ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CAATGCTGGACTGATTGTCACATGGATTACTGATCCTATGCATGGAAACACCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTGgtgagtcacgttccaccaggaacttcttgttcattcttctctagtatgcaatgcatttctattatgataaatctgaacgaatctcagttttgtttcggca...

Basic information

species	Zea mays
transcript	GRMZM2G365160_T02
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G365160_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os07g42960.2 (Oryza sativa), 5'ss of exon 3

CAATGCTGGACTGATTGTCACATGGATTACTGATCCTATGCATGGAAACACCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTGgtgagtcacgttccacca-ggaacttcttgttc------attcttctctagtatgcaatgcatttctattatgataaatctgaacgaatc--tcagttttgtttcggca
|||  |||||| |||||||||||||||||||||||| ||||||||||||||||||||||| || ||||| ||||||||||||||||| || |||||||||||||||    |||  | |  | | | | | ||       || |||  ||||||||  |||||     | |  | | ||||| |   ||    | |   |  || |    
CAACTCTGGACAGATTGTCACATGGATTACTGATCCCATGCATGGAAACACCATCAAGGCTCCATGTGGTCTGAAGACTCGTCCATTCGATTCCATTCTGgtgagtatttttctgctacagcattccatatttgctagtatcctttcctagtatg--atgcaac---aatccggtcaatctcacataaggaattaccctcattcc----

upper sequence: GRMZM2G365160_T02 (Zea mays), 5'ss of exon 4
lower sequence: AT1G22410.1 (Arabidopsis thaliana), 5'ss of exon 4

CAATGCTGGACTGATTGTCACATGGATTACTGATCCTATGCATGGAAACACCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTGgtgagtcacgttccaccaggaacttc--ttgttcattcttctctagtatgc-aatgcattt-ctattatgataaatctgaacgaatctcagttttgtttcggca
   |||||||| |||||| || ||| | | |||||| ||||| ||||||||||| ||||| |||||||| || ||||||||||| |||||| ||||  ||||  ||    |  | |    ||||     |  | |||      |  ||| | ||||  |    | || |||| | |   || || |   | |     | |    
ACGTGCTGGACAGATTGTGACTTGGGTCAGTGATCCAATGCACGGAAACACCATTAAGGCTCCTTGTGGTCTCAAGACTCGTCCCTTTGACGCCATCTTGgtacgttttttaactcataaaactctaactaatgattacaaattgttataccaatgtttaggttcttttgatcattgcaaatga-tagaaataggaatact---

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|95107805|gb|EB740034.1|EB740034

EST:     GACTCGTCCATTTGACTCCATTCTG                         GCTGAAGTGCGTGCCTTCTTCGATGTGCATGACCAAGAAGGAAGCCACCCT
genomic: GACTCGTCCATTTGACTCCATTCTGgtgagtcacg ... tctctaacagGCTGAAGTGCGTGCCTTCTTCGATGTGCATGACCAAGAAGGAAGCCACCCT

EST: gi|32840706|gb|CD980387.1|CD980387

EST:     CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTG                         GCTGAAGTGCGTGCCTTCTTCGATGTGCATG
genomic: CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTGgtgagtcacg ... tctctaacagGCTGAAGTGCGTGCCTTCTTCGATGTGCATG

EST: gi|78025844|gb|DV494231.1|DV494231

EST:     CCATCAAGGCCCTTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTG                         GCTGAAGTGCGTGCCTTCTTCGATGTGCATGACCAAGAAGGAAGCCACCCT
genomic: CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTGgtgagtcacg ... tctctaacagGCTGAAGTGCGTGCCTTCTTCGATGTGCATGACCAAGAAGGAAGCCACCCT

EST: gi|211371610|gb|FK948449.1|FK948449

EST:     CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTG                         GCTGAAGTGCGTGCCTTCTTCGATGTGCATGACCAAGAAGGAAGCCACCCT
genomic: CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTGgtgagtcacg ... tctctaacagGCTGAAGTGCGTGCCTTCTTCGATGTGCATGACCAAGAAGGAAGCCACCCT

EST: gi|38568918|gb|CF974803.1|CF974803

EST:     CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTG                         GCTGAAGTGCGTGCCTTCTTCGATGTGCATGACCAAGAAGGAAGCCACCCT
genomic: CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTGgtgagtcacg ... tctctaacagGCTGAAGTGCGTGCCTTCTTCGATGTGCATGACCAAGAAGGAAGCCACCCT

EST: gi|211371609|gb|FK948448.1|FK948448

EST:     CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTG                         GCTGAAGTGCGTGCCTTCTTCGATGTGCATGACCAAGAAGGAAGCCACCCT
genomic: CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTGgtgagtcacg ... tctctaacagGCTGAAGTGCGTGCCTTCTTCGATGTGCATGACCAAGAAGGAAGCCACCCT

EST: gi|71533870|gb|DR784629.1|DR784629

EST:     CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTG                         GCTGAAGTGCGTGCCTTCTTCGATGTGCATGACCAAGAAGGAAGCCACCCT
genomic: CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTGgtgagtcacg ... tctctaacagGCTGAAGTGCGTGCCTTCTTCGATGTGCATGACCAAGAAGGAAGCCACCCT

EST: gi|38568956|gb|CF974841.1|CF974841

EST:     CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTG                         GCTGAAGTGCGTGCCTTCTTCG
genomic: CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTGgtgagtcacg ... tctctaacagGCTGAAGTGCGTGCCTTCTTCG

EST: gi|40287021|gb|CK327413.1|CK327413

EST:     CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTG                         GCTGAAGTGCGTGCCTTCTTCGATGTGCATGACCAAGAAGGAAGCCACCCT
genomic: CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTGgtgagtcacg ... tctctaacagGCTGAAGTGCGTGCCTTCTTCGATGTGCATGACCAAGAAGGAAGCCACCCT

EST: gi|71449372|gb|DR830422.1|DR830422

EST:     CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTG                         GCTGAAGTGCGTGCCTTCTTCGATGTGCATGACCAAGAAGGAAGCCACCCT
genomic: CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTGgtgagtcacg ... tctctaacagGCTGAAGTGCGTGCCTTCTTCGATGTGCATGACCAAGAAGGAAGCCACCCT

EST: gi|23357722|gb|BU645371.1|BU645371

EST:     CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTG                         GCTGAAGTGCGTGCCTTCTTCGATGTGCATGACCAAGAAGGAAGCCACCCT
genomic: CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTGgtgagtcacg ... tctctaacagGCTGAAGTGCGTGCCTTCTTCGATGTGCATGACCAAGAAGGAAGCCACCCT

EST: gi|32841201|gb|CD980882.1|CD980882

EST:     CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTG                         GCTGAAGTGCGTGCCTTCTTCGATGTGCATG
genomic: CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTGgtgagtcacg ... tctctaacagGCTGAAGTGCGTGCCTTCTTCGATGTGCATG

EST: gi|166488930|gb|EG318091.1|EG318091

EST:     CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTG                         GCTGAAGTGCGTGCC
genomic: CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTGgtgagtcacg ... tctctaacagGCTGAAGTGCGTGCC

EST: gi|211371608|gb|FK948447.1|FK948447

EST:     CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTG                         GCTGAAGTGCGTGCCTTCTTCGATGTGCATGACCAAGAAGGAAGCCACCCT
genomic: CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTGgtgagtcacg ... tctctaacagGCTGAAGTGCGTGCCTTCTTCGATGTGCATGACCAAGAAGGAAGCCACCCT

EST: gi|71533894|gb|DR784653.1|DR784653

EST:     CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTG                         GCTGAAGTGCGTGCCTTCTTCGATGTGCATGACCAAGAAGGAAGCCACCCT
genomic: CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTGgtgagtcacg ... tctctaacagGCTGAAGTGCGTGCCTTCTTCGATGTGCATGACCAAGAAGGAAGCCACCCT

EST: gi|78025351|gb|DV493738.1|DV493738

EST:     CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTG                         GCTGAAGTGCGTGCCTTCTTCGATGTGCATGACCAAGAAGGAAGCCACCCT
genomic: CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTGgtgagtcacg ... tctctaacagGCTGAAGTGCGTGCCTTCTTCGATGTGCATGACCAAGAAGGAAGCCACCCT

EST: gi|32866392|gb|CF006074.1|CF006074

EST:     CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTG                         GCTGAAGTGCGTGCCTTCTTCGATGTGCATGACCAAGAAGGAAGCCACCCT
genomic: CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTGgtgagtcacg ... tctctaacagGCTGAAGTGCGTGCCTTCTTCGATGTGCATGACCAAGAAGGAAGCCACCCT

EST: gi|32866393|gb|CF006075.1|CF006075

EST:     CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTG                         GCTGAAGTGCGTGCCTTCTTCGATGTGCATGACCAAGAAGGAAGCCACCCT
genomic: CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTGgtgagtcacg ... tctctaacagGCTGAAGTGCGTGCCTTCTTCGATGTGCATGACCAAGAAGGAAGCCACCCT

EST: gi|32840781|gb|CD980462.1|CD980462

EST:     CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTG                         GCTGAAGTGCGTGCCTTCTTCGATGTGCATGA
genomic: CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTGgtgagtcacg ... tctctaacagGCTGAAGTGCGTGCCTTCTTCGATGTGCATGA

EST: gi|32840917|gb|CD980598.1|CD980598

EST:     CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTG                         GCTGAAGTGCGTGCCTTCTTCGATGTGCATGAC
genomic: CCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTGgtgagtcacg ... tctctaacagGCTGAAGTGCGTGCCTTCTTCGATGTGCATGAC

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: 29

CAATGCTGGACTGATTGTCACATGGATTACTGATCCTATGCATGGAAACACCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTGgtgagtcacg ... tctctaacagGCTGAAGTGCGTGCCTTCTTCGATGTGCATGACCAAGAAGGAAGCCACCCTGGGGGCGTCCACCTTGAAATGACTGGGCAGAATGTGACCGAGTGCATCG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 17

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 20

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 102

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAATGCTGGACTGATTGTCACATGGATTACTGATCCTATGCATGGAAACACCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTGgtgagtcacgttccaccaggaacttcttgttcattcttctctagtatgcaatgcatttctattatgataaatctgaacgaatctcagttttgtttcggca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA