ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

gtagtctctttgtgcctcggcaacctcggaccatgctagctagctgtttccattcatccttgctttcgtgttggtgacttggtgtgtgaagCTGAGGACGGTGATGACCAGTCTCGGGGAGAAGATGACCGACGAGGAGGTTGAACAGATGATCAGGGAAGCAGACACCGACGGTGACGGTCAGGTGAACT

Basic information

species	Zea mays
transcript	GRMZM2G149923_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G149923_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g53200.1 (Oryza sativa), 3'ss of exon 3

gtagtctctttgtgcctcggcaacctcggaccat--gctagctagctgtttccattcatccttgctttcgtgttggtgacttggtgtgtgaagCTGAGGACGGTGATGACCAGTCTCGGGGAGAAGATGACCGACGAGGAGGTTGAACAGATGATCAGGGAAGCAGACACCGACGGTGACGGTCAGGTGAACT
   ||   || || ||||    |  || ||||||    |  | |||||||  |  ||||   ||    | ||||  ||  ||  |||||| |||||||||| |||||||||| ||| |||||||||||||| |||||||||||||| |||||||| ||||| || || ||||| || ||||| ||||||||||
---gtggtttagtacctcaagcagttcagaccattaattttcaagctgttatccatcatttctgac--catgttcttg--ttcatgtgtgcagCTGAGGACAGTGATGACCAATCTTGGGGAGAAGATGACAGACGAGGAGGTTGAGCAGATGATAAGGGAGGCGGATACCGATGGCGACGGGCAGGTGAACT

upper sequence: GRMZM2G149923_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ32870 (Selaginella moellendorffii), 3'ss of exon 3

gtagtctctttgtgcctcggcaacctcggaccatgctagctagctgtttccattcatccttgctttcgtgttggtgacttgg---tgtgtgaagCTGAGGACGGTGATGACCAGTCTCGGGGAGAAGATGACCGACGAGGAGGTTGAACAGATGATCAGGGAAGCAGACACCGACGGTGACGGTCAGGTGAACT
                        ||  ||      | | |   || |    ||  || || | ||  ||    ||||| |    | |    || |||||   ||||||| || ||| || |||||| |||||||||||||||| ||| |||||||| | || || ||||  ||||| |||||||| || ||||
----------------------gtctgtgagagacatggattcttggtcttgtttctcgtttcctttttgac--tgactggaatttcttcccagTTGAGGGACGTGATGATCAATCTGGGCGAGAAGCTGACCGACGAGGAGGTAGAAGAGATGATCCGCGAGGCTGACATGGACGGCGACGGTCACGTTAACT

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|6827394|gb|AW331037.1|AW331037

EST:     CCTTTGAGGTCCTGGACAAAGACCAGAACGGCTTCATCTCCCCGGTTGAG                         CTGAGGACGGTGATGACCAGTCTCGGGGAGAAGATGACCGACGAGGAGGTT
genomic: CCTTTGAGGTCCTGGACAAAGACCAGAACGGCTTCATCTCCCCGGTTGAGgtagtctctt ... gtgtgtgaagCTGAGGACGGTGATGACCAGTCTCGGGGAGAAGATGACCGACGAGGAGGTT

EST: gi|211012915|gb|FL112608.1|FL112608

EST:     CCTTTGAGGTCCTGGACAAAGACCAGAACGGCTTCATCTCCCCGGTTGAG                         CTGAGGACGGTGATGACCAGTCTCGGGGAGAAGATGACCGACGAGGAGGTT
genomic: CCTTTGAGGTCCTGGACAAAGACCAGAACGGCTTCATCTCCCCGGTTGAGgtagtctctt ... gtgtgtgaagCTGAGGACGGTGATGACCAGTCTCGGGGAGAAGATGACCGACGAGGAGGTT

EST: gi|211012910|gb|FL112603.1|FL112603

EST:     CCTTTGAGGTCCTGGACAAAGACCAGAACGGCTTCATCTCCCCGGTTGAG                         CTGAGGACGGTGATGACCAGTCTCGGGGA
genomic: CCTTTGAGGTCCTGGACAAAGACCAGAACGGCTTCATCTCCCCGGTTGAGgtagtctctt ... gtgtgtgaagCTGAGGACGGTGATGACCAGTCTCGGGGA

EST: gi|4887307|gb|AI677406.1|AI677406

EST:     CCTTTGAGGTCCTGGACAAAGACCAGAACGGCTTCATCTCCCCGGTTGAG                         CTGAGGACGGTGATGACCAGTCTCGGGGAGAAGATGACCGACGAGGAGGTT
genomic: CCTTTGAGGTCCTGGACAAAGACCAGAACGGCTTCATCTCCCCGGTTGAGgtagtctctt ... gtgtgtgaagCTGAGGACGGTGATGACCAGTCTCGGGGAGAAGATGACCGACGAGGAGGTT

EST: gi|211505742|gb|FL354865.1|FL354865

EST:     CCTTTGAGGTCCTGGACAAAGACCAGAACGGCTTCATCTCCCCGGTTGAG                         CTGAGGACGGTGATGACCAGTCTCGGGGAGAAGATCACCGACGA
genomic: CCTTTGAGGTCCTGGACAAAGACCAGAACGGCTTCATCTCCCCGGTTGAGgtagtctctt ... gtgtgtgaagCTGAGGACGGTGATGACCAGTCTCGGGGAGAAGATGACCGACGA

EST: gi|211015687|gb|FL112613.1|FL112613

EST:     CCTTTGAGGTCCTGGACAAAGACCAGAACGGCTTCATCTCCCCGGTTGAG                         CTGAGGACGGTGATGA
genomic: CCTTTGAGGTCCTGGACAAAGACCAGAACGGCTTCATCTCCCCGGTTGAGgtagtctctt ... gtgtgtgaagCTGAGGACGGTGATGA

EST: gi|211012913|gb|FL112606.1|FL112606

EST:     CCTTTGAGGTCCTGGACAAAGACCAGAACGGCTTCATCTCCCCGGTTGAG                         CTGAGGACGGTGATGACCAGTCTCGGGGAGAAGATGACCGACGAGGAGGTT
genomic: CCTTTGAGGTCCTGGACAAAGACCAGAACGGCTTCATCTCCCCGGTTGAGgtagtctctt ... gtgtgtgaagCTGAGGACGGTGATGACCAGTCTCGGGGAGAAGATGACCGACGAGGAGGTT

EST: gi|78026108|gb|DV494495.1|DV494495

EST:     CCTTTGAGGTCCTGGACAAAGACCAGAACGGCTTCATCTCCCCGGTTGAG                         CTGAGGACGGTGATGACCAGTCTCGGGGAGAAGATGACCGACGAGGAGGTT
genomic: CCTTTGAGGTCCTGGACAAAGACCAGAACGGCTTCATCTCCCCGGTTGAGgtagtctctt ... gtgtgtgaagCTGAGGACGGTGATGACCAGTCTCGGGGAGAAGATGACCGACGAGGAGGTT

EST: gi|211015685|gb|FL112611.1|FL112611

EST:     CCTTTGAGGTCCTGGACAAAGACCAGAACGGCTTCATCTCCCCGGTTGAG                         CTGAGGACGGTGATGACCAGTCTCGGGGAGAAGATGACCGACGAGGAGGTT
genomic: CCTTTGAGGTCCTGGACAAAGACCAGAACGGCTTCATCTCCCCGGTTGAGgtagtctctt ... gtgtgtgaagCTGAGGACGGTGATGACCAGTCTCGGGGAGAAGATGACCGACGAGGAGGTT

EST: gi|211012908|gb|FL112601.1|FL112601

EST:     CCTTTGAGGTCCTGGACAAAGACCAGAACGGCTTCATCTCCCCGGTTGAG                         CTGAGGACGGTGATGACCAGTCTCGGGGAGAAGATGACCGACGAGGAGG
genomic: CCTTTGAGGTCCTGGACAAAGACCAGAACGGCTTCATCTCCCCGGTTGAGgtagtctctt ... gtgtgtgaagCTGAGGACGGTGATGACCAGTCTCGGGGAGAAGATGACCGACGAGGAGG

EST: gi|211012916|gb|FL112609.1|FL112609

EST:     CCTTTGAGGTCCTGGACAAAGACCAGAACGGCTTCATCTCCCCGGTTGAG                         CTGAGGACGGTGATGACCAGTCTCGGGGAGAAGATGWCCGACGAGGAGGTT
genomic: CCTTTGAGGTCCTGGACAAAGACCAGAACGGCTTCATCTCCCCGGTTGAGgtagtctctt ... gtgtgtgaagCTGAGGACGGTGATGACCAGTCTCGGGGAGAAGATGACCGACGAGGAGGTT

EST: gi|211012914|gb|FL112607.1|FL112607

EST:     CCTTTGAGGTCCTGGACAAAGACCAGAACGGCTTCATCTCCCCGGTTGAG                         CTGAGGACGGTGATGACCAGTCTCGGGGGAGAAGATGACCGACGAGGAGGT
genomic: CCTTTGAGGTCCTGGACAAAGACCAGAACGGCTTCATCTCCCCGGTTGAGgtagtctctt ... gtgtgtgaagCTGAGGACGGTGATGACCAGTCTCGGGG-AGAAGATGACCGACGAGGAGGT

EST: gi|211012911|gb|FL112604.1|FL112604

EST:     CCTTTGAGGTCCTGGACAAAGACCAGAACGGCTTCATCTCCCCGGTTGAG                         CTGAGGACGGTGATGACCAGTCTCGGGGAGAAGATGACCGACGAAGAGGTT
genomic: CCTTTGAGGTCCTGGACAAAGACCAGAACGGCTTCATCTCCCCGGTTGAGgtagtctctt ... gtgtgtgaagCTGAGGACGGTGATGACCAGTCTCGGGGAGAAGATGACCGACGAGGAGGTT

EST: gi|211012917|gb|FL112610.1|FL112610

EST:     CCTTTGAGGTCCTGGACAAAGACCAGAACGGCTTCATCTCCCCGGTTGAG                         CTGAGGACGGTGATGACCAGTCTCGGGGAGAAGAWGACCGACGAGGAGGTT
genomic: CCTTTGAGGTCCTGGACAAAGACCAGAACGGCTTCATCTCCCCGGTTGAGgtagtctctt ... gtgtgtgaagCTGAGGACGGTGATGACCAGTCTCGGGGAGAAGATGACCGACGAGGAGGTT

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: 45 (upstream exon), 36 (downstream exon)
Score: 4

GATGGCGACGGCGACGAAGAGCTCAAGGAAGCCTTTGAGGTCCTGGACAAAGACCAGAACGGCTTCATCTCCCCGGTTGAGgtagtctctt ... gtgtgtgaagCTGAGGACGGTGATGACCAGTCTCGGGGAGAAGATGACCGACGAGGAGGTTGAACAGATGATCAGGGAAGCAGACACCGACGGTGACGGTCAGGTGAACT

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 12

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 39

Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 17

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtctctttgtgcctcggcaacctcggaccatgctagctagctgtttccattcatccttgctttcgtgttggtgacttggtgtgtgaagCTGAGGACGGTGATGACCAGTCTCGGGGAGAAGATGACCGACGAGGAGGTTGAACAGATGATCAGGGAAGCAGACACCGACGGTGACGGTCAGGTGAACT

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