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

...ttaaggatgtattatctttcatactcttttccttttttttgtgtttgcctttactatcttacaagtaacgataaaaaacattggttgatctgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTCAATGATGGAGCTGTTGAGTATGAGGATGGTACTC

Basic information

species	Zea mays
transcript	GRMZM2G032367_T04
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G032367_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g23620.1 (Oryza sativa), 3'ss of exon 6

-----ttaaggatgtattatctttcatactcttttccttttttttgtgtttgcctttactatcttacaagtaacgataaaaaacattggttgatctgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTCAATGATGGAGCTGTTGAGTATGAGGATGGTACTC
     ||    |  | | || |||||  ||  ||   || | ||    ||||| ||    |   | |||   |  |  |||  |  |||||||| ||||| |||||| ||||||||| |||| ||||| |||||||||||||||||||||||||| |||||||||||||| |  |||||||||||||| ||||| ||||||||||
gttatttttctagctgtaatttttcaagctggttgtgttctgtt---atttgctttctgcagtgtgcaac--attagtaaactctctggttgatttgtattctagATCCGTGAGGGTTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCTATGCCCAAGATGCTTATAGATGGAGCTGTTGAATATGAAGATGGTACTC

upper sequence: GRMZM2G032367_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT5G40810.2 (Arabidopsis thaliana), 3'ss of exon 4

ttaaggatgtattatctttcatactcttttccttttttttgtgtttgc--ctttactatcttacaagtaacgataaaaaacattggttgatctgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTCAATGATGGAGCTGTTGAGTATGAGGATGGTACTC
       |  ||| ||| || || | ||| | ||    ||||  || |  ||| |   | ||  |||| | || | ||  |  ||  | |   |||    ||||  | ||||| || |||||||| || || ||||||||||| || || || ||||| || |||||||| |||| |||||| || ||||| ||||| ||||
------gtaaatt-tctctcctatt-tttgctttagacttgttattacaacttcaaattgttggaagtta-gaaataatcctgtgactaacgggtac---agATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGCAATCGCTATGCCAAAAATGCTCAACGATGAAGCTGTGGAATATGAAGATGGAACTC

upper sequence: GRMZM2G032367_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT3G27240.1 (Arabidopsis thaliana), 3'ss of exon 5

ttaaggatgtattatctttcatactcttttccttttttttgtgtttgcctttactatcttacaagtaacgataa-aaaacattggttgatctgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTCAATGATGGAGCTGTTGAGTATGAGGATGGTACTC
                     ||   || ||   ||||     ||   |||       ||  ||||   | | |  ||| ||  | ||||   | | | ||||| | |||||  | |||||||| || || |||||||| || || || || ||||| || ||||||||||||| ||||||||||||||| ||||||   |
--------------------gtaagtttctctcattttccacattgaacttcttcgaattcaaagtgctggttatgaaaaatccgatgataactgtac-agATTAGAGAGGGGTTACACTACAATCCTTATTTCCCTGGGGGAGCAATTGCTATGCCGAAAATGCTCAATGATGAAGCTGTTGAGTATGAAGATGGTGTCC

upper sequence: GRMZM2G032367_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv09s0002g05950.t01 (Vitis vinifera), 3'ss of exon 4

ttaaggatgtattatcttt-catactcttttccttttttttgtgtttgcctttactatcttacaagtaacgataaaaaacattg--gttgatctgtatcc-tagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTCAATGATGGAGCTGTTGAGTATGAGGATGGTACTC
     |||  || |||||  | |    |||  | |  |||  |   |   | | |  ||||  ||  || | |  |      ||   |||| || | ||  |||||||| || || |||||||| || || || ||||||||||| || ||||| |||||||| |||||||  ||||| |||||||||||||| |||||||| |
---ccgata-atcatcttgacttgggttttgtcatcatttgattgctctttctgcattcttttaatgaatgttccatcctgatgtcattgaactctttctgtagATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCTATGCCCAAAATGCTCATCGATGGTGCTGTTGAGTATGAAGATGGTACCC

upper sequence: GRMZM2G032367_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv14s0171g00330.t01 (Vitis vinifera), 3'ss of exon 5

--ttaaggatgtattatctttcatactcttttccttttttttgtgtttgcctttactatcttacaagtaacgataaaaaacattggttgatctgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTCAATGATGGAGCTGTTGAGTATGAGGATGGTACTC
   | |   | | |||| ||| ||  |  |   | | || | ||   ||         || |  |  |||  |   ||    ||     || | | |  ||||| || || ||  |||||||||| || ||||||||||| ||||| || || ||||| || ||||||| |||||| ||  |||||||||| |||||||| |
tgctgatttttttttattttttatgtttatggacatattct-gttcatgatgacctattcctctacctaatcaatcaagttgttcacaaatattt-ttgtagATCCGAGAAGGGTTGCACTACAATCCTTACTTCCCTGGGGGTGCAATTGCTATGCCTAAAATGCTCATTGATGGTGCACTTGAGTATGAAGATGGTACGC

upper sequence: GRMZM2G032367_T01 (Zea mays), 3'ss of exon 5
lower sequence: EDO96204 (Chlamydomonas reinhardtii), 3'ss of exon 7

--ttaaggatgtattatctttcatactcttttccttttttttgtgtttgcctttacta-tcttacaagtaacgataaaaaacattggttgatctgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTCAATGATGGAGCTGTTGAGTATGAGGATGGTACTC
  ||||  |   || |  | | |  | |           | |     |  | | |||| || |  | | |||  | |    ||   |   | | | | |  |||| || ||||| ||| ||||||||||||||||||| || || ||||| |||||||||||||||||    || || | ||| ||||| ||||| || || |
tcttaattaatcatgaa-tgtaaccccccccaaagagggtctaccactttcgtaactaatcatgaatgcaaccctcaccctcaaccgcc-acccgga-cgcagATCCGCGAGGGCCTGTACTACAACCCCTACTTCCCGGGCGGCGCCATCGCCATGCCCAAGATGCTGGTGGACGGCGGTGTGGAGTACGAGGACGGCACGC

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|71763205|gb|DR961142.1|DR961142

EST:     ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAGgtactttact ... tgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC

EST: gi|14245130|gb|BG873712.1|BG873712

EST:     ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAGgtactttact ... tgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC

EST: gi|76290228|gb|DV029796.1|DV029796

EST:     ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAGgtactttact ... tgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC

EST: gi|71757789|gb|DR955726.1|DR955726

EST:     ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAGgtactttact ... tgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC

EST: gi|211323657|gb|FL286663.1|FL286663

EST:     ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAGgtactttact ... tgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC

EST: gi|37386374|gb|CF630373.1|CF630373

EST:     ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAGgtactttact ... tgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC

EST: gi|29947382|gb|CB816627.1|CB816627

EST:     ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAGgtactttact ... tgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC

EST: gi|78026464|gb|DV494851.1|DV494851

EST:     ATTTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAG                         ATTTGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAGgtactttact ... tgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC

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), 49 (downstream exon)
Score: 122

GCTTACTGTTTGCATTGCATTCATCCAGGCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAGgtactttact ... tgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTCAATGATGGAGCTGTTGAGTATGAGGATGGTACTC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 178

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 151

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 163

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tgcctttactatcttacaagtaacgataaaaaacattggttgatctgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTCAATGATGGAGCTGTTGAGTATGAGGATGGTACTC

                         ataaaaaacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaaggatgtattatctttcatactcttttccttttttttgtgtttgcctttactatcttacaagtaacgataaaaaacattggttgatctgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTCAATGATGGAGCTGTTGAGTATGAGGATGGTACTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG