ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

AGGTCTCAGAGGAGGAGCTCAGCCAGTACGACGGCTCCGACCCTAAGAAGCCGCTCCTCATGGCCATCAAGGGCCAGATCTACGACGTCACCCAGAGCAGgtctgttctttgcactaaaacactaacttacctccctgtcttcatgaatcgatcactgtttagtgattaaattttgttgcgctggcctgattctaccata...

Basic information

species	Zea mays
transcript	GRMZM2G107444_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G107444_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os10g35870.1 (Oryza sativa), 5'ss of exon 1

AGGTCTCAGAGGAGGAGCTCAGCCAGTACGACGGCTCCGACCCTAAGAAGCCGCTCCTCATGGCCATCAAGGGCCAGATCTACGACGTCACCCAGAGCAGgtctgttctttgcactaaaacactaacttacctccctgtcttcatgaatcgatcactgtt-tagtgatt--aaattttgttgcgctggcctgattctaccata---
||||||| |||||||||||| ||||||||||||| ||||| || |||||||| ||||||||||||||||||||||||||||| |||||||| ||||||||||| |||| || |         | || | |  ||| | | | | |     |||| ||||  |  || ||   | ||  |  | | | || || ||||||  ||   
AGGTCTCCGAGGAGGAGCTCCGCCAGTACGACGGGTCCGATCCCAAGAAGCCCCTCCTCATGGCCATCAAGGGCCAGATCTATGACGTCACGCAGAGCAGgtccgttccttacgtc----tccgaaatcatatccttttttcctttg--tgatcgctgtgatgatgctttcgatttgggaggtggttgcatgtttctactgtagtc

upper sequence: GRMZM2G107444_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA09G25940.1 (Glycine max), 5'ss of exon 1

AGGTCTCAGAGGAGGAGCTCAGCCAGTACGACGGCTCCGACCCTAAGAAGCCGCTCCTCATGGCCATCAAGGGCCAGATCTACGACGTCACCCAGAGCAGgtctgttctttgcactaaaacactaacttacctccctgtcttcatgaatcgatcactgtttagtgattaaattttgttgcgctggcctgattctaccata----
||||| | ||||| || ||||     ||||||||| |||| ||  ||||||| ||||||||||||||||||||||||||||| || ||  |||||||||||| |  |  || ||  | | |  ||| | | |   ||  |  ||| ||   | |||   ||  || ||  ||||| ||    |       || |    |     
AGGTCACCGAGGACGACCTCAAGGCCTACGACGGCACCGATCCCGAGAAGCCTCTCCTCATGGCCATCAAGGGCCAGATCTATGATGTTTCCCAGAGCAGgtatagttatt-catcatagctttaattgaaccaact--cagcat-aacaaaacacccctttttgtttttatttttttattttttttgagttttgttctttttg

upper sequence: GRMZM2G107444_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA20G29660.1 (Glycine max), 5'ss of exon 1

AGGTCTCAGAGGAGGAGCTCAGCCAGTACGACGGCTCCGACCCTAAGAAGCCGCTCCTCATGGCCATCAAGGGCCAGATCTACGACGTCACCCAGAGCAGgtctgttctttgcactaaaacactaacttacctcc---ctgtcttcatgaatcgatcactgtttagtgattaaattttgttgcgctggcctgattctaccata
|| || ||| |||||||||||     ||||||||| |||| ||  |||||||  | |||||||||||||||| ||||||||| || ||| |||||||||||| |  | | | ||| ||| |     |||   |||    ||  ||  |  |    | | ||| ||  | | |  ||  |||  |      | |||     || 
AGATCACAGCGGAGGAGCTCAAGGCCTACGACGGCACCGATCCCGAGAAGCCCTTGCTCATGGCCATCAAGGCCCAGATCTATGATGTCTCCCAGAGCAGgtttactgtct-cacaaaacccacccctttgttccaaattgcatttttttaattttgattgtcta-cgctcattttaggttttgggtattttatttatttat-

upper sequence: GRMZM2G107444_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA10G38150.1 (Glycine max), 5'ss of exon 1

AGGTCTCAGAGGAGGAGCTCAGCCAGTACGACGGCTCCGACCCTAAGAAGCCGCTCCTCATGGCCATCAAGGGCCAGATCTACGACGTCACCCAGAGCAGgtctgttctttgcactaaaacactaacttacctccctgtcttcatgaatcgatcactgtttagtgattaaattttgttgcgctggcctgattctaccata----
|| || | | |||||||||||     ||||||||| |||| ||  |||||||  | |||||||||||||||| ||||||||| || ||| |||||||||||| |  | | |    |||||| | | | |   | |     | ||  | |   |     |||  |   |  |||||| ||  ||   || ||| ||   |     
AGATCACGGCGGAGGAGCTCAAGGCCTACGACGGCACCGATCCCGAGAAGCCCTTGCTCATGGCCATCAAGGCCCAGATCTATGATGTCTCCCAGAGCAGgtttactgtctcacataaaacccaaccctttgttctaaattgca--attt--ttgtgtttttttctcttcattttgatggtctatgctcattttaggttgtggg

upper sequence: GRMZM2G107444_T01 (Zea mays), 5'ss of exon 1
lower sequence: EFJ25427 (Selaginella moellendorffii), 5'ss of exon 1

AGGTCTCAGAGGAGGAGCTCAGCCAGTACGACGGCTCCGACCCTAAGAAGCCGCTCCTCATGGCCATCAAGGGCCAGATCTACGACGTCACCCAGAGCAGgtctgttctttgcactaaaacactaacttacctccctgtcttcatgaatcgatcactgtttagtgattaaattttgttgcgctggcctgattctaccata
||||| | || ||||||||||||   ||||| |||   ||       |||||||| |||||||||||||||||||| ||||| |||||| ||  |  |||||               | |  ||  |  |  ||  |     ||    |   | |   ||  | ||||  |                             
AGGTCACGGAAGAGGAGCTCAGCGCCTACGATGGCAAGGATGACTCCAAGCCGCTGCTCATGGCCATCAAGGGCCAAATCTATGACGTCTCCATGTCCAGgt----------agaagagattcttccccatttcgtttgtgccactggt--gtgatctttgggagatttcag----------------------------

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|89759054|gb|DY687998.1|DY687998

EST:     CCGCTCCTCATGGCCATCAAGGGCCAGATCTACGACGTCACCCAGAGCAG                         AATGTTCTATGGACCTGGTGGACCATACGCCCTATTCGCCGGCAAAGACGC
genomic: CCGCTCCTCATGGCCATCAAGGGCCAGATCTACGACGTCACCCAGAGCAGgtctgttctt ... ccctgtgcagAATGTTCTATGGACCTGGTGGACCATACGCCCTATTCGCCGGCAAAGACGC

EST: gi|60397186|gb|DN230002.1|DN230002

EST:     CCGCTCCTCATGGCCATCAAGGGCCAGATCTACGACGTCACCCAGAGCAG                         AATGTTCTATGGACCTGGTGGACCATACGCCCTATTCGCCGGCAAAGACGC
genomic: CCGCTCCTCATGGCCATCAAGGGCCAGATCTACGACGTCACCCAGAGCAGgtctgttctt ... ccctgtgcagAATGTTCTATGGACCTGGTGGACCATACGCCCTATTCGCCGGCAAAGACGC

EST: gi|50333704|gb|CO528830.1|CO528830

EST:     CCGCTCCTCATGGCCATCAAGGGCCAGATCTACGACGTCACCCAGAGCAG                         AATGTTCTATGGACCTGGTGGACCATACGCCCTATTCGCCGGCAAAGACGC
genomic: CCGCTCCTCATGGCCATCAAGGGCCAGATCTACGACGTCACCCAGAGCAGgtctgttctt ... ccctgtgcagAATGTTCTATGGACCTGGTGGACCATACGCCCTATTCGCCGGCAAAGACGC

EST: gi|149011209|gb|EE042286.2|EE042286

EST:     CCGCTCCTCATGGCCATCAAGGGCCAGATCTACGACGTCACCCAGAGCAG                         AATGTTCTATGGACCTGGTGGACCATACGCCCTATTCGCCGGCAAAGACGC
genomic: CCGCTCCTCATGGCCATCAAGGGCCAGATCTACGACGTCACCCAGAGCAGgtctgttctt ... ccctgtgcagAATGTTCTATGGACCTGGTGGACCATACGCCCTATTCGCCGGCAAAGACGC

EST: gi|211176746|gb|FL087623.1|FL087623

EST:     ACCCAGAGCAG                         AATGTTCTATGGACCTGGTGGACCATACGCCCTATTCGCCGGCAAAGACGC
genomic: ACCCAGAGCAGgtctgttctt ... ccctgtgcagAATGTTCTATGGACCTGGTGGACCATACGCCCTATTCGCCGGCAAAGACGC

EST: gi|148973100|gb|EE024165.2|EE024165

EST:     GCCATCAAGGGCCAGATCTACGACGTCACCCAGAGCAG                         AATGTTCTATGGACCTGGTGGACCATACGCCCTATTCGCCGGCAAAGACGC
genomic: GCCATCAAGGGCCAGATCTACGACGTCACCCAGAGCAGgtctgttctt ... ccctgtgcagAATGTTCTATGGACCTGGTGGACCATACGCCCTATTCGCCGGCAAAGACGC

EST: gi|21432191|gb|BQ547681.1|BQ547681

EST:     CCGCTCCTCATGGCCATCAAGGGCCAGATCTACGACGTCACCCAGAGCAG                         AATGTTCTATGGACCTGGTGGACCATACGCCCTATTCGCCGGCAAAGACGC
genomic: CCGCTCCTCATGGCCATCAAGGGCCAGATCTACGACGTCACCCAGAGCAGgtctgttctt ... ccctgtgcagAATGTTCTATGGACCTGGTGGACCATACGCCCTATTCGCCGGCAAAGACGC

EST: gi|32926446|gb|CF031258.1|CF031258

EST:     CCGCTCCTCATGGCCATCAAGGGCCAGATCTACGACGTCACCCAGAGCAG                         AATGTTCTATGGACCTGGTGGACCATACGCCCTATTCGCCGGCAAAGACGC
genomic: CCGCTCCTCATGGCCATCAAGGGCCAGATCTACGACGTCACCCAGAGCAGgtctgttctt ... ccctgtgcagAATGTTCTATGGACCTGGTGGACCATACGCCCTATTCGCCGGCAAAGACGC

EST: gi|60343332|gb|DN210305.1|DN210305

EST:     CCGCTCCTCATGGCCATCAAGGGCCAGATCTACGACGTCACCCAGAGCAG                         AATGTTCTATGGACCTGGTGGACCATACGCCCTATTCGCCGGCAAAGACGC
genomic: CCGCTCCTCATGGCCATCAAGGGCCAGATCTACGACGTCACCCAGAGCAGgtctgttctt ... ccctgtgcagAATGTTCTATGGACCTGGTGGACCATACGCCCTATTCGCCGGCAAAGACGC

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: 369

AGGTCTCAGAGGAGGAGCTCAGCCAGTACGACGGCTCCGACCCTAAGAAGCCGCTCCTCATGGCCATCAAGGGCCAGATCTACGACGTCACCCAGAGCAGgtctgttctt ... ccctgtgcagAATGTTCTATGGACCTGGTGGACCATACGCCCTATTCGCCGGCAAAGACGCCAGCAGAGCCCTAGCGAAGATGTCCTTCGAGCCACAGGATCTGACCGGC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 286

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 263

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 267

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGTCTCAGAGGAGGAGCTCAGCCAGTACGACGGCTCCGACCCTAAGAAGCCGCTCCTCATGGCCATCAAGGGCCAGATCTACGACGTCACCCAGAGCAGgtctgttctttgcactaaaacactaacttacctccctgtcttcatgaatcgatcactgtttagtgattaaattttgttgcgctggcctgattctaccata

- - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctccctg