ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CGCGGCCGGACCGTGGAGATCTTCAACAGCTTCGAGCTCGTGCTCGACCCCGTCTCCGGAACCCTCGACCGCGCCTTCCTCGACAAGAAGCAGGAGCTCTgtaagctggggcattttgttttttgtttcacggcttcatctttcacgacgcctggaatcctagggaacgctagggtttcgcggatggtttgatgatgctggtgctttgttacggccgtggatgtgcag

Basic information

species	Zea mays
transcript	GRMZM2G080652_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G080652_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA04G12890.1 (Glycine max), 5'ss of exon 1

CGCGGCCGGACCGTGGAGATCTTCAACAGCTTCGAGCTCGTGCTCGACCCCGTCTCCGGAACCCTCGACCGCGCCTTCCTCGACAAGAAGCAGGAGCTCTgtaagctggggcattttgttttttgtttcacggcttcatctttcacgacgcctggaatcctagg-gaacgctagggtttcgcggatggtttgatgatgctggtgctttgttacggccgtggatgtgcag
   ||||| |||||||||||||||||||||||||| ||| |   ||| ||   ||||    ||||||| ||| |||||||||| |||||||| || ||||||    |    | || | | |    |||  |   ||    |||||       || |||  |    | |    |  |      | |   ||  | ||   |                             
AAGGGCCGCACCGTGGAGATCTTCAACAGCTTCGAACTCCTCTACGATCCTTCCTCCCACTCCCTCGATCGCACCTTCCTCGAGAAGAAGCAAGAACTCTgttcagtattcctttctctctcaactttttcaatttttaatttcaatttttatgcaattgtgactgcatttgacagcaatttgaaaccttgaacgacctt-----------------------------

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|89248438|gb|DY620224.1|DY620224

EST:     CGTCTCCGGAACCCTCGACCGCGCCTTCCTCGACAAGAAGCAGGAGCTCT                         ATAAGAAGGTGTTCCCCGACTTCTACGTGCTCGGTTGGTACTCCACTGGAA
genomic: CGTCTCCGGAACCCTCGACCGCGCCTTCCTCGACAAGAAGCAGGAGCTCTgtaagctggg ... ggatgtgcagATAAGAAGGTGTTCCCCGACTTCTACGTGCTCGGTTGGTACTCCACTGGAA

EST: gi|101391113|gb|EB817490.1|EB817490

EST:     CGTCTCCGGAACCCTCGACCGCGCCTTCCTCGACAAGAAGCAGGAGCTCT                         ATAAGAAGGTGTTCCCCGACTTCTACGTGCTCGGTTGGTACTCCACTGGAA
genomic: CGTCTCCGGAACCCTCGACCGCGCCTTCCTCGACAAGAAGCAGGAGCTCTgtaagctggg ... ggatgtgcagATAAGAAGGTGTTCCCCGACTTCTACGTGCTCGGTTGGTACTCCACTGGAA

EST: gi|211380203|gb|FL080414.1|FL080414

EST:     CGTCTCCGGAACCCTCGACCGCGCCTTCCTCGACAAGAAGCAGGAGCTCT                         ATAAGAAGGTGTTCCCCGACTTCTACGTGCTCGGTTGGTACTCCACTGGAA
genomic: CGTCTCCGGAACCCTCGACCGCGCCTTCCTCGACAAGAAGCAGGAGCTCTgtaagctggg ... ggatgtgcagATAAGAAGGTGTTCCCCGACTTCTACGTGCTCGGTTGGTACTCCACTGGAA

EST: gi|31360794|gb|CD445151.1|CD445151

EST:     CGTCTCCGGAACCCTCGACCGCGCCTTCCTCGACAAGAAGCAGGAGCTCT                         ATAAGAAGGTGTTCCCCGACTTCTACGTGCTCGGTTGGTACTCCACTGGAA
genomic: CGTCTCCGGAACCCTCGACCGCGCCTTCCTCGACAAGAAGCAGGAGCTCTgtaagctggg ... ggatgtgcagATAAGAAGGTGTTCCCCGACTTCTACGTGCTCGGTTGGTACTCCACTGGAA

EST: gi|78117501|gb|DV535888.1|DV535888

EST:     CGTCTCCGGAACCCTCGACCGCGCCTTCCTCGACAAGAAGCAGGAGCTCT                         ATAAGAAGGTGTTCCCCGACTTCTACGTGCTCGGTTGGTACTCCACTGGAA
genomic: CGTCTCCGGAACCCTCGACCGCGCCTTCCTCGACAAGAAGCAGGAGCTCTgtaagctggg ... ggatgtgcagATAAGAAGGTGTTCCCCGACTTCTACGTGCTCGGTTGGTACTCCACTGGAA

EST: gi|50325208|gb|CO520334.1|CO520334

EST:     CGTCTCCGGAACCCTCGACCGCGCCTTCCTCGACAAGAAGCAGGAGCTCT                         ATAAGAAGGTGTTCCCCGACTTCTACGTGCTCGGTTGGTACTCCACTGGAA
genomic: CGTCTCCGGAACCCTCGACCGCGCCTTCCTCGACAAGAAGCAGGAGCTCTgtaagctggg ... ggatgtgcagATAAGAAGGTGTTCCCCGACTTCTACGTGCTCGGTTGGTACTCCACTGGAA

EST: gi|211380204|gb|FL080415.1|FL080415

EST:     CGTCTCCGGAACCCTCGACNGCGCCTTCCTCGACAAGAAGCAGGAGCTCT                         ATAAGAAGGTGTYCCCGGACTTCTACGTGCTCGGTTGGTACTCCACTGGAA
genomic: CGTCTCCGGAACCCTCGACCGCGCCTTCCTCGACAAGAAGCAGGAGCTCTgtaagctggg ... ggatgtgcagATAAGAAGGTGTTCCCCGACTTCTACGTGCTCGGTTGGTACTCCACTGGAA

EST: gi|71330852|gb|DR802224.1|DR802224

EST:     CGTCTCCGGAACCCTCGACCGCGCCTTCCTCGACAAGAAGCAGGAGCTCT                         ATAAGAAGGTGTTCCCCGACTTCTACGTGCTCGGTTGGTACTCCACTGGAA
genomic: CGTCTCCGGAACCCTCGACCGCGCCTTCCTCGACAAGAAGCAGGAGCTCTgtaagctggg ... ggatgtgcagATAAGAAGGTGTTCCCCGACTTCTACGTGCTCGGTTGGTACTCCACTGGAA

EST: gi|89248430|gb|DY620216.1|DY620216

EST:     CGTCTCCGGAACCCTCGACCGCGCCTTCCTCGACAAGAAGCAGGAGCTCT                         ATAAGAAGGTGTTCCCCGACTTCTACGTGCTCGGTTGGTACTCCACTGGAA
genomic: CGTCTCCGGAACCCTCGACCGCGCCTTCCTCGACAAGAAGCAGGAGCTCTgtaagctggg ... ggatgtgcagATAAGAAGGTGTTCCCCGACTTCTACGTGCTCGGTTGGTACTCCACTGGAA

EST: gi|71447371|gb|DR828421.1|DR828421

EST:     CGTCTCCGGAACCCTCGACCGCGCCTTCCTCGACAAGAAGCAGGAGCTCT                         ATAAGAAGGTGTTCCCCGACTTCTACGTGCTCGGTTGGTACTCCACTGGAA
genomic: CGTCTCCGGAACCCTCGACCGCGCCTTCCTCGACAAGAAGCAGGAGCTCTgtaagctggg ... ggatgtgcagATAAGAAGGTGTTCCCCGACTTCTACGTGCTCGGTTGGTACTCCACTGGAA

EST: gi|76294373|gb|DV033941.1|DV033941

EST:     CGTCTCCGGAACCCTCGACCGCGCCTTCCTCGACAAGAAGCAGGAGCTCT                         ATAAGAAGGTGTTCCCCGACTTCTACGTGCTCGGTTGGTACTCCACTGGAA
genomic: CGTCTCCGGAACCCTCGACCGCGCCTTCCTCGACAAGAAGCAGGAGCTCTgtaagctggg ... ggatgtgcagATAAGAAGGTGTTCCCCGACTTCTACGTGCTCGGTTGGTACTCCACTGGAA

EST: gi|61119643|gb|DN560604.1|DN560604

EST:     CGTCTCCGGAACCCTCGACCGCGCCTTCCTCGACAAGAAGCAGGAGCTCT                         ATAAGAAGGTGTTCCCCGACTTCTACGTGCTCGGTTGGTACTCCACTGGAA
genomic: CGTCTCCGGAACCCTCGACCGCGCCTTCCTCGACAAGAAGCAGGAGCTCTgtaagctggg ... ggatgtgcagATAAGAAGGTGTTCCCCGACTTCTACGTGCTCGGTTGGTACTCCACTGGAA

EST: gi|101386958|gb|EB815496.1|EB815496

EST:     CGTCTCCGGAACCCTCGACCGCGCCTTCCTCGACAAGAAGCAGGAGCTCT                         ATAAGAAGGTGTTCCCCGACTTCTACGTGCTCGGTTGGTACTCCACTGGAA
genomic: CGTCTCCGGAACCCTCGACCGCGCCTTCCTCGACAAGAAGCAGGAGCTCTgtaagctggg ... ggatgtgcagATAAGAAGGTGTTCCCCGACTTCTACGTGCTCGGTTGGTACTCCACTGGAA

EST: gi|71309454|gb|DR791014.1|DR791014

EST:     GCAGGAGCTCT                         ATAAGAAGGTGTTCCCCGACTTCTACGTGCTCGGTTGGTACTCCACTGGAA
genomic: GCAGGAGCTCTgtaagctggg ... ggatgtgcagATAAGAAGGTGTTCCCCGACTTCTACGTGCTCGGTTGGTACTCCACTGGAA

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: 72

CGCGGCCGGACCGTGGAGATCTTCAACAGCTTCGAGCTCGTGCTCGACCCCGTCTCCGGAACCCTCGACCGCGCCTTCCTCGACAAGAAGCAGGAGCTCTgtaagctggg ... ggatgtgcagATAAGAAGGTGTTCCCCGACTTCTACGTGCTCGGTTGGTACTCCACTGGAAGCGATGTGCACGACACCGACATGCTAATCCACAAATCA

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 70

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 60

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 91

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCGGCCGGACCGTGGAGATCTTCAACAGCTTCGAGCTCGTGCTCGACCCCGTCTCCGGAACCCTCGACCGCGCCTTCCTCGACAAGAAGCAGGAGCTCTgtaagctggggcattttgttttttgtttcacggcttcatctttcacgacgcctggaatcctagggaacgctagggtttcgcggatggtttgatgatgctggtgctttgttacggccgtggatgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT