTTTGAGGATACTAAGgtgaatattt ... tgtgatgcagTATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTATGGCCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGAAAACA

Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 11

Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 15

Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 36

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttgaatttatgttcattttgggtttcatatgatctgttgaatttatgtgatgcagTATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTATGGCCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGAAAACA