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

...cgtatagattgtgctaccgcattcccttgtttgccaatgggaaaaaaaaatatgcgctgcatttcgtttcattgcctaatacctattccattgatatcagTGCCACAGCTTATGGAATCCTGATCTTTCTGGGTTCATTGTTTGGGGATCTTGTCGAGTCTCTGATCAAGCGTGACGCTGGTGTCAAGGACTCTGGATCA

Basic information

species	Zea mays
transcript	GRMZM2G027043_T01
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G027043_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g03460.1 (Oryza sativa), 3'ss of exon 4

cgtat---agattgtgctaccgcattcccttgtttgccaatgggaaaaaaaaatatgcgctgcatttcgtttcattgcctaatacctattccattgatatcagTGCCACAGCTTATGGAATCCTGATCTTTCTGGGTTCATTGTTTGGGGATCTTGTCGAGTCTCTGATCAAGCGTGACGCTGGTGTCAAGGACTCTGGATCA
 || |   | | | || ||     ||| ||||  ||   |   | |  ||| || | |    || || ||||   |  ||||   ||||| || |||||||||||| || ||||| |||||| |||||||||||||||| ||||| |||||||||||||||||||||||||||||||| |||||||| |||||||||||||||
tgtgttcaaaactttgataggttgttcacttgcatgttcacaagtagcaaatatttccttaacacttggttttgataactaa---ctatttcactgatatcagTGCTACTGCTTACGGAATCTTGATCTTTCTGGGTTCGTTGTTCGGGGATCTTGTCGAGTCTCTGATCAAGCGTGATGCTGGTGTGAAGGACTCTGGATCA

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|71763393|gb|DR961330.1|DR961330

EST:     ACCACTGTGCTGCTGTCAACTGCCTTACGCTGGCCAAGATCACTGTTGAG                         TGCCACAGCTTATGGAATCCTGATCTTTCTGGGTTCATTGTTTGGGGATCT
genomic: ACCACTGTGCTGCTGTCAACTGCCTTACGCTGGCCAAGATCACTGTTGAGgtgtgaattc ... ttgatatcagTGCCACAGCTTATGGAATCCTGATCTTTCTGGGTTCATTGTTTGGGGATCT

EST: gi|91056794|gb|EB167212.1|EB167212

EST:     ACCACTGTGCTGCTGTCAACTGCCTTACGCTGGCCAAGATCACTGTTGAG                         TGCCACAGCTTATGGAATCCTGATCTTTCTGGGTTCATTGTTTGGGGATCT
genomic: ACCACTGTGCTGCTGTCAACTGCCTTACGCTGGCCAAGATCACTGTTGAGgtgtgaattc ... ttgatatcagTGCCACAGCTTATGGAATCCTGATCTTTCTGGGTTCATTGTTTGGGGATCT

EST: gi|91056795|gb|EB167213.1|EB167213

EST:     ACCACTGTGCTGCTGTCAACTGCCTTACGCTGGCCAAGATCACTGTTGAG                         TGCCACAGCTTATGGAATCCTGATCTTTCTGGGTTCATTGTTTGGGGATCT
genomic: ACCACTGTGCTGCTGTCAACTGCCTTACGCTGGCCAAGATCACTGTTGAGgtgtgaattc ... ttgatatcagTGCCACAGCTTATGGAATCCTGATCTTTCTGGGTTCATTGTTTGGGGATCT

EST: gi|89759341|gb|DY688206.1|DY688206

EST:     ACCACTGTGCTGCTGTCAACTGCCTTACGCTGGCCAAGATCACTGTTGAG                         TGCCACAGCTTATGGAATCCTGATCTTTCTGGGTTCATTGTTTGGGGATCT
genomic: ACCACTGTGCTGCTGTCAACTGCCTTACGCTGGCCAAGATCACTGTTGAGgtgtgaattc ... ttgatatcagTGCCACAGCTTATGGAATCCTGATCTTTCTGGGTTCATTGTTTGGGGATCT

EST: gi|71435126|gb|DR816176.1|DR816176

EST:     ACCACTGTGCTGCTGTCAACTGCCTTACGCTGGCCAAGATCACTGTTGAG                         TGCCACAGCTTATGGAATCCTGATCTTTCTGGGTTCATTGTTTGGGGATCT
genomic: ACCACTGTGCTGCTGTCAACTGCCTTACGCTGGCCAAGATCACTGTTGAGgtgtgaattc ... ttgatatcagTGCCACAGCTTATGGAATCCTGATCTTTCTGGGTTCATTGTTTGGGGATCT

EST: gi|89247373|gb|DY619159.1|DY619159

EST:     CTTACGCTGGCCAAGATCACTGTTGAG                         TGCCACAGCTTATGGAATCCTGATCTTTCTGGGTTCATTGTTTGGGGATCT
genomic: CTTACGCTGGCCAAGATCACTGTTGAGgtgtgaattc ... ttgatatcagTGCCACAGCTTATGGAATCCTGATCTTTCTGGGTTCATTGTTTGGGGATCT

EST: gi|60348161|gb|DN215134.1|DN215134

EST:     ACCACTGTGCTGCTGTCAACTGCCTTACGCTGGCCAAGATCACTGTTGAG                         TGCCACAGCTTATGGAATCCTGATCTTTCTGGGTTCATTGTTTGGGGATCT
genomic: ACCACTGTGCTGCTGTCAACTGCCTTACGCTGGCCAAGATCACTGTTGAGgtgtgaattc ... ttgatatcagTGCCACAGCTTATGGAATCCTGATCTTTCTGGGTTCATTGTTTGGGGATCT

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: 47 (upstream exon), 49 (downstream exon)
Score: 58

CTAAGAAAACCTTGGAGGGTGCTTTAGCTGGCCTAGCTGGCTGTGTGCTGACCACTGTGCTGCTGTCAACTGCCTTACGCTGGCCAAGATCACTGTTGAGgtgtgaattc ... ttgatatcagTGCCACAGCTTATGGAATCCTGATCTTTCTGGGTTCATTGTTTGGGGATCTTGTCGAGTCTCTGATCAAGCGTGACGCTGGTGTCAAGGACTCTGGATCA

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 37

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 32

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

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

aaaaatatgcgctgcatttcgtttcattgcctaatacctattccattgatatcagTGCCACAGCTTATGGAATCCTGATCTTTCTGGGTTCATTGTTTGGGGATCTTGTCGAGTCTCTGATCAAGCGTGACGCTGGTGTCAAGGACTCTGGATCA

                                        ttccatt  CT-rich tract
                                            attgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgtatagattgtgctaccgcattcccttgtttgccaatgggaaaaaaaaatatgcgctgcatttcgtttcattgcctaatacctattccattgatatcagTGCCACAGCTTATGGAATCCTGATCTTTCTGGGTTCATTGTTTGGGGATCTTGTCGAGTCTCTGATCAAGCGTGACGCTGGTGTCAAGGACTCTGGATCA

- - - - - -tgctacc
- - - - - - - - - gcattcc
- - - - - - - - - - - - - -tgtttgc
- - - - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - -gcgctgc