ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GTGCTGCTCACTGTGAGAATGAGCATTTTACTTATGATATCACGTCTAAGGTGAAGACAAAGTTCTTGGGAAATTCATTGGAAATCTATCCAGTTGGAAGgttaattgttagaattgtatttctttcttggagatctgtatggcttaaaaatattttattggaataaaatggaaacctttttgaaggctgaattgggaccagttattctaatccctgctgtaatataatttccatgtcacag

Basic information

species	Zea mays
transcript	GRMZM2G114126_T01
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G114126_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g16690.1 (Oryza sativa), 5'ss of exon 6

GTGCTGCTCACTGTGAGAATGAGCATTTTACTTATGATATCACGTCTAAGGTGAAGACAAAGTTCTTGGGAAATTCATTGGAAATCTATCCAGTTGGAAGgttaattgttagaattgtatttctttcttggagatctgtatggcttaaaaatattttattggaataaaatggaaacctttttgaaggctgaattgggaccagttattctaatccctgctgtaatataatttccatgtcacag
|||| ||||||||||| ||||  |||||||| ||||| ||||| || ||| ||||||| || |||||||| || ||  ||||| | |||||| ||||||||| | ||  |  || |||  || ||||     |||   ||||  | ||  |  | ||  |    |||| |||     |||||     ||| ||                                                 
GTGCCGCTCACTGTGAAAATGCACATTTTACATATGACATCACCTCCAAGTTGAAGACCAAATTCTTGGGGAACTCTCTGGAAGTTTATCCACTTGGAAGgtaattttgtcaaactgtgattgtttc---aggat---tatgaataaaccagctctttatatcctaaa-tgg-----ttttttgtttctgcatcacag--------------------------------------------

upper sequence: GRMZM2G114126_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA11G14770.1 (Glycine max), 5'ss of exon 6

GTGCTGCTCACTGTGAGAATGAGCATTTTACTTATGATATCACGTCTAAGGTGAAGACAAAGTTCTTGGGAAATTCATTGGAAATCTATCCAGTTGGAAGgttaattgttagaattgtatttctttcttggagatctgtatggcttaaaaatattttattggaataaaatggaaacctttttgaaggctgaattgggaccagttattctaatccctgctgtaatataatttccatgtcacag
||||||| ||    ||||||||||||||||| |||||| | || || ||| |||| || ||||| |||||||||||  | ||  | || || |||||||||| |    |    |||| |||| |||   | |||| |     | |  | |   | |||||                ||| |||         |||     | |  ||| | | ||  || |                     
GTGCTGCGCATGCCGAGAATGAGCATTTTACATATGATGTGACTTCAAAGTTGAAAACTAAGTTTTTGGGAAATTCTGTTGATGTTTACCCTGTTGGAAGgtgacaaat--atattgcatttgttt--agtagatttcctctgtt--atatcgtcttatt----------------cttcttgttactgatgttgtttgtattatttcaagttccaactctg--------------------

upper sequence: GRMZM2G114126_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA15G04210.1 (Glycine max), 5'ss of exon 6

GTGCTGCTCACTGTGAGAATGAGCATTTTACTTATGATATCACGTCTAAGGTGAAGACAAAGTTCTTGGGAAATTCATTGGAAATCTATCCAGTTGGAAGgttaattgttagaattgtatttctttcttggagatctgtatggcttaaaaatatttt-attggaataaaatggaaacctttttgaaggctgaattgggaccagttattctaatccctgctgtaatataatttccatgtcacag
||||||  ||   |||||||||||||||||| |||||| | || || ||| | ||||| ||||| |||||||||||  | ||  | || || ||||||||||  ||   || | ||| |||| |||  | ||   |  |||      |   |||||| |||| | | |  |         ||  ||      ||||   |||                                         
GTGCTGGGCATGCTGAGAATGAGCATTTTACATATGATGTGACTTCAAAGTTAAAGACTAAGTTTTTGGGAAATTCTGTTGATGTTTACCCTGTTGGAAGgt-gatcaataca-ttgcatttgtttggtagattaccttattatcctattctatttttattgtacttattttttgtatccttccaacttcctattgct-ccat----------------------------------------

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|211454957|gb|FL196641.1|FL196641

EST:     GTGAAGACAAAGTTCTTGGGAAATTCATTGGAAATCTATCCAGTTGGAAG                         GACTAGAGTGACACTTAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACC
genomic: GTGAAGACAAAGTTCTTGGGAAATTCATTGGAAATCTATCCAGTTGGAAGgttaattgtt ... catgtcacagGACTAGAGTGACACTTAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACC

EST: gi|91055718|gb|EB166136.1|EB166136

EST:     GTGAAGACAAAGTTCTTGGGAAATTCATTGGAAATCTATCCAGTTGGAAG                         GACTAGAGTGACACTTAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACC
genomic: GTGAAGACAAAGTTCTTGGGAAATTCATTGGAAATCTATCCAGTTGGAAGgttaattgtt ... catgtcacagGACTAGAGTGACACTTAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACC

EST: gi|67040089|gb|CO466344.1|CO466344

EST:     GTGAAGACAAAGTTCTTGGGAAATTCATTGGAAATCTATCCAGTTGGAAG                         GACTAGAGTGACACTTAAAAAATCTGGNTGTCGTGTTGGGATTTGGTGCCA
genomic: GTGAAGACAAAGTTCTTGGGAAATTCATTGGAAATCTATCCAGTTGGAAGgttaattgtt ... catgtcacagGACTAGAGTGACACTTAAAAAATCTGG-TGTCGTGTTGG-ATTTGGTGCCA

EST: gi|67022184|gb|CO450933.1|CO450933

EST:     TGAAGACAAAGTTCTTGGGGAAATTCATTGGAAATCTATCCAGTTGGAAG                         GACTAGAGTGACACTTTAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCTC
genomic: TGAAGACAAAGTTCTT-GGGAAATTCATTGGAAATCTATCCAGTTGGAAGgttaattgtt ... catgtcacagGACTAGAGTGACAC-TTAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCAC

EST: gi|61118185|gb|DN559146.1|DN559146

EST:     AAGACAAAGTTCTTGGGAAATTCATTGGAAATCTATCCAGTTGGAAG                         GACTAGAGTGACACTTAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACC
genomic: AAGACAAAGTTCTTGGGAAATTCATTGGAAATCTATCCAGTTGGAAGgttaattgtt ... catgtcacagGACTAGAGTGACACTTAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACC

EST: gi|78120438|gb|DV538822.1|DV538822

EST:     GTGAAGACAAAGTTCTTGGGAAATTCATTAGAAATCTATCCAGTTGGAAG                         GACTAGAGTGACACTTAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACC
genomic: GTGAAGACAAAGTTCTTGGGAAATTCATTGGAAATCTATCCAGTTGGAAGgttaattgtt ... catgtcacagGACTAGAGTGACACTTAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACC

EST: gi|67032806|gb|CO461555.1|CO461555

EST:     GTGAAGACAAAGTTCTTGGGAAATTCATTGGAAATCTATCCAGTTGGAAG                         GACTAGAGTGACACTTAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACC
genomic: GTGAAGACAAAGTTCTTGGGAAATTCATTGGAAATCTATCCAGTTGGAAGgttaattgtt ... catgtcacagGACTAGAGTGACACTTAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACC

EST: gi|148961873|gb|EE012659.2|EE012659

EST:     GTGAAGACAAAGTTCTTGGGAAATTCATTGGAAATCTATCCAGTTGGAAG                         GACTAGAGTGACACTTAAAAAATCTGGTGTCGTGTTGGATTTCGTGCCACC
genomic: GTGAAGACAAAGTTCTTGGGAAATTCATTGGAAATCTATCCAGTTGGAAGgttaattgtt ... catgtcacagGACTAGAGTGACACTTAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACC

EST: gi|78120437|gb|DV538821.1|DV538821

EST:     GTGAAGACAAAGTTCTTGGGAAATTCATTGGAAATCTATCCAGTTGGAAG                         GACTAGAGTGACACTTAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACC
genomic: GTGAAGACAAAGTTCTTGGGAAATTCATTGGAAATCTATCCAGTTGGAAGgttaattgtt ... catgtcacagGACTAGAGTGACACTTAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACC

EST: gi|8367795|gb|BE050740.1|BE050740

EST:     GTGAAGACAAAGTTCTTGGGAAATTCATTGGAAATCTATGCAGTTGGAAG                         GACTAGAGTGACACTTAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACC
genomic: GTGAAGACAAAGTTCTTGGGAAATTCATTGGAAATCTATCCAGTTGGAAGgttaattgtt ... catgtcacagGACTAGAGTGACACTTAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACC

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), 48 (downstream exon)
Score: 119

GTGCTGCTCACTGTGAGAATGAGCATTTTACTTATGATATCACGTCTAAGGTGAAGACAAAGTTCTTGGGAAATTCATTGGAAATCTATCCAGTTGGAAGgttaattgtt ... catgtcacagGACTAGAGTGACACTTAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACCACTAACAAAGGTTAACAACCTGATATTTGGGCGTACTTGGGTTGATTCT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 340

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 327

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 142

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGCTGCTCACTGTGAGAATGAGCATTTTACTTATGATATCACGTCTAAGGTGAAGACAAAGTTCTTGGGAAATTCATTGGAAATCTATCCAGTTGGAAGgttaattgttagaattgtatttctttcttggagatctgtatggcttaaaaatattttattggaataaaatggaaacctttttgaaggctgaattgggaccagttattctaatccctgctgtaatataatttccatgtcacag

- - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG