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

...ctgtgagaggcaacgcatgatatgctgtcagttcaaagtatagatgactattgtcttttcttgtgatatctcacaagtttgcattgctatatttggacagGGACATCACCACTACATTTCCAAGCTTTGTCTTTCACTCTCAGGTTGATGATAACTGAAATTGATGGGGTTACTTTGAAAAGAAACATTAGAAGATATTC

Basic information

species	Zea mays
transcript	GRMZM2G173424_T02
intron #	8
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G173424_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os12g40510.1 (Oryza sativa), 3'ss of exon 8

ctgtgagaggcaacgcatgatatgctgtcagttcaaagtatagatgactattgt-----cttttcttgtgatatctcacaagtttgcattgctatatttggacagGGACATCACCACTACATTTCCAAGCTTTGTCTTTCACTCTCAGGTTGATGATAACTGAAATTGATGGGGTTACTTTGAAAAGAAACATTAGAAGA-TATTC
     | |   |     || |         |||||| || || |  | | ||||     ||||| || |  |||  |||||| |    |||| | || ||  |||||||||||||||||||||||||||||||||||| || || ||||| ||||| | ||||| ||  |||  ||  ||  |    || ||| |||||| |  ||
----aaaaaagattaggtgttcataaaaatgttcaa-gtctataaaaatgttgtagacacttttgtttttctatagcacaagctaatcttgccacatgtgtgcagGGACATCACCACTACATTTCCAAGCTTTGTCTTCCATTCCCAGGTCGATGACACCTGAA-TTCTTGGATTTGTTTGAACTCAAACCATCAGAAGAATGCTC

upper sequence: GRMZM2G173424_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA07G39940.1 (Glycine max), 3'ss of exon 8

-ctgtgagaggcaacgcatgatatg-ctgtcagttcaaagtatagatgactattgtcttttcttgtgatatctca-caagtttgcattgctatatttggacagGGACATCACCACTACATTTCCAAGCTTTGTCTTTCACTCTCAGGTTGATGATAACTGAAATTGATGGGGTTACTTTGAAAAGAAACATTAGAAGATATTC
 || |  |            ||| |  |  |   |||  |  ||  | | | || ||      |   || |  || |    ||  |||| |   ||  | ||| || ||||| ||||||||||| || ||||| |||||||| || ||||||||||  |||     |       |        ||   || |       | | 
gctatttggatttggcaccaatacgattaccttctcagggactattttatt-ttatcaagctctagaatctaacatctgacttaaattgtttcctt--ggcagAGATATCACTACTACATTTCCCAGTTTTGTTTTTCACTCACAAGTTGATGATACTTGAGGCAAACCACAGCATCCATGTCAGTTTCAGTGTTCTTGACTG

upper sequence: GRMZM2G173424_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA18G08230.1 (Glycine max), 3'ss of exon 9

---ctgtgagaggcaacgcatgatatgctgtcagttcaaagtatagatgactattgtctttt-cttgtgatatctcacaagtttgcattgctatatttggacagGGACATCACCACTACATTTCCAAGCTTTGTCTTTCACTCTCAGGTTGATGATAACTGAAATTGATGGGGTTACTTTGAAAAGAAACATTAGAAGATATTC---
   || ||| |  |    | |||  | ||  ||  |     | |   |   |  ||| |||  || ||| | ||| | |   ||   ||  | | ||||| ||||||||||||||| ||||| || |||||||| ||||| || || || || ||||  ||||  | ||     | |  ||        | || |     ||     
gtcctttgatacacttgccgtgaactactaacatct---gtttttcctttttcctgtatttcactggtgttttctgatatccttt--ttaatgtgtttgggcaggGACATCACCACAACATTCCCGAGCTTTGTATTTCATTCACAAGTAGACGATACTTGAAGATAATT--TCTCCCATGGCTTCTTCCTTTGGGCTGCATGGCCA

upper sequence: GRMZM2G173424_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA17G00830.1 (Glycine max), 3'ss of exon 8

ctgtgagaggcaacgcatgatatg-ctgtcagttcaaagtatagatgactattgtcttttcttgtgat-----atctcaca---agtttgcattgctatatttggacagGGACATCACCACTACATTTCCAAGCTTTGTCTTTCACTCTCAGGTTGATGATAACTGAAATTGATGGGGTTACTTTGAAAAGAAACATTAGAAGATATTC
       |    |    | ||||| || |   ||  |  | |    ||||||| | |||| |   | |     |||| |||      ||  |||| |   ||  | ||| || ||||||||||||||||| || ||||| |||||||| || ||||||||||  |||     |       |        ||   || |       | | 
-------ataacatttctaatatgtctatgtattatacttctcagggactattttattttatcaagctctagaatctaacatctgacttaaattgtttcctt--ggcagAGATATCACCACTACATTTCCCAGTTTTGTTTTTCACTCACAAGTTGATGATACTTGAGGCAAACTACAGCATCCATGTCAGTTTCAGTGTTCTTGACTG

upper sequence: GRMZM2G173424_T02 (Zea mays), 3'ss of exon 8
lower sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 9

-----------------------ctgtgagaggcaacgcatgatatgctgtcag-ttcaaagtatagatga-ctattgtcttttctt-gtgatatctcacaa-gtttgcattgctat-----atttgg---acagGGACATCACCACTACATTTCCAAGCTTTGTCTTTCACTCTCAGGTTGATGATAACTGAAATTGATGGGGTTACTTTGAAAAGAAACATTAGAAGATATTC
                        | | |   | |  | ||  ||| |   ||  |||    | | | |   || |  ||| ||||   |||||| | | || | | |   | || |       |||     |||||| ||||| ||||| |||||||||||||| || || ||||||||||| |||| ||||||  |     |  |     |  ||   ||  | |  ||  | 
gtgagttccaaatctttctatttatataaccaggattgaatc-tattcaaccaaattccttctctggtttctctttcttctattctccatgatatgtaataaaggtcgtgatcctgttgtgtgcttgctctgcagGGATATCACGACTACGTTTCCAAGCTTTGTGTTCCATTCTCAGGTTGAAGATACCTGAAAAAGCAAAAGCAAAAGCAAGCAGCGGCAAGACATCATTGTA

upper sequence: GRMZM2G173424_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv00s1569g00020.t01 (Vitis vinifera), 3'ss of exon 7

ctgtgagaggcaacgcatgatatgctgtcagttcaaagtatagatgactattgtcttttcttgtgatatctcacaagt-ttgcattgctatatttgg-acagGGACATCACCACTACATTTCCAAGCTTTGTCTTTCACTCTCAGGTTGATGATAACTGAAATTGATGGGGTTACTTTGAAAAGAAACAT-TAGAAGATATTC-
  | |  |||      || |||| |  |   |||| | |    |       ||||  |     |  |  || |||  | || |||   | | ||    |||| ||||||||||||||||| ||||| ||||| |||||||| || || ||||| |  |||   |    | | ||| |  |     | ||| | ||| |      
-gggggcaggtttaaaatcatatac-ataccttcataatggcaaaagtctgtgtcactgggcttagttactaacatctgtttcatccgtttcttgaacacagAGACATCACCACTACATTCCCAAGTTTTGTGTTTCACTCACAAGTGGATGACACTTGAG--TTGCAGAGCTACATCAAGTTCTATCATCTTGAACAGGGATG

upper sequence: GRMZM2G173424_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv00s0194g00040.t01 (Vitis vinifera), 3'ss of exon 2

ctgtgagaggcaacgcatgatatgctgtcagttcaaagtatagatgactattgtcttttcttgtgatatctcacaagt-ttgcattgctatatttgg-acagGGACATCACCACTACATTTCCAAGCTTTGTCTTTCACTCTCAGGTTGATGATAACTGAAATTGATGGGGTTACTTTGAAAAGAAACATT---AGAAGATATTC
  | |  |||      || |||| |  |   |||| | |    |       ||||  |     |  |  || |||  | || |||   | | ||    |||| ||||||||||||||||| ||||| ||||| |||||||| || || ||||| |  |||   |    | | ||| |  |     | |||    || ||  ||  
-gggggcaggtttaaaatcatatac-ataccttcataatggcaaaagtctgtgtcactgggcttagttactaacatctgtttcatccgtttcttgaacacagAGACATCACCACTACATTCCCAAGTTTTGTGTTTCACTCACAAGTGGATGACACTTGAG--TTGCAGAGCTACATCAAGTTCTATCATCTTGAGCAGGGATG-

upper sequence: GRMZM2G173424_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv19s0015g01070.t01 (Vitis vinifera), 3'ss of exon 7

-ctgtgagaggcaacgcatgatatgctgtcagttcaaagtatagatgactattgtcttttcttgtgat--atctcaca--agtttgcattgctatatttggacagGGACATCACCACTACATTTCCAAGCTTTGTCTTTCACTCTCAGGTTGATGATAACTGAAATTG-ATGGGGTTACTTTGAAAAGAAAC-ATTAGAAGATATTC
  | |   |    || | | ||   |    | | |||    | |||| ||||   ||| ||     |   | || |      ||||  ||  |   |||| |||||||||||||||| ||||| ||||||||||||||||| ||||| ||||| || | ||||| |   ||      |  ||||   |      |||  |  |    
cttttatcattgtacactt-atggacaaaaaatgcaat---tggatg-ctatgagcttctcaaaccactcaactgatgttgatttgttttatttcctttgaacagGGACATCACCACCACATTCCCAAGCTTTGTCTTTCATTCTCAAGTTGACGACACCTGAAGTCCCATACATGAAAGTTGACTGGTTTTTGTTAATAATTGC--

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|211119821|gb|FL462978.1|FL462978

EST:     GTCATTCGGCATCCTTCTTTGCTGAAGAACATGACTCTTCAGTACCTCAA                         GGACATCACCACTACATTTCCAAGCTTTGTCTTTCACTCTCAGGTTGATGA
genomic: GTCATTCGGCATCCTTCTTTGCTGAAGAACATGACTCTTCAGTACCTCAAgtaaggaacc ... atttggacagGGACATCACCACTACATTTCCAAGCTTTGTCTTTCACTCTCAGGTTGATGA

EST: gi|32940052|gb|CF044871.1|CF044871

EST:     GTCATTCGGCATCCTTCTTTGCTGAAGAACATGACTCTTCAGTACCTCAA                         GGACATCACCACTACATTTCCAAGCTTTGTCTTTCACTCTCAGGTTGATGA
genomic: GTCATTCGGCATCCTTCTTTGCTGAAGAACATGACTCTTCAGTACCTCAAgtaaggaacc ... atttggacagGGACATCACCACTACATTTCCAAGCTTTGTCTTTCACTCTCAGGTTGATGA

EST: gi|88755366|gb|DY539507.1|DY539507

EST:     GTCATTCGGCATCCTTCTTTGTTGAAGAACATGACTCTTCAGTACCTCAA                         GGACATCACCACTACATTTCCAAGCTTTGTCTTTCACTCTCAGGTTGATGA
genomic: GTCATTCGGCATCCTTCTTTGCTGAAGAACATGACTCTTCAGTACCTCAAgtaaggaacc ... atttggacagGGACATCACCACTACATTTCCAAGCTTTGTCTTTCACTCTCAGGTTGATGA

EST: gi|74244689|gb|DT652603.1|DT652603

EST:     GTCATTCGGCATCCTTCTTTGCTGAAGAACATGACTCTTCAGTACCTCAA                         GGACATCACCACTACATTTCCAAGCTTTGTCTTTCACTCTCAGGTTGATGA
genomic: GTCATTCGGCATCCTTCTTTGCTGAAGAACATGACTCTTCAGTACCTCAAgtaaggaacc ... atttggacagGGACATCACCACTACATTTCCAAGCTTTGTCTTTCACTCTCAGGTTGATGA

EST: gi|71307467|gb|DR789938.1|DR789938

EST:     GTCATTCGGCATCCTTCTTTGCTGAAGAACATGACTCTTCAGTACCTCAA                         GGACATCACCACTACATTTCCAAGCTTTGTCTTTCACTCTCAGGTTGATGA
genomic: GTCATTCGGCATCCTTCTTTGCTGAAGAACATGACTCTTCAGTACCTCAAgtaaggaacc ... atttggacagGGACATCACCACTACATTTCCAAGCTTTGTCTTTCACTCTCAGGTTGATGA

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: 271

CAGACACAAAGCATGATGGAAGAATTGACAAGGAAGAGTGGCGCAATCTAGTCATTCGGCATCCTTCTTTGCTGAAGAACATGACTCTTCAGTACCTCAAgtaaggaacc ... atttggacagGGACATCACCACTACATTTCCAAGCTTTGTCTTTCACTCTCAGGTTGATGATAACTGAAATTGATGGGGTTACTTTGAAAAGAAACATTAGAAGATATTC

Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 182

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 215

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 139

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gactattgtcttttcttgtgatatctcacaagtttgcattgctatatttggacagGGACATCACCACTACATTTCCAAGCTTTGTCTTTCACTCTCAGGTTGATGATAACTGAAATTGATGGGGTTACTTTGAAAAGAAACATTAGAAGATATTC

                      atctcac  putative branch site (score: 139)
                                          tatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgtgagaggcaacgcatgatatgctgtcagttcaaagtatagatgactattgtcttttcttgtgatatctcacaagtttgcattgctatatttggacagGGACATCACCACTACATTTCCAAGCTTTGTCTTTCACTCTCAGGTTGATGATAACTGAAATTGATGGGGTTACTTTGAAAAGAAACATTAGAAGATATTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - acgcatg
- - - - - - - - - - - tgctgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgcatt