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

...agtcatctctgtcgatgaaatggatgtgcgcacatgtaattgtgaagcaagagcgtttccatcctctttactactaattggcaaagcattgcacgagtagGTCTACGCAAATGTCTCAGGAGAGGCACCGCTGGATGAGCCCATGATTGACGTGAGCTCGAGTCAGTTCTACGGTGAAGGATACGATGATAGCGACAAGA

Basic information

species	Zea mays
transcript	GRMZM2G063949_T01
intron #	7
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G063949_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g73790.1 (Oryza sativa), 3'ss of exon 7

agtcatctctgtcgatgaaatggatgtgcgcacatgtaattgtgaagcaagagcgtttccatcctctttactactaattggcaaagcattgcacgagt---------agGTCTACGCAAATGTCTCAGGAGAGGCACCGCTGGATGAGCCCATGATTGACGTGAGCTCGAGTCAGTTCTACGGTGAAGGATACGATGATAGCGACAAGA
                             | ||||  | | | |  ||||      ||  | | | | |  |||| ||   | |||  || || |  |         ||||||| |||||||||||||||||| |||| |||||||| || |||||||||||||| ||||  |||||||| ||||||||||| |||||||| || ||||
-----------------------------gtacat-cattagcgtggcaatgtttctttgagcgtttctgttactcatgccctaagtcttacatggttgtcctgtacagGTCTATGCAAATGTCTCAGGAGAGCCACCACTGGATGAACCTATGATTGACGTGAGTTCGAAGCAGTTCTATGGTGAAGGATATGATGATAGTGATAAGA

upper sequence: GRMZM2G063949_T01 (Zea mays), 3'ss of exon 7
lower sequence: EFJ07025 (Selaginella moellendorffii), 3'ss of exon 7

agtcatctctgtcgatgaaatggatgtgcgcacatgtaattgtgaagcaagagcgtttccatcctctttactactaattggcaaagcattgcacgagtagGTCTACGCAAATGTCTCAGGAGAGGCACCGCTGGATGAGCCCATGATTGACGTGAGCTCGAGTCAGTTCTACGGTGAAGGATACGATGATAGCGACAAGA
                                  |||  ||   | |      |  || |     |||  || |  | |    |    |  |||    |||| ||| |||| ||    ||   | | | |||||| |||||||  || |||||||||||||   |||| ||||| || ||||||||||| ||||||||| 
--------------------------------gttgtttttaaaacgttctttcagtttcccaggcttatcttcatacttctcattggtgccac--acagGTGTACACAAAAGTTAGCGGCAGGCCGCAGCTGGACGAGCCCACAATCGACGTGAGCTCGAAGGAGTTTTACGGGGAGGGATACGATGACAGCGACAAGC

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|93281900|gb|EB674164.1|EB674164

EST:     ATCCGAACAATGAAGTTACCGTTAGGGAGTTGGCCCAAATGATGACAGAG                         GTCTACGCAAATGTCTCAGGAGAGGCACCGCTGGATGAGCCCATGATTGAC
genomic: ATCCGAACAATGAAGTTACCGTTAGGGAGTTGGCCCAAATGATGACAGAGgtatgccata ... gcacgagtagGTCTACGCAAATGTCTCAGGAGAGGCACCGCTGGATGAGCCCATGATTGAC

EST: gi|40337281|gb|CK371351.1|CK371351

EST:     ATCCGAACAATGAAGTTACCGTTAGGGAGTTGGCCCAAATGATGACAGAG                         GTCTACGCAAATGTCTCAGGAGAGGCACCGCTGGATGAGCCCATGATTGAC
genomic: ATCCGAACAATGAAGTTACCGTTAGGGAGTTGGCCCAAATGATGACAGAGgtatgccata ... gcacgagtagGTCTACGCAAATGTCTCAGGAGAGGCACCGCTGGATGAGCCCATGATTGAC

EST: gi|60356652|gb|DN223625.1|DN223625

EST:     ATCCGAACAATGAAGTTACCGTTAGGGAGTTGGCCCAAATGATGACAGAG                         GTCTACGCAAATGTCTCAGGAGAGGCACCGCTGGATGAGCCCATGATTGAC
genomic: ATCCGAACAATGAAGTTACCGTTAGGGAGTTGGCCCAAATGATGACAGAGgtatgccata ... gcacgagtagGTCTACGCAAATGTCTCAGGAGAGGCACCGCTGGATGAGCCCATGATTGAC

EST: gi|32868566|gb|CF008248.1|CF008248

EST:     ATCCGAACAATGAAGTTACCGTTAGGGAGTTGGCCCAAATGATGACAGAG                         GTCTACGCAAATGTCTCAGGAGAGGCACCGCTGGATGAGCCCATGATTGAC
genomic: ATCCGAACAATGAAGTTACCGTTAGGGAGTTGGCCCAAATGATGACAGAGgtatgccata ... gcacgagtagGTCTACGCAAATGTCTCAGGAGAGGCACCGCTGGATGAGCCCATGATTGAC

EST: gi|149086196|gb|EE175736.2|EE175736

EST:     ATCCGAACAATGAAGTTACCGTTAGGGAGTTGGCCCAAATGATGACAGAG                         GTTTACGCAAATGTCTCAGGAGAGGCACCGCTGGATGAGCCCATGATTGAC
genomic: ATCCGAACAATGAAGTTACCGTTAGGGAGTTGGCCCAAATGATGACAGAGgtatgccata ... gcacgagtagGTCTACGCAAATGTCTCAGGAGAGGCACCGCTGGATGAGCCCATGATTGAC

EST: gi|7137694|gb|AW499223.1|AW499223

EST:     TCCGAACAATGAAGTTACCGTTAGGGAGTTTGGCCCAAATGATGACAGAG                         GTCTACACAAATGTCTCAGGAGAGGCACCGCTGGATGAGCCCATGATTGAC
genomic: TCCGAACAATGAAGTTACCGTTAGGGAGTT-GGCCCAAATGATGACAGAGgtatgccata ... gcacgagtagGTCTACGCAAATGTCTCAGGAGAGGCACCGCTGGATGAGCCCATGATTGAC

EST: gi|211216490|gb|FL245940.1|FL245940

EST:     ATCCGAACAATGAAGTTACCGTTAGGGAGTTGGCCCAAATGATGACAGAG                         GTCTACGCAAATGTCTCAGGAGAGGCACCGCTGGATGAGCCCATGATTGAC
genomic: ATCCGAACAATGAAGTTACCGTTAGGGAGTTGGCCCAAATGATGACAGAGgtatgccata ... gcacgagtagGTCTACGCAAATGTCTCAGGAGAGGCACCGCTGGATGAGCCCATGATTGAC

EST: gi|60353566|gb|DN220539.1|DN220539

EST:     ATCCGAACAATGAAGTTACCGTTAGGGAGTTGGCCCAAATGATGACAGAG                         GTCTACGCAAATGTCTCAGGAGAGGCACCGCTGGATGAGCCCATGATTGAC
genomic: ATCCGAACAATGAAGTTACCGTTAGGGAGTTGGCCCAAATGATGACAGAGgtatgccata ... gcacgagtagGTCTACGCAAATGTCTCAGGAGAGGCACCGCTGGATGAGCCCATGATTGAC

EST: gi|149098033|gb|EE183980.2|EE183980

EST:     ATCCGAACAATGAAGTTACCGTTAGGGAGTTGGCCCAAATGATGACAGAG                         GTCTACGCAAATGTCTCAGGAGAGGCACCGCTGGATGAGCCCATGATTGAC
genomic: ATCCGAACAATGAAGTTACCGTTAGGGAGTTGGCCCAAATGATGACAGAGgtatgccata ... gcacgagtagGTCTACGCAAATGTCTCAGGAGAGGCACCGCTGGATGAGCCCATGATTGAC

EST: gi|211213926|gb|FL245933.1|FL245933

EST:     ATCCGAACAATGAAGTTACCGTTAGGGAGTTGGCCCAAATGATGACAGAG                         GTCTACGCAAATGTCTCAGGAGAGGCACCGCTGGATGAGCCCATGATTGAC
genomic: ATCCGAACAATGAAGTTACCGTTAGGGAGTTGGCCCAAATGATGACAGAGgtatgccata ... gcacgagtagGTCTACGCAAATGTCTCAGGAGAGGCACCGCTGGATGAGCCCATGATTGAC

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), 48 (downstream exon)
Score: 253

GAAAATCCTGCTCGAGCCAATGGCCACATCTTCAATGTTGGGAATCCGAACAATGAAGTTACCGTTAGGGAGTTGGCCCAAATGATGACAGAGgtatgccata ... gcacgagtagGTCTACGCAAATGTCTCAGGAGAGGCACCGCTGGATGAGCCCATGATTGACGTGAGCTCGAGTCAGTTCTACGGTGAAGGATACGATGATAGCGACAAGA

Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 92

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 48

Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 134

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

agcaagagcgtttccatcctctttactactaattggcaaagcattgcacgagtagGTCTACGCAAATGTCTCAGGAGAGGCACCGCTGGATGAGCCCATGATTGACGTGAGCTCGAGTCAGTTCTACGGTGAAGGATACGATGATAGCGACAAGA

                          tactaat  putative branch site (score: 134)
                          tactaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtcatctctgtcgatgaaatggatgtgcgcacatgtaattgtgaagcaagagcgtttccatcctctttactactaattggcaaagcattgcacgagtagGTCTACGCAAATGTCTCAGGAGAGGCACCGCTGGATGAGCCCATGATTGACGTGAGCTCGAGTCAGTTCTACGGTGAAGGATACGATGATAGCGACAAGA

- - - - - - - - - -atggatg
- - - - - - - - - - - - - - - - catgtaa
- - - - - - - - - - - - - - - - - - - - - tgaagca